The 2021 continuation of my COVID emails.... You can go back to 2020 if you dare. Some later clarifications are italicized.

Jan. 4. A holiday COVID hangover?. Local numbers.

Well, this time a quick note. Arguments continue on just how infectious the UK variant is; no doubt this will continue for awhile (it has now been found in CO, CA, FL, and NY). Also arguments on how to deploy the vaccines, which is kind of an embarrassment (presumably this discussion was opened up when the UK took their unusual approach public. Keep in mind this is the same government that was considering a herd immunity approach at one point, so I think it fair to question their logic). While there are rumblings that LA county is seeing a Christmas surge on top of already high numbers, it is hard to tell anything here in Colorado. Hospitalizations continue a slow decline, including (finally) here in Boulder. Boulder’s average case numbers continue to go down, but very slowly. Today’s release of 155 new cases probably is mainly catchup for the holidays plus a typical Monday higher total, but this is the highest number since 12/6. Maybe later this week we’ll really have an idea where we stand.

Meantime, we are all back to level orange, though only Boulder, Broomfield and now Larimer counties in the urban Front Range really might merit that change. This mainly affects restaurants (can reopen indoor dining at a reduced level) and gyms (and technically getting together with another household).

Sometime Thursday we’ll probably have a decent notion of what is up.

Jan. 5. Getting in COVID vaccine line.... The rules.

I was asked about info on vaccine availability. The state has set the guidelines for vaccine distribution but decisions on when to move from phase 1a to 1b and 1b to 2 are being made county-by-county. Although the governor was looking to push those over 70 up in line, most counties appear to be completing other phase 1b groups prior to trying to immunize those 70 and older.

The state’s guidance is at https://covid19.colorado.gov/for-coloradans/vaccine/vaccine-for-coloradans, which described who qualifies for each phase of vaccine distribution and includes a link for an app to track any post-inoculation side effects. The state’s answer to “when do I know its my turn?” is "If you are in phase 1A or 1B and have not been notified by or received your vaccine through your employer, you can either try contacting a vaccine provider https://drive.google.com/file/d/1wM9W1pf2gUj2vp3PSXzvRgoL7-dm-omX/view nearest you or wait for additional providers to come onboard in early January -- those providers will serve members of the 1A group first.”

Boulder County was deluged in questions and so now has a form you can fill out to be notified when you are eligible for a vaccine: https://bouldercounty.wufoo.com/forms/z14hos8502vdgjr/. The county’s general vaccine information page is https://www.bouldercounty.org/families/disease/covid-19/vaccines/

Broomfield County has a page describing where that county stands: https://broomfield.org/3378/COVID-19-Vaccine; this includes a sign-up link to be notified when you are eligible https://forms.gle/pP82PHUA22vJMJ438.

JeffCo’s vaccine page is https://www.jeffco.us/4210/Vaccine; some info on their site is dated (they misstate the phases being used in Colorado in an FAQ). They say they are in phase 1a and just a bit in phase 1b, so residents over 70 are not being inoculated yet.

Larimer County’s page is https://www.larimer.org/coronavirus-covid-19/covid-19-vaccine; there is no sign-up, and the county expects to remain in phase 1a for quite awhile; they suggest checking the website frequently.

Weld County has no specific vaccine page, though they are surveying those getting doses in phase 1a. https://www.weldgov.com/departments/health_and_environment/2019_novel_coronavirus

Hopefully this is of help.

Jan. 6. Yes Virginia, there was a Christmas COVID bump.... How big?, vacation hotspots, Pac-12 compare, Alpha tests, vaccination updates, self tests, bad messaging?, capitol attack a super spreader?

…but is it a little bump or a spike?

While the full extent won’t be clear for a few more days, the rise in positivity rates (over 10% statewide for a few days) even as testing moves back towards pre-holiday levels points to some increase in cases. Positive test numbers are still well below the early November peak statewide, and some of this is catching up to the backlog that probably developed over the holidays, but it is beginning to look like there is more than just backfill going on. This is particularly true of the Boulder county numbers, which have now returned to level red values. The question and concern is, just how large a bump might this be? In Boulder so far, the increase isn’t too alarming though it was abrupt. For now, hopefully, this is mainly a function of erratic testing more than the start of something big. But keep your eye on the reported numbers the next few days: if you start seeing 130, 140 new cases for Boulder County in the paper, we’re heading downhill.

You’ll recall looking again at Estes Park and Eagle County as possible canaries in the coal mine for a holiday bump owing to their positions as destinations for out-of-state groups. So with somewhat more complete numbers, Estes had 18 cases 12/12-12/18, 7 for 12/19-12/25, and *34* for 12/26-1/1. Ouch—though if you average over those last two weeks, this might reflect whether testing was available or pursued, and cases since the first have dropped down a fair bit. Eagle County, in contrast, had a relatively minor post-Christmas increase (over the same weeks, numbers of cases were 192, 178, and 205), but it does seem numbers are still slowly rising in the new year. So, nothing terribly dramatic—which is hopefully a good sign.

So was Gov. Polis’s gamble that case numbers would continue to decline a bad bet? It is hard to say: statewide, numbers have come up a bit, but not dramatically so, so we might be looking at an artifact of testing timing. Given how some other places are seeing substantial post-holiday increases (Phoenix is very bad, LA still high, Dallas and New York both have turned higher), Colorado is looking pretty good—though still the numbers are higher than we really want. Again, we were still the first state to find the UK variant and so things could go poorly quite rapidly.

While that question festers, of more immediate concern is, how high will this go? The 1/4 new cases in Boulder is about as high as the post-Thanksgiving peak, and odds are higher numbers of cases might be out there.

A different way of looking at what is going on regionally is our occasional review of COVID numbers in the Pac-12. This set of numbers is from 1/5: Numbers from COVIDactnow.org (last looked at 12/17):

Rank nowlast timecollegecounty case rate per 100kRt oldcase rateRt new
13Washington King county 26.90.9712.90.76
24Oregon State Benton county 27.51.1316.40.81
32Oregon Lane county 24.41.0621.90.96
41Washington State Whitman county 22.80.7824.20.87
55CU Boulder county 35.30.8629.61.00
66Cal Alameda county 48.31.3045.10.98
77Stanford Santa Clara county 61.01.2561.21.01
88Utah Salt Lake county 74.90.9374.81.01
910Arizona Pima county 100.81.19103.71.03
109Arizona State Maricopa county 86.21.13116.11.13
11t11tUCLA/USC LA county 129.21.28134.11.01

As usual, the Pacific Northwest seems best able to deal with this, and while their exact position in our rankings is juggled again, these top four schools have generally been in that top four a lot. Otherwise things are pretty stagnant, with conditions worsening in Arizona and SoCal.

On to the variant virus, where things are getting clearer that the UK variant [Alpha, later on] is quite likely more contagious than the other common strains, as summarized by Science News https://www.sciencemag.org/news/2021/01/viral-mutations-may-cause-another-very-very-bad-covid-19-wave-scientists-warn. While it isn’t really airtight, as one scientist said, “We’re relying on multiple streams of imperfect evidence, but pretty much all that evidence is pointing in the same direction now.” There is a bit of clarity in terms of what this means: some of the work in Britain suggests that the Rt for the non-new strain was about 1.0 and the new strain was about 1.5. According to the state’s COVID public health board, we’ve seen Rt of 1.5 during the spike in mid-September through October while Rt of 1.0 was about late August; the only time Rt was so low that we would avoid a spike with this new variant was in late May. This brings up the issue of the paucity of routine sequencing of the virus in the U.S.; apparently the British are sequencing 10% of all positive tests; we are *way* behind that https://www.nytimes.com/2021/01/06/health/coronavirus-variant-tracking.html. While there are scattered labs doing sequencing, there is not a nationally coordinated effort. Given the vast number of cases in the U.S., it seems quite plausible that we are breeding our own variants (and certainly many in California have been wondering if LA County is dealing with a variant), yet we are nearly blind to any such mutated virii. It seems likely that this oversight will be addressed by the new administration, but will it be in a timely fashion? Some good news is that the state has asked commercial labs doing COVID testing to provide samples that are missing the S-protein that could then reflect the B.1.1.7 variant so that the state can more fully sequence the sample, and in addition those who have a test that could possibly be the UK variant are asked to isolate more strictly even prior to completion of sequencing. So far there are still only the 2 positive tests from the Colorado National Guard members. (The state lab is also monitoring for other variants).

And back to vaccinations: Colorado Public Radio has a useful article detailing some of the issues with vaccine distribution in Colorado: https://www.cpr.org/2021/01/05/whos-next-colorados-covid-19-vaccine-plan-creates-confusion-for-most-competition-for-some/. As we’ve noted before, Polis kind of upended a lot of the existing planning, and then with the allocations being made county-by-county, we’ve had some counties work down their list more than others. Perhaps most surprising is how confused many doctors are about the priority lists. in Boulder County, the public health folks are keeping track of how many doses have been given. To date, 618 people have had both shots and 7388 have received their first shot. So we are over 1% vaccinated… The Daily Camera ran a story on where those over 70 might look for getting vaccinated: https://www.dailycamera.com/2021/01/07/covid-vaccine-colorado-schedule-70-older/. That story grew out of Polis’s news conference this week https://www.cpr.org/2021/01/06/watch-video-polis-colorado-coronavirus-update-53/, where he mentioned that educators would be in group 1b (after 70+ individuals)—overall there are 1.3 million in group 1b, about 7 times group 1a (which should be complete statewide on 15 January). He expects educators to start getting vaccinated in March (though some had already made appointments to get the vaccine). (I’m not quite sure that we should be counted as educators in this context, especially those of us teaching remotely, but I am unsure.) The state is currently getting 70,000 vaccines/week. It sounds like Polis is hoping to have drive-thru vaccination clinics (they have had a couple already in more rural communities) in addition to distribution through hospitals and health care facilities (which is where most vaccinations will occur). The state is specifically emphasizing that those 70 and up should be getting the vaccine in the earliest part of phase 1b, with all getting the vaccine by the end of February. The basic advice is to contact your health care provider, but the state has assembled a page with links to various major providers (like UCHealth, Kaiser, etc.) at https://covid19.colorado.gov/for-coloradans/vaccine/vaccine-for-coloradans. In general you sign up to be on the list and will get an appointment through either first come-first served or some random drawing setup; several of these groups will immunize folks who are not presently in their systems. A lot more gory details are on the state’s page of vaccine providers https://covid19.colorado.gov/vaccine-providers. It is kind of interesting that the state is not responsible for vaccinating long-term care facilities; this is done through a federal program with CVS and Walgreens and so is out of the state’s control (the state has apparently been asking if they can help accelerate this process). Phase 2 is far enough out that there is no specific discussion about how that will be run.

Interestingly the state is one of three states to have made arrangements to use at-home coronavirus tests from Binax; these will be distributed through schools to test symptomatic or exposed individuals or even as surveillance testing. They expect to get one million tests per month to help make in-person education in schools (presumably K-12) safer. Those of you with school-age children might keep an eye on this.

Polis was asked about the point of the COVID dial when he just superseded the metrics that are present. His defense was that he didn’t think level red was something that could be suffered for a long time, and he felt that with the trends he was seeing justified moving down to level orange (a not entirely fair answer). It sounds like they might be reworking the dial yet again. Polis did note that the state’s rules affect maybe 20% of infection rates, where 80% is driven by personal decisions (as we discussed some time ago—interesting that he is well aware of the limits of his actions). Polis was also chastised by one reporter for what his newsroom felt was chaotic messaging from the governor and the state—Polis’s defense is that he felt movement forward was more important than getting all the ducks in a row first, and he notes that Colorado is ahead of many states in getting people vaccinated (e.g., https://www.nytimes.com/interactive/2020/us/covid-19-vaccine-doses.html).

Finally, an oldie-but-goodie: the super spreader event. Where was this one? Try the Capital building in Washington, DC. Between the aggressively anti-mask Trump supporters swarming into the building and the members of Congress and their staffs huddling in close contact with (again) a number of (predominantly) GOP members remaining maskless, odds are excellent that we have not seen the end of the death toll from the yesterday’s insurrection. Given that three of the mob that descended on the Capital building died of medical conditions, this might not be the healthiest group around to start with. And of course Congress is awash in 70 and 80 year olds who are at greater risk, and so two GOP members of Congress announcing they have tested positive for COVID-19 presumably sent shivers down a few spines. You’d think after losing one new member of Congress to this disease that there might be less posturing and more sanity, but it appears that is not the case. https://arstechnica.com/science/2021/01/capitol-insurrection-was-recipe-for-covid-superspreader-event/ https://www.nytimes.com/2021/01/07/health/coronavirus-capitol-riot.html.

Honestly, when things seem like they can’t get any crazier, we learn that we just underestimate just how crazy it can get.

OK, the light at the end of the tunnel is getting brighter. Some of you might be seeing somebody with a sharp needle in the near future- and be grateful for it.

Jan. 11. COVID's End: Bang or Whimper? Another spike to come? Minimal holiday spike, how many infected, a national spike.

With vaccinations now underway, we might ponder the way the next few months might play out. I think there are two possibilities. The first is kind of what you might expect extrapolating from where we are: that with the holidays now behind us and vaccinations ramping up, that COVID numbers will start heading down a long, slow decline to insignificant sometime in the early or middle summer.

The other? I am suspecting that we will see one more decent wave of infections. Odds are that we will see the restrictions on businesses be reduced in the coming weeks as the pressure on the hospital system starts to recede. Combined with a few weeks of generally good news by late January and the still potent fatigue many feel on keeping COVID at bay, it seems possible that folks will relax their guard a bit too early. Because this will increasingly be in a younger part of the population, COVID numbers might not seem to be spiking until they really accelerate, and it might prove challenging to reinstitute some of the restrictions one last time. For Boulder, toss in the uncertainty about how returning students will behave, and one last time watching cases rise seems plausible. If so, its end will probably be the end of COVID as such a dominant part of our lives, for between the increasing vaccinations and the increased immunity from those having had the disease, it is possible that Rt will suddenly crash well below 1 and the pandemic as we have known it will end. [Hmm. Well, there was a spring spike, but that sadly was hardly the end]

Of course a wild card is the UK variant. It still seems that there are only those 2 cases in the state.

For now, the immediate question is the magnitude of the holiday spike. So far it looks mild: Boulder and Colorado cases might have topped out in the past few days about half as high as the November peak—this should be clear by late in the week. Hospitalizations are down as well. With the resumption of testing at pre-holiday levels, positivity is returning to 4% (Boulder) to 6% (state). Still, it will take about a week to return to case levels appropriate for level orange—we are still at a pretty high level of cases and have been for a couple of months.

The state’s team of infectious disease experts released a new report on 1/8. They argued that Rt was 0.7, which is pretty low, but this was working with numbers before the holidays (COVIDactnow has us at 1.05 now after a low of 0.85 before the holidays). If this holds, hospitalizations will drop to under 500 by the end of the month. About 1 in 100 Coloradans might now be infectious; they think only about 1 in 5 infections are being identified by testing. They calculate that nearly a quarter of the state’s population has been infected at some point, which is almost a third of the way to herd immunity even before vaccinations start up (in Boulder, though, they think a bit under 10% of the population has been infected). In general, Boulder has done better than most of the other urban counties in the state (in Adams and Denver counties they estimate that nearly 30% of the population has been infected; in addition, the eastern plains as a whole see equally high proportions of infection. The lowest? Regionally, southwest Colorado at 7.1% and in the metro area JeffCo and Douglas at about 7.5%). In mid-December the state thought 1 in 400 in Boulder were infectious, and the numbers today are similar enough that that is probably in the ballpark now.

So we’re probably over the worst of this—and quite fortunate if so, as other parts of the country are in dire straits. Nationally, a holiday spike is pretty evident. LA is now having its “New York Moment” with new cases at a level twice of the worst we have seen in Boulder, which is also the case for Phoenix. LA now has the freezer trucks and the patients lining corridors and waiting for hours in ambulances. Even New York city’s metro area is now above our worst level. Nationally, deaths continue on the rise, and we might pass 400,000 before Trump leaves office. So while we aren’t doing as badly, it behooves us to keep in mind that it doesn’t take much to fall down that rabbit hole once again.

Oh, and that super-spreader event in the capital? The first legislator to test positive since huddling in a safe room has blamed that episode on her infection https://arstechnica.com/science/2021/01/congressional-doctor-warns-insurrection-may-have-been-superspreader-event/.

The end is in sight, just don’t trip on your own shoelaces on the way there….

Jan. 14. COVID college chaos, spring edition. CU's ahead, damage from college cases, scaling up immunizations, (old) age before job, local numebers OK, national ones bad.

While the rest of the news universe spins out of control, we’ll tighten our focus a bit on COVID and universities.

Well, for once CU is ahead of the curve. With COVID numbers nationwide at record high levels, many institutions are suddenly pulling the plug on starting in-person classes about now. While CU’s announcement last month was not the best timed, it was at least long enough ago that we aren’t facing the same kind of panicked reaction some other schools are https://www.wsj.com/articles/as-covid-19-surges-colleges-make-last-minute-changes-to-spring-calendars-11609848003.

Don’t celebrate just yet. Along those lines, the CDC has calculated just how much damage reopening colleges for in-person education was in the fall, and it isn’t pretty https://www.cdc.gov/mmwr/volumes/70/wr/mm7001a4.htm. Counties where colleges and universities restarted in-person education saw COVID numbers increase by over 50%. Counties where schools stayed remote from the start saw a *decrease* in COVID levels of 18% and counties lacking universities saw a 6% decrease over the same time periods. Arguably the decisions to reopen campuses killed people—probably a lot of people. While that might be defensible for past times—there wasn’t certainty at the time that this would be the case (though we all thought it highly likely)- *knowing* this is the case now potentially puts campuses in a position of recklessly putting communities at risk if they don’t take adequate measures to prevent spread. And right now, the spread of COVID in most other states is higher or *way* higher than here, so reasserting the 15 Feb start for in-person classes might be premature. However, that latest missive from campus carries good news: it appears all who set foot on campus will have to submit to a weekly COVID test. This is wonderful news (a second test per week would be even better, but we'll take this). As yet, it isn’t clear how this will be enforced (if it isn’t enforced, it isn’t that big a help). A Chronicle of Higher Ed piece follows up on the CDC reported study https://www.chronicle.com/article/where-campuses-reopened-covid-19-cases-spiked-where-colleges-went-remote-they-declined. A similar but separate study that explicitly includes CU as an example was recently published and profiled by Inside HigherEd https://www.insidehighered.com/news/2021/01/13/college-openings-led-increase-community-cases-research-says. This last study notes that while campuses were generally able to corral their student spikes fairly quickly, the broader communities around campuses were not as nimble.

What will we see this spring? It does seem that there are a few students already back in the Boulder area. Will we be seeing the return of stupid parties? I would think Boulder County Public Health is watching very closely...

Immunization plans are still in flux; nationwide there is a lot of finger pointing going on and the numbers are quite confusing. Here in Colorado, for instance, Colorado Public Radio has pointed out that numbers from federal sources suggest a lot of vaccine is sitting in freezers https://www.cpr.org/2021/01/12/coloradans-age-65-69-will-soon-be-eligible-for-the-early-vaccine-plan-but-the-pace-remains-slow/. In his weekly news conference, the governor was challenged by CPR’s Andrea Dukakis on this; the governor said that the state receives the vaccine on Monday and by the following Sunday there is nearly none left in the state. A subsequent interview Dukakis had with the state’s director for vaccine distribution, Brig. Gen. Scott Sherman, cleared up some of the confusion: a lot of the vaccine listed as sitting on shelves was earmarked for second shots, a designation that is about to be removed. Even so, Sherman said that there aren’t enough places for people to get shots right now, and that is their main focus. Interestingly the hospitals managing immunizations (Centura, UC Health) say that they are ready to scale up and that the current limited immunization rates are due to supply issues, so presumably the issues Sherman refers to are for reaching the population farther from these hospital organizations. It appears that about 500,000 total doses have entered Colorado and the state has administered about 300,000, another 100,000 has either been administered or will be by Walgreens and CVS under federal contract for long term care facilities, and the remainder is being used or being released from second shot reserves right now. The state’s goal is to be inoculating ~120,000 a week, but the state is only getting 70,000 or so doses a week. It appears that the main hope is that either the Johnson and Johnson or Oxford/Astra Zeneca vaccines will be available in the coming weeks, though J&J has said they probably cannot contribute until March owing to manufacturing difficulties.

In terms of policy, Polis has gotten far clearer that Colorado's primary concern is to get older Coloradans immunized; while there is now national guidance to get down to those 65 and older as soon as possible, the state wants to be sure that those 70 and older get their shots first and so is holding off on extending down to age 65. Polis claimed in his press briefing that we have a lot of people over 70 (about 7% of the population—but Colorado is in fact a state at the very low end of numbers of seniors), so limiting to that group at present isn’t limiting doses going out the door. Of particular interest is that the state recognizes that age is the primary risk factor and other comorbidities are a far lower risk (which is correct). CU Health is randomly assigning vaccination times both for their eligible patients (who should get an invitation from CUHealth as their time approaches) and those who have entered their information into the CUHealth COVID site (next week they will add a phone option to sign up). Centura’s online option for non-members should be up soon (and apparently walk-ins can sign up in person, though the governor was trying to discourage that as risking them getting swamped). Both UCHealth and Centura maintain a list of will-calls of those 70 and up in case there is some leftover vaccine (e.g., somebody fails to show for an appointment), so they say that there is no waste of vaccine.

As for the state of the pandemic, numbers in the region continue to trend down slowly from the thankfully small holiday spike. This is clearer for Boulder than the state as a whole—except Boulder now has one of the five B.1.1.7 cases in the state and hospitalizations in the county jumped up a little today. Cases connected to CU apparently rose by nearly a factor of two in our holiday spike; the connection of these cases to CU isn’t clear (are these faculty? grad students? undergrad?). Whatever the case, CU-connected cases are now about 10% of the new positive tests in the county after being about 5% over December. This might be a bit of a warning that CU is still positioned to be a problem for the county. There are still strange discrepancies in numbers: so far as I can tell, we are well above the 350 cases/14 days/100,000 people level marking the upper limit for level orange, but the county (and state) put us right on the edge of 350. I’m not sure if they know something I don’t or if their math is off.

Nationally the train wreck continues. 379,000-385,000+ have died (depends on whose count you look at), and at the current rate by Wednesday’s inauguration we’ll likely exceed 400,000. The west and south are the areas with the biggest problems right now, but nobody is doing great. COVID-19 has now been present in the U.S. almost a year; 400,000 puts it in yelling distance of cancer for the #2 spot; over the past month or so COVID-19 has been the number one killer by far (85,000 have died in the past 31 days; over a year that would be over 1 million compared to ~650,000 killed annually by heart disease and 600,000 by cancer).

Hopefully you all are well positioned for the resumption of education this week. In a week the inauguration will be behind us and, hopefully, any and all drama from armed confrontations. Then, perhaps, the nation might return to facing the continued high levels of infection and death from COVID-19.

Jan. 18. COVID chaos: Vaccine edition. No stockpile, cost of reopening, Colorado's success at vaccinating, a California variant, cabinet-level science, Pac-12 update, local trends good.

Kind of unbelievable, but as you no doubt noticed, the federal government, after saying they would release the stockpile held back for second shots, revealed that there was no stockpile. Their interpretation is that the announcement was just that they were not going to hold back any future reserve, which is certainly not the way a number of governors understood it (including Polis). But today we learned that many Colorado hospitals were in fact holding back the second shot; the state has now instructed them to use those second shots now and trust that the production lines will keep up and the second shots can be taken from future shipments. This last major fumble of the Trump administration stains their success in pushing Operation Warp Speed forward. We are fortunate that Colorado, unlike many other states, had not opened up vaccinations to all over 65 as those states can hardly backtrack and yet this will delay older people at far greater risk from getting vaccinated. The coming months will see whether Reagan was right or wrong in saying that the most feared words in the English language were “I’m from the government and I’m here to help.” Biden has basically made the claim that government can help; solving this crisis would go a long ways to justifying that claim.

A review of the successes and failures of Operation Warp Speed is at Politico https://www.politico.com/news/2021/01/17/crash-landing-of-operation-warp-speed-459892. And with the anniversary of the first recognized US case, the New York Times has a lengthy retrospective (including a quote or two from Polis) about just where things went wrong https://www.nytimes.com/2021/01/17/us/covid-deaths-2020.html. The piece points to reopenings in late April as the missed chance to corral the disease; my missive from 22 April responded to the governor’s announcement reopening businesses went this way: "To be clear, the goal now is to keep infection rates low enough that hospitals are not overwhelmed while opening up things as much as possible. This strategy will probably end up resulting in ~11,000 Colorado deaths by my math, assuming that the plateau we are on continues forward (20 deaths/day over next 18 months). Realistically, nobody is certain how well these phased openings will work out; we're going to find out one state at a time.” It is worth noting that the governor has been consistent in pursuing these goals(e.g., revising level red and creating level purple). We are about halfway through that 18 month period and we are at 5386 deaths, almost exactly halfway to the 11,000 I had feared. So while the plateau didn’t continue as feared, the resurgence of the virus more than made up for our relatively quiet summer. (If you are wondering, Colorado has the 17th fewest total deaths per capita of the 50 states (947/million vs 1180/million nationally)—we are still worse than California overall but better since July).

Colorado is something of a success story in getting vaccines out, as noted by a CNN story https://www.cnn.com/2021/01/15/health/states-vaccinating-faster-west-virginia/index.html. Frankly a big reason is that Colorado hasn’t gotten fancy, especially once the governor rejiggered the line to emphasize age. An aspect that hasn’t been clear prior to this story is that the state will not allow vaccine doses to sit with any provider more than 72 hours. The state’s use it or lose it philosophy has apparently motivated groups to get shots done (today’s advice to not hold on to second shots at hospitals will also move in this direction). On the other end of the spectrum, a NY Times piece points out how some states are burying the vaccination process in paperwork, with New York being a fine example. In Colorado, by focusing on age only right now, paperwork is minimal. Where things will get sticky is once we are done with the over-65 crowd sometime in March; below that threshold you start looking at preexisting conditions, ethnicity, and exposure as important factors. Balancing those against a rapid expansion of injections will be an interesting challenge. Some ideas are in a NY Times op-ed https://www.nytimes.com/2021/01/15/opinion/coronavirus-vaccine.html.

Meanwhile in California, a newly recognized variant of COVID-19 has been found in outbreaks in Santa Clara county and elsewhere in southern California https://www.latimes.com/california/story/2021-01-17/covid-19-coronavirus-vaccine-update-pandemic. This mutation has three changes to the spike protein, so it is suspicious, but with the hit-or-miss level of sequencing being done, it isn’t clear if it is behaving any differently than all the other “regular” versions out there, but it could be more widespread and more transmissible. It might, though, make some sense of the difficulties that SoCal has had. And just how bad are those difficulties? "So many people have died in Los Angeles County that officials have temporarily suspended air-quality regulations that limit the number of cremations.”

And in quasi-COVID news that might be of interest, Biden has elevated the science advisor to a cabinet level post https://www.nytimes.com/2021/01/15/science/biden-science-cabinet.html. This is a first. Recall it took the Trump administration two years to nominate a science advisor. Ars Technica slugged this "As it turns out, the Biden administration will listen to scientists” https://arstechnica.com/science/2021/01/as-it-turns-out-the-biden-administration-will-listen-to-scientists/.

In honor of the CU women’s basketball team’s victory over #1 and previously undefeated Stanford (only the third time *any* CU team has beaten a #1 team, the other two came from the volleyball team; if you didn’t watch it, you missed out—made up for heartbreak a year ago), we’ll revisit our Pac-12 COVID board. (As an aside, Stanford has not played in Palo Alto for months: the county there has banned any kind of team sports. Of course in a COVID world, “home” games aren’t the advantage they usually are—CU might be a bit different with the altitude--but Stanford’s 11-0 record prior to playing CU speaks to a disciplined team). Numbers from COVIDactnow.org (last looked at 1/5):

Rank nowlast timecollegecounty case rate per 100kRt oldcase rateRt new
12Oregon State Benton county 16.40.8122.01.14
23Oregon Lane county 21.90.9622.51.08
35CU Boulder county 29.61.0023.60.94
44Washington State Whitman county 24.20.8724.80.91
51Washington King county 12.90.7627.41.19
66Cal Alameda county 45.10.9855.61.06
78Utah Salt Lake county 74.81.0168.01.02
87Stanford Santa Clara county 61.21.0168.91.03
99Arizona Pima county 103.71.03112.31.05
1010Arizona State Maricopa county 116.11.13118.71.07
11t11tUCLA/USC LA county 134.11.01139.11.02
Well, not only the basketball team doing well, but CU has marched into the top 3 and could become the least infectious part of the Pac-12 given the sub-1.0 Rt estimate. Things have curdled in the northwest, especially in Seattle. The bottom half of the standings remain nearly unchanged with Utah sneaking above Stanford. The CU women might want to be careful on their road trip to the Arizona schools as things there continue to be poor.

Finally, the numbers. The state now has the infection rate in Boulder dropping into level orange numbers. While that maybe deserves a sigh of relief, it doesn’t merit celebration: these are still higher numbers than we want to see and that UK variant is a wildcard still out there. The decline might be slowing, though the holiday weekend is interfering with numbers some; things should be clearer later in the week. Statewide hospitalizations have dropped below 800 for the first time since the start of November, and positive tests statewide have resumed dropping down. So trends are good even if levels are still too high.

This is the last of my missives during the Trump administration. We’ll see if anything changes by the next update...

Jan. 21. CU COVID miscellany. Limited on-campus testing, hands off the off-campus, level red criteria, vaccine rules, variant risks, no-flu.

Well CU has resumed their weekly COVID zooms, and the first one of 2021 wasn’t all that thrilling. There is still no specific guideline for how the requirement that all who step on campus will have to be taking reconnaissance tests (though that requirement was restated again). Apparently CU thinks it can manage 20-25,000 such tests a week, which would seem to imply that thousands of students won’t be on campus at all. For those stepping onto campus who don’t live there, food is once again available at the Weathertek Cafe and the Alferd Packer Grill. And while campus leaders like to say that how things are done on campus is tightly aligned with the state’s COVID dial, this is mostly overstatement, as there is no certainty that a return to level red would cause an end to in-person classes (going remote is only encouraged, not required), nor would a change to level yellow or green change much as far as campus is run (it would open up some indoor dining and more social activities). We were told that overall, half of classes this term are remote, 30% will be in-person and the remainder hybrid.

Something those of us teaching might want to keep in mind is that while the pass-fail choice deadline remains the 10th Friday of the term, the temporary rules have lapsed that permitted a pass/fail grade choice for some of those courses that usually have to be graded to count toward a degree.

Several questions were asked about off-campus students and their behavior. First, students are indeed back in Greek houses and apartments at some level (campus dorms start to reopen about 7 Feb). Nothing has really changed from campus’s perspective: if they learn of misbehavior (big parties, etc.), they will enforce academic penalties. Nobody from the city was on the call, so it isn’t clear just how carefully the city is watching those fraternities; you would hope they are watching quite closely. Those students coming back is probably why we’re seeing CU-affiliates’ fraction of the new COVID cases rising to over 10% of all cases (it was around 4% after Christmas). This will bear watching as our November spike was seeded by the September spike in college-age adults.

Another question bouncing around is, what does it take to reinstitute level red after the governor just dropped it without regard to any criteria? CU leaders are as in the dark as the rest of us, it seems. Well, Pitkin County returned to level red this past Sunday. Why? The two-week incidence per 100,000 hit about 3000; it was the county public health board that voted to return to level red https://www.aspentimes.com/news/pitkin-county-moving-to-red-level-restrictions-closing-indoor-dining/. Yep, 3% of Pitkin County’s population tested positive over two weeks. How bad is that? Boulder is now a bit under 350 cases over 14 days per 100,000; the highest level in the November peak in Boulder was about 1000. You might recall that Aspen (which is in Pitkin Co) was one of the epicenters of spread last March. With a little under half of the county’s population, Aspen has 67% of the COVID cases (and so had an infection rate over 4% while the rest of the county was under 2%). Guess we should have watched them instead of Estes or Vail. That public health board has decided that 700 cases over 14 days per 100,000 is now the threshold between orange and red in Pitkin County; we’ll see if anybody else adopts that threshold. [Oddly, the *town* of Pitkin is in Gunnison County, where the COVID dial is at level yellow—for now]. Plenty of other west slope counties west of Pitkin County are only doing a little better at ~1000/100,000 this past 2 weeks.

And on to vaccines. First up, CU, which has been asked to partner with BCPH in vaccine distribution. It sounded like about 100 doses have come through CU to their health staff and first responders. Is CU In line for earlier vaccinations because we are officially “educators”? Right now, campus doesn’t know (and the statements that there has not been transmission in the classrooms would seem to undercut any argument that CU faculty are at any greater risk because of their jobs). There is certainly a big difference between spending 2-6 hours a week in a classroom with enhanced ventilation teaching adults and spending 6 hours a day in a classroom with children who might have difficulties with masks and distancing and all that.

FWIW Boulder County’s vaccine page lists providers and what they are doing: https://www.bouldercounty.org/families/disease/covid-19/vaccines/. CU is not on this list (UC Health is). About 1% of county residents are fully immunized and over 5% have had one shot.

A bit more craziness on how vaccines will be distributed. Apparently Washington, DC is using body-mass index as a means of choosing who should get vaccinated. Their threshold of BMI of 25 is well below any medically observed threshold of increased risk (BMI of 40 seems the boundary for increased chance of death), and more than half of DC residents qualify. This is a logistical nightmare at so many levels (throwing open the doors to large numbers of people with very limited vaccine, having a criterion that is going to require some investigation—will there be a scale at every vaccination site?). The more I’ve seen of equally well-intentioned but realistically stupid attempts to be super equitable, the more necessary a simple strategy seems to be. I suspect that the most successful set-ups are going to fall into three types. One is simply by age; all you need is a standard ID or just at least know your birthdate. Appointments are required to avoid long lines. A second is by workplace: much of the racial inequities in outcomes is because minorities are employed in larger proportions of “essential” and hard-to-socially-distance jobs. So having a mobile vaccine setup that visits these workplaces and vaccinates all the employees would not require a lot of paperwork or passing criteria tests. The third are clinics for communities that have poor access to health care and a history of suspicion about big medicine. Colorado recognized this as an issue in testing for COVID-19 and made a point of having smaller satellite testing setups in churches in such communities. These might be set up in advance through community groups. Implementing these three approaches while vaccines are relatively rare seems the fastest way to get immunizations to the groups that need them the most. After that, throwing open the doors to everyone through hospitals and pharmacies would seem fair game. My read of how things have evolved here in Colorado is that this might well be the strategy than Polis is apt to embrace. I think the tricky part is workplace vaccinations; for the brief time when educators were near the front of phase 1b, they were making appointments at pharmacies. It might be painful if pharmacies have to be the gatekeepers (how do you prove you are an educator?). Here in Colorado we are probably more than a month away from actually having to worry about those under the age of 70.

And what of the feds? Incoming Biden administration people are saying they are appalled at a lack of existing plans, which sounds like they want to take over vaccine administration. This could be heaven or hell: North Dakota has done a fine job of getting vaccines into arms, but the peculiar health care landscape in that state isn’t like what is in New York or California and so may be a poor model. There has been talk of having very large vaccination centers around the country—could work in urban areas, not so great in rural regions. Polis has said he doesn’t think that these are the best way forward: he claims that efficiencies of scale plateau out in the few hundred to few thousand vaccinations a day range and thus more distributed medium-size sites with only a few Pepsi-center scale sites makes the most sense. An overly centralized federal response could upset some of the more careful planning in some states while rescuing residents of others from poorly thought-through plans. So this will bear watching.

Concern continues to exist in the media that the variants of COVID-19 might slip past the current vaccines https://www.cnn.com/2021/01/21/health/coronavirus-variant-problem-vaccines/index.html. This isn’t about the UK variant (B.1.1.7 later alpha) but one from South Africa (1.351 later beta) that seems most concerning. These are early lab studies, but one would expect that Moderna and Pfizer are both looking at what they might want to modify in the existing vaccines and exploring what regulatory hurdles might exist. They have said that it takes them about six weeks to actually update the produced vaccine. Frankly, it is hardly surprising that there are variants showing up: you put rapidly reproducing organisms in a hundred million people and odds are good you’ll generate a few more successful strains. And it might be this California strain (CAL.20C) that is of greater concern for us; this appears to be responsible for over a third of cases in southern California seen in recent weeks https://www.cedars-sinai.org/newsroom/local-covid-19-strain-found-in-over-one-third-of-los-angeles-patients/. This behavior is very reminiscent of what happened in England (and is hardly a surprise with how cases exploded in SoCal). To date there is no indication that it is more or less susceptible to the vaccines, though research is underway https://www.sandiegouniontribune.com/news/science/story/2021-01-20/san-diego-california-variant-coronavirus; like the UK variant, it rise within the COVID cases suggests it is a more transmissible strain. This variant has been found in many other states (not Colorado, so far), but the non-uniform testing for genome means we really aren’t sure how prevalent it is across the country. This is certainly on the radar of the new administration.

OK, here’s something you aren’t hearing about. There are virtually no cases of flu in Colorado this season, which is a side effect of everybody protecting themselves from COVID-19. This is not unexpected after the southern hemisphere saw nearly no cases this past northern summer. So there is your glimmer of good news this go round. (If there is still anybody claiming this is just like a bad flu year, this chart should make it clear we’re *way* out of that range: https://www.cdc.gov/flu/weekly/weeklyarchives2020-2021/NCHS01.html). (If you want to find flu, appears Tennessee is the only state with even a mild outbreak).

On to the numbers around town and the state. Cases continue to decline; in both Colorado and Boulder we are back to late October values (and Boulder is solidly in level orange criteria). Still, will take about three weeks to get down to level yellow at our current rate of decline. All students taking in-person classes will be back by then, so it seems plausible that we’ll have numbers start to scoot back up rather than continue down. Boulder hospitalizations are slowly declining (but actually back to mid-October numbers) as are state numbers (which are like start of November numbers).

With things returning to a routine we’ll probably start just seeing incremental changes. The next big event is the arrival of all the on-campus students in a few weeks.

Jan. 25. COVID collegians return. CU cases rising?, local declines, vaccine the previously infected?, So African variant (beta), UK variant (alpha) and California variant.

More and more I am watching the percentage of cases attributed to people affiliated with CU. Over the past week, 12% of new cases are associated with the university (when full, campus is about 10% of Boulder County’s population). Now this could be professors and staff, but also well over a quarter of the new cases in the past week are from 18-24 year olds, a substantial increase from a few weeks ago. In fact, of all the age groups BCPH provides numbers on, only this group is showing a rising number of cases. So yes, it is the students who are returning. This feels like a rerun of September when the 18-22 year old range spiked spectacularly. Right now there are no noises coming from anyone about this, but this will prove crucial; if we see this group spike up again, we will have another serious wave of COVID here in Boulder. Somebody needs to step up NOW and address this before we see the main wave of student returns in the next couple of weeks.

For now, though, county cases are slowly declining, with the emphasis on slowly. We might actually be stuck on a plateau of about 68 cases/day—well below the threshold of 82 that was the lower edge of level red, but far above the level of 41/day for level yellow. Hospital numbers also are on a slow decline both countywide and statewide. Broomfield, on the other hand, seems to be headed in the wrong direction, and it isn’t clear why; cases there are increasing by about 30/100,000 per day over the last week, roughly, while Boulder is down near 20/100,000/day of late; the state as a whole is halfway between these two. A couple weeks ago the two counties were very close. One thing that is special about Broomfield is that restaurants that meet the five star program’s criteria can operate as though they are at level yellow (i.e., more capacity). I would expect that to be changed in the near future; is there the possibility that this was the cause of the spike? You do have to wonder.

As vaccinations proceed, some interesting puzzles. For instance, there are estimates that more than 60% of North Dakotans have had COVID-19. Does it make sense to immunize those people? Indeed, the state as a whole is approaching the kinds of numbers where you might expect to see herd immunity start to slow things down (which, perhaps, is the main reason that North Dakota numbers finally started falling in mid-November). Some other states have had very low levels of COVID; would it make sense to divert vaccines where there are proportionally more vulnerable people? Right now this doesn’t seem to be affecting distribution discussions.

We’re hearing more and more out of South Africa about their variant (501Y.V2 later called beta). Aside from the lab experiments described before, reinfections with the new variant are numerous enough that there is a suspicion that natural immunity is not working well against the variant https://www.nature.com/articles/d41586-021-00121-z, though Moderna and Pfizer are saying that the current vaccine will protect against these variants. As I said before, hard to imagine that Pfizer and Moderna are not all over this (indeed, this has now been documented https://www.nytimes.com/2021/01/25/health/coronavirus-moderna-vaccine-variant.html. This does suggest more and more that COVID-19 will be with us for years to come, with updated vaccinations being a thing for awhile. Will it eventually die out as the opportunities for mutation fade away? It will probably take quite some time to find out.

Meanwhile, the UK variant is now being pegged as not only more transmissible but also more deadly. Oh, good. Current hotspots we know of (recall sequencing the virus is scattershot) are San Diego and Florida. And work continues on the California strain (now B.1.246) to determine if it was part of the reason things went so bad in SoCal over the past couple of months. And a case of reinfection of an individual with this new strain is causing the same worries we’ve been seeing for the other variants (maybe it can sneak past antibodies or even vaccines) https://www.latimes.com/science/story/2021-01-23/coronavirus-california-strain-homegrown. Well, worries multiply like dust bunnies; for the moment there is little doubt that the best path forward remains continued vigilance and more vaccine.

Finally keep in mind that California is a major source of CU undergrads. Hopefully they won’t be bringing any of these variants along with them...

Jan. 28. Looking in the COVID crystal ball. Alpha's cost, CO forecasts, why constant Rt is bad assumption, Europe, a spring forecast, CU rules.

I’m leading off with some speculation that kind of underlies my expectations for the coming months. The immediate local outlook is at the end of the email.

The CDC has made a quick and dirty model of how the growth of the UK variant (later alpha) is apt to affect the decline of COVID in the face of vaccination (figure attached) https://www.cdc.gov/mmwr/volumes/70/wr/mm7003e2.htm. Some folks have looked at this and said, oh, not that bad—there isn’t another spike in there from the UK variant, just takes a bit longer to shut down COVID-19. But there is a lot of misery in the difference between the “Current variants” line and the “Total” line that includes an impact from the UK variant—keep in mind that 10 daily cases/100,000 per day maps to about 1,000,000 additional cases per month nationally. The CDC is assuming that the UK variant is just more transmissive but otherwise identical to the other variants currently in play.

CDC forecast

A related effort was made by the Colorado Public Health advisory group https://coloradosph.cuanschutz.edu/docs/librariesprovider151/default-document-library/co_modeling_report_01_20_2021.pdf?sfvrsn=2b2a92b9_0. Their modeling incorporated both vaccinations and increasing levels of the UK (B.1.1.7) virus within the Colorado demographic. As with the CDC analysis, the assumption is just one of increased transmissibility. If we continue with behaviors at present, they find that infections and hospitalizations will continue to slowly decline and the presence of the B.1.1.7 version has little impact. However only a slight decrease in social distancing (from 78% to 70%) would result in a spike in April [this actually is what happened as alpha took over]. I am a bit suspicious about this model, for while it supposedly includes demographics and successful vaccination of most of those over 70, the ratios of daily active infections per 100,000:number hospitalized:ICU beds used seems nearly constant over the entire pandemic at about 100:75:21, which makes little sense going forward if the most frequently hospitalized are immunized.

What the CDC and state advisory board aren't including in this analysis is that new variants might cause reinfection, that new variants might reduce the efficacy of vaccines, or that new variants could be more deadly or produce longer recoveries. All three of these possibilities are now in the mix for the UK (B.1.1.7), South Africa (1.351), Brazil (P.1), and California (B.1.426) variants https://www.latimes.com/california/story/2021-01-25/new-coronavirus-strains-urgent-threat-what-to-know. Simply put, the CDC analysis here is, arguably, a best-case scenario. What nobody can include are any other emerging variants; the longer we have lots of people being infected, the greater the chances of some combination of mutations proving to be a problem. If we were lucky, we could get a variant that is a lot less severe but transmissible enough to take over from the more deadly versions—in essence, for COVID-19 to evolve into the common cold. So far there is no sign of that happening. Furthermore, these models assume a constant Rt throughout the time period. This is hopelessly unrealistic: we’ve already seen that Rt rises back up again as people feel safer and rules are loosened. It is easy to imagine that we start down the path where Rt is 0.9 to early March and then shift to the path where Rt rises to 1.1 as people mix more or use masks less. Nationally, cases would rise from 10-20 cases/100,000/day to ~40 in late April—even in the presence of immunizations. A more significant relaxation would produce a bigger spike. The inference that there won’t be another wave of COVID is naive; arguably the factor that might tamp down another spike might well be a return to warm weather, which did seem to help.

It is worth noting that we still know very little about these variants. Estimates of transmissibility depend on epidemiological models of how a variant comes to be dominant in a population, and there are considerable uncertainties in that analysis. Whether a variant is more deadly takes longer to ascertain as of course deaths lag infections and not all cases are tested for the variant, so the statistics aren’t as robust. The mechanisms of increased transmissibility seem unclear and of increased mortality (if present) even less clear, though changes to the spike protein seem most plausible. So far experts seem to feel that the vaccines currently available are effective against the new variants, though there is suspicion that they are somewhat less effective against the South African (1.351) variant. Efforts are underway for a possible booster vaccine should it be necessary. So there are grounds for both pessimism and optimism; only time will tell. Frankly, a smart response to this possible threat would be to proactively have a lockdown, especially if funds to help those most affected came out of DC. With low enough infections, immunizations could overtake any variants before trouble emerged.

While we’ve been focused on Colorado and the U.S., it is worth a moment to look to Europe. Portugal relaxed rules for Christmas; they now have the highest infection and death rate per 100,000 of any country in the world https://apnews.com/article/travel-pandemics-europe-coronavirus-vaccine-portugal-ce002bdf1a21c540ece3adfedc193bc8. And it is worth recalling that the big increase in UK cases was associated with holidays. In addition to the UK, which we hear about the most, several European countries are returning to outright lockdowns and curfews. These countries have not been asleep at the switch quite the way we have and yet they are facing difficulties. We aren’t out of the woods yet.

For the near future, it seems likely that COVID rates will decline some more, but probably not all the way to level yellow here in Boulder. My guess is that we will see a plateau develop (if we aren’t already there), probably in the next month but maybe a bit later, that would locally be driven by students returning to Boulder and then statewide by relaxing rules and behaviors plus whatever happens with these variants. Whether that plateau then turns up into a new spike or not will depend on vaccination rates, the way rules are changed or not, how prevalent and how transmissive any new variants turn out to be. With older people being vaccinated, we might well see a spike in cases but a far smaller increase in hospitalizations; it is entirely possible that the state will decide to loosen restrictions as risks to the health care system decline (Gov. Polis hinted as much this week; https://www.cpr.org/2021/01/26/polis-will-dial-down-coronavirus-restrictions-once-vaccines-take-hold/). Decoupling of cases from hospitalizations from deaths is a likely (indeed, desired) outcome of the current vaccination strategy, but it will also complicate public health rules. Only 10% of Boulder County deaths are among those younger than 65, so once all those over 65 are vaccinated we could see COVID levels spike up while deaths continue to drop (statewide it might be a touch higher than 10%). What I haven’t seen are numbers on the fraction of cases for those under 65 that lead to longterm health problems.

So how common are the variants in Colorado? As of earlier in the week, 10 cases of the UK variant have been found in Colorado (1 in Boulder County) and none of the California, South Africa or Brazil variants https://www.denverpost.com/2021/01/26/colorado-covid-hospitalizations-cases-falling/. (One case from Brazil has been found in Minnesota https://www.npr.org/sections/coronavirus-live-updates/2021/01/25/960566484/a-more-contagious-coronavirus-variant-from-brazil-is-found-in-minnesota). So little impact so far, but we aren’t isolated from these.

As I mentioned above, the latest state modeling report showed up on Tuesday (while dated 1/20, it wasn’t available until then). We are only now coming down to levels of estimated infection equal to the peak last March (by a measure including an estimate of infections that were never tested). At the peak in late November, the state thinks about 2.5% of the population was infectious; this was down to about 0.9% in mid-January. They think 24% of the state’s population has been infected to this point.

The weekly campus and BCPH zooms were not all that illuminating and in one regard a bit distressing. Instead of requiring all who come on campus to participate in the surveillance testing, campus will only merely encourage those living off campus to get tested regularly. Sorry gang, not good enough: at minimum, the BuffPass should get tied to having participated in testing; at best, access to campus buildings would be denied if a student doesn’t get tested. I mean, students were leaving quarantine, so expecting perfect behavior on testing is unrealistic. There were sounds that group living environments will be contacted by CU directly and, in some instances, testing will be required (I suspect this is a remnant of the fall conditions placed on some houses by Boulder Public Health). As for the county and city, they are returning to the effort in the fall as far as reaching out and having more patrols on the Hill and asking folks to report any parties; they will pass on to CU info on any students breaking the rules. It’s worth recalling that those efforts were insufficient in the fall. There was no mention of reinstating the order specific to 18-22 year olds (that had expired in December). The “are CU profs educators?” question remains unanswered. On the campus call, a number of questions from parents indicated they are hopeful that CU will be vaccinating students. While campus representatives pretty much said they have no idea, barring a massive increase in vaccines, I’d be astonished if any CU students were vaccinated during the spring term. We’ll barely get through phase 1 by April.

As for the current numbers, we are still in level orange territory by new case rates, but the decline looks to be flattening out: the average of new cases over the past week is nearly identical to the previous week. Hospitalizations also are essentially flat. This is much higher that we really want to be, especially as there is one identified case of the UK variant (B.1.1.7) in the county. And the fraction of cases associated with CU continues to grow; it is now over 15% of new cases. Statewide numbers are a bit rosier with new cases and hospitalizations continuing to decline, though the rate is slowing. If you were wondering about vaccines, 41% of those over 70 in the county have received at least one shot, about 7.5% have had both shots (of those 18-69, about 4-5% have gotten a shot because of their employment in health care, extended care facilities or as first responders). Boulder has been administering about 1000 doses a day, though the numbers have been swinging up and down a fair bit. At that rate it would take nearly three months to finish immunizing all those over 69, much longer than Gov. Polis had indicated, so we need to see this increase substantially. The county feels that they are in position to manage higher levels of inoculation should the vaccines show up; they will also reach out to parts of the community that are either hesitant to or having difficulty with getting the vaccine.

The next couple weeks will be crucial here in Boulder; if the current trends are really indicating a resumption of student-led illnesses, we could have a rocky ride into March. And if one of the more contagious variants takes hold here, could be very unpleasant. On the other hand, BCPH will be watching the student population, and maybe CU will push off-campus students harder on getting tested. As it has been so often, we walk a narrow path; falling off so close to vaccine nirvana would be painful.

Feb. 1. March of the COVID variants. Variant horserace, variant breeding, vaccines and variants, dial 2.0, when to relax?, local cases flattening, return of students in a week.

Welcome to February, often called the cruelest month as spring just seems so far away. This year, it has the added stress of the month when it seems like vaccines are just staying out of reach as variant virii are multiplying somewhere.

There are estimates out there that sometime in March we might be seeing one of the COVID variants as the main source of infection in the country. What is increasingly clear is that this will be a horse race with several entries. Right now B.1.1.7 (or 501Y.v1), the UK variant, is in the lead, and that might be the one to root for as it apparently is blocked by the current vaccines out there, although this one is most clearly more transmissible and there is some evidence it might be more fatal. In contrast, the South Africa variant, B.1.351 or 501Y.v2, is more worrying as we now have some direct evidence from the phase 3 trials of two other vaccines that show that they are noticeably less effective against that variant https://www.latimes.com/science/story/2021-01-29/as-coronavirus-variants-threaten-immunity-the-race-to-vaccinate-shows-pitfalls. This variant finally was found in the US late last week, but as usual, given the haphazard approach to sequencing variants in the U.S. it is quite possible it is rattling around elsewhere. Then we have the California variant (B.1.246 or CAL.20C or L452R), which we know precious little about and which is not getting national attention but which is almost certainly the most prevalent in the U.S. of the four variants being examined (this variant first showed up in Denmark in March but only became important in California in the past few months; this is sounding more like a fluky growth to prominence during rapid growth of illnesses in SoCal than an inherently more dangerous variant). The continued absence of mention in the media is starting to indicate it isn’t a real issue, but I guess we will see. Finally we have the Brazilian variant (P.1 or 501Y.v3), which has a lot of similarities to the South African one, though there is not yet direct evidence of it being as challenging for the current vaccines as B.1.351 or as infectious as B.1.1.7. A handy summary of the variants is at Are Technical’s https://arstechnica.com/science/2021/01/coronavirus-variants-what-they-do-and-how-worried-you-should-be/

If you wonder where these variants come from, an article in the LA Times reveals the history of a “long-haul” patient in Boston who seemed to accumulate mutations due in part to issues with his immune system https://www.latimes.com/science/story/2021-01-30/long-term-covid-19-patients-are-incubating-dangerous-new-coronavirus-strains. Something like this was suggested to be the origin of the UK variant.

In a way we are seeing a reprise of the situation just under a year ago: we have a new flavor of disease, not yet very common but potentially quite dangerous; how are we going to stop it? If we really wanted this in the rear view mirror, a return to a real shutdown combined with focusing vaccinations on essential workers might keep the variants at bay for long enough that we could crush coronavirus before the variants made enough headway to be a threat. Politically this won’t happen. Next best would be a massive increase in sequencing the genome of positive test samples and aggressively doing contact tracing on these variants. But that takes time we might not have. So instead we get to watch this horserace to see which variant(s) gain the upper hand. This could get complicated: those fully vaccinated with the current vaccines might be inclined to be less careful (which is fully understandable—that was the point of getting vaccinated) and might then be vulnerable to 1.351 and might end up spreading it much as the original virus was spread early last year. But it seems if B.1.1.7 is the winner, the vaccines might shut it down just fine. We’ll want to watch all this carefully; odds are good that the Moderna and Pfizer vaccines will be updated or have a booster to deal with this; a question that has not yet been addressed is what kinds of regulatory hurdles might be required of a rejiggered vaccine—if it is a full run back through all the trials, that six week turnaround mentioned by the companies will be meaningless. It is less clear whether the AstraZenica or Johnson and Johnson vaccines can be updated as nimbly. And it is worth keeping in mind that these will not be the last variants to show up, particularly as long as hundreds of thousands of people are infected daily. On the other hand, even a less effective vaccine will help to knock down Rt and maybe get us on track for a normal life (albeit one where the COVID shot might be as common as the flu shot).

For now the advice is to carry on with the usual precautions, perhaps upping your mask game a bit by doing things like working to make a mask fit well or getting an N95 mask. I personally use a KN95 mask when going indoors someplace for more than five minutes (which is usually once a week to visit the market late at night); most of the time these masks sit in paper bags marked with the date of last use. This seems acceptable https://www.nytimes.com/2021/01/29/opinion/coronavirus-masks.html.

Gotta say, this seems a lousy time for Polis to be touting a Dial 2.0 that is more lenient. Hints from a Denver Post article are that right now it will just be loosening the criteria that determine the levels, which Polis effectively did when he moved everyone to level orange who had been in level red. I guess it is consistent with his mantra that as long as the hospitals aren’t overflowing, everything should be as open as possible. Fewer people dying is still people dying, and not striving to squash the pandemic before any of the variants take hold is missing an opportunity. Politically, though, you can see what he’s thinking. Again, keep in mind just how high prevalence of the disease still remains—we are almost at the same level as early April.

The flip side are public health authorities doing interviews where they say we need to follow all the guidelines until everyone is vaccinated. Um, really? First, we are *never* vaccinating everyone; presumably they mean all those who want it, and the vaccines are not yet approved for children. Second, this advice feels too extreme, and while you probably don’t want to be in a mosh pit anytime soon, you might think that relaxing some restrictions on get-togethers of people who are immunized might be OK. It does seem that the tension between the public health people and politicians isn’t apt to go away any time soon.

Locally numbers are pretty flat and looking like new cases might be asymptotic to 60/day, about 50% above the (current) threshold for going down to level yellow. We have only had one day in the past two weeks where new cases were reported to be less than that threshold, so that isn’t happening soon. Most age groups are seeing a steady decline, the exception being 18-22 year olds who now have an infection rate roughly double all other age groups (though to be fair, one has to wonder what the estimated denominator is for a population that is kind of transient). The percentage of new cases associated with CU keeps rising and is now above 15%. You do wonder at what point the authorities are finally going to acknowledge that this is a problem. Hospitalizations are slowly but erratically declining. Because we are at level orange case levels, the newly approve 5-star program for businesses allows those who meet the criteria to operate at level yellow restrictions, mainly meaning restaurants and gyms can have more people. Statewide cases and hospitalizations continue a slow decline; new cases are back down to late October values but still four times what we had in late August.

We’re a week away from the dorms refilling, so the thing to watch locally will be the numbers as students from out of state come back with little viral gifts for us all…

Feb. 4. COVID exponents. Asymmetric spikes, vaccines and breakthrough cases, Astra-Zeneca strangeness, county moving to 1B.2 vaccinations, downgrades of dial 2.0, encouraging off-campus testing, local numbers decline.

Maybe it interests only me, but the run-up of statewide hospitalizations in October and November was, you might recall, kind of scary as it was well-fit (R^2 of 0.9925) with an exponential doubling every 16.6 days [Boulder County cases were scarier, doubling every 9 days for awhile]. That slowed some on 20 Nov and then turned around almost on a dime on 2 Dec. Since then, statewide hospitalizations have been declining on another exponential, but with a halving time of 36.5 days (R^2 0.9881)—more than twice the time from the uphill side of things. So while it took about 70 days for things to hit a peak, it will take about 140 days or so to return to where we were in late September—which would be late March. So half the year dealing with one spike. Assuming of course there are no changes. Oddly, the Boulder hospitalization curve is nearly symmetric, but the county case data seems to mirror the asymmetry of the state’s hospitalization data (case data is far noisier). Go figure.

One of the concerns we’ve been watching is the degree to which vaccines will reduce transmission of the disease (Recall that the testing was solely on preventing symptomatic cases). Some earlier indications were that they do reduce infection and the possibility of retransmission, and now the AstraZeneca vaccine has shown a reduction in presence of the virus in those vaccinated https://www.nytimes.com/live/2021/02/03/world/covid-19-coronavirus/astrazeneca-coronavirus-vaccine. While they did see asymptomatic infections in some who were vaccinated (so while COVID is widespread, those vaccinated should still be using a mask), nobody got seriously ill (I have seen indications that there were no hospitalizations of those immunized in the phase 3 trials for the four main vaccines; I haven’t tracked down the published studies to verify that). This means that Rt will drop as vaccinations proceed, but not to the degree that hospitalizations will decline as some immunized might transmit the disease.

Another curious feature of the AstraZeneca work is that they find their vaccine is more effective when the spread between the two shots is stretched out to ~3 months. This is cheerful news for Great Britain, where both a decision was made to first get as many people as possible their first shot before doing a second round and the AstraZeneca vaccine was already approved. Whether anything like that is in the cards for the US vaccines currently in play is unclear, but probably unlikely as there apparently wasn’t a variation in time between shots in the testing for either vaccine and there is no stomach with the federal health authorities for ad-libbing the vaccination rules.

The weekly Boulder County Public Health zoom had a lot of focus on vaccinations. The county thinks they can currently get 20,000 - 22,000 people vaccinated per week if that much vaccine shows up (which would mean that were the vaccine available, the county could fully vaccinate everybody in about 30 weeks). In contrast the county had only 800 doses last week but 7000 this week. More than 50% of those over 70 have gotten at least one shot, so the county starting to look at next phase (1B.2): K-12 and pre-K teachers (~10,000 people) and 65-69 year old (18,000 people); that may be starting next week. The phase after that (1B.3) is murky and large (front line workers, those with two or more other conditions), so a lot unknown about that phase still.

The other focus was the coming changes to the COVID dial https://drive.google.com/file/d/1XUgKViQH1_vk2B9xDM4LVcmNg6qqVruo/view; as proposed, Boulder County would immediately drop into level yellow restrictions and quite possibly to level green in short order. While these new levels loosen the number of cases that a given level allows by a lot (about a factor of three), the positivity numbers actually get somewhat tighter (but Boulder has been doing well there of late, <4%). Apparently part of the logic in increasing the number of cases is that the state expects to move counties far more quickly between levels—before it might be a month after a county saw higher cases before it might be formally moved to the higher level; now it is expected to be within a week. The thought is that a quicker response will head off a greater rise over time while allowing more commercial activity. A less obvious change is that hospitalizations will now be counted against the county a person resides in, and not the county where the hospital is; this comes into play for level red. While the rules will remain the same at each level, dropping to Yellow or Green mean increases in restaurant capacity (from 25% to 50% indoors), last call (an hour later each level), gyms (50% capacity), hair and nail care (50%) and many other events, including some campus events. The flip side of this change is that an increase in cases would move a county more rapidly to a higher level of concern. We’ll probably see the new dial officially introduced soon. According to Jeff Zayach of BCPH, the state’s COVID modeling group has looked at this and thinks this will not drop us to lower levels of social distancing (which they now wasn’t to call “transmission control”—which sounds like a task at NASA flight control for avoiding people talking over one another).

Campus messaging has now tried the verb “expected” (to replace “encouraged”) as in "all who live off campus are “expected” to participate in the surveillance testing" (this includes faculty and staff). They have added some incentives, saying that participation will enroll you for a drawing for gift cards or Buff gear, so that is something. Hopefully free stuff will encourage student participation. There is text saying that those regularly on campus should have an assigned day for testing; no idea where you learn that (perhaps this is aimed at students). Supposedly there are enhancements to the BuffPass so that you will get test results through it (I do not see this yet); guess this is “watch this space” territory. Presumably all enhancements will need to be online late next week.

Nothing much new on case numbers. Statewide, hospitalizations continue a slow decline as do new cases; we are back to ~20 October on cases and ~27 October on hospitalizations. Sometime in the next month we should start to see the connection between cases and hospitalizations decouple; exactly when depends on the completion of vaccination of those over 70. There might be hints that immunizations are starting to have an effect. For the first time since late October, nobody over 75 died from COVID-19 this past week in the county. CU now accounts for about 17% of new cases over the past week and 18-24 year olds 28%, but those numbers might finally be stabilizing, though that might be a temporary reprieve until the rest of the students return in the coming week. County cases resumed trending downward after being stuck for a couple of weeks, though we are still quite a ways above the current threshold for level yellow, though we have had a couple days down below the ~42 new case/day level to go down to yellow. Presumably COVID dial 2.0 will be out before we get all the way down.(Pitkin, by the ways, dropped back to level orange after their big spike).

So one more week of fully remote instruction before campus gets a bit busier.

Feb. 8. Dialing down COVID? Ski areas high, Boulder level yellow, what to do?, state models, herd immunity not happening?, UK (alpha) variant spreading, Boulder numbers level, vaccine update, waiting for student tests.

So last Friday the state officially announced the anticipated COVID dial 2.0 and implemented it on Saturday. Well, kind of implemented it on Saturday as it seems this was a one-way street: four counties (Grand, Lake, Crowley, and San Miguel) are at case levels justifying level red even under the new COVID dial and yet they remain at level orange. You might notice that Grand, Lake and San Miguel are associated with ski areas (Lake has Ski Cooper but more to the point, is where a large number of Vail and Copper resort employees live, Grand has Winter Park and Granby Ranch, San Miguel is home to Telluride) and all four are small (Grand, with 15,000, is the largest of the four). There are special rules for counties with less than 20,000 people (Colorado Public Health then looks at positivity rates—which leaves Grand as a problem as the positivity there is 19% (!!-vs 3% in Boulder)); even so, you get the sense that moving a county up to a higher level of restrictions is not going to be quick or level red is going to depend on issues at hospitals. We in Boulder (indeed much of the Front Range) are solidly in level yellow.

So the state says you *can* now do these things; the question remains, should you? Ideally the answer remains no—most of the lessened restrictions are in some of the most troublesome places for infection (restaurants and gyms); in a way I suspect that the governor is hoping people will be super cautious about returning to these businesses so that he can get a win-win: cases continue to decline as folks worried about COVID stay home while pressure from businesses is relaxed and the associated bad press of health authorities shutting down restaurants goes away. The reality remains, case levels remain quite high. But your odds of encountering someone with the disease have dropped: the new regional report from the state COVID modeling group estimates one in 391 Boulder County residents were contagious as of 1/26. Cases have dropped about 10% since then, so maybe a bit fewer than 1 in 400 are contagious. Back in the summer it was probably one in 2,000; in mid-November it was estimated to be 1 in under 150. (in contrast, Denver was estimated to have 1 in 104 infectious in late January—in other words, the worst we’ve seen in Boulder is significantly better than the current situation in Denver—so if you must visit a restaurant, better to stay in Boulder). So we still have a ways to go, though.

The modeling group for the state issued a new report dated the third (posted today). They see social distancing (aka transmission control) as increasing a bit (from 77% to 79%) and Rt around 0.8 (down from ~0.85 in previous weeks, but this is based on hospitalizations, so reflects the situation a couple weeks before—even so there is a trend line that looks to be better than that 79%). Right now the urban parts of the state are doing better than the rural (mountains, west slope and southeastern plains). The total number of infectious Coloradans is now thought to be a bit lower than last April’s peak. So yeah, still pretty high. If we can stay at or near this 79% transmission control number, expansion of the UK variant won’t matter too much, but if that number drops, we will see a resurgence. Will COVID Dial 2.0 encourage people to go out more? If so, that resurgence will be at the governor’s doorstep. None of their current models predicts Colorado exceeding ICU capacity (which is the one red line the governor seems to have). If things continue, we’ll return to summer levels of infection sometime in mid-April (not far from my exponential fit’s guess of late March). Unusually, a regional report was also posted today, with numbers estimating where we were near 1/25. At that point they think Boulder’s Rt was 0.4; this has probably increased in the past week (COVIDActNow never had us that low—low points have been about 0.85).

A chilling quote from a South African scientist in charge of a study finding a relatively poor performance of the AstraZeneca vaccine on the South African variant: “These findings recalibrate thinking about how to approach the pandemic virus and shift the focus from the goal of herd immunity against transmission to the protection of all at risk individuals in population against severe disease.” In other words, this isn’t going away any time soon, and we might expect that instead of a return to normal, we will be forging a new normal. We still aren’t sure how the two US-approved vaccines do against the South African variant, so maybe things won’t be quite that dire.

In equally un-cheery news, the UK variant (B.1.1.7 later alpha) is apparently rapidly spreading in the U.S. (California and Florida being hot spots), supporting the notion that this is truly a more transmissible form of the virus (in Colorado it is thought to still be under 2% of cases). At minimum, this indicates that decline in cases will slow; at worst, that another significant bump is on the way.

On the good side, the FDA has basically said that any adjustments to the vaccines for variants will only need information similar to what is routinely done for the annual flu vaccine. https://arstechnica.com/science/2021/02/tweaking-covid-vaccines-to-fight-variants-wont-require-big-trials-fda-says/. So it does seem like these vaccine makers will be able to make adjustments fairly quickly. However, it is also beginning to smell a bit like we’re headed to an annual COVID vaccine that is built to anticipate the strains of the disease in the coming year.

Meanwhile, Boulder’s 7-day case numbers bottomed on the third and have started a rise away from level blue; hospitalizations have similarly stalled. Or maybe there is just another little burp on the way down, it is too early to know (we’ve had a couple in January like that). On the good side, the infection rate in 18-22 year olds has dropped a lot and the fraction of cases assigned to CU has also dropped. If CU can keep that up in the next two weeks, we’ll be past the last predictable potential spike. State numbers continue to decline; announced deaths over the past week finally dropped below 100 for the first time since early November (keep in mind that announced deaths usually trails actual deaths by a week or two).

Over 32,000 Boulderites have received at least one dose (over a third of them have had both). So we should be closing in on the end of vaccinating those 70 and older. Hopefully the county will avoid scenes like that in Denver where a text broadcast to all employees of the JeffCo school district noting that some extra vaccine was available if you could get to the site within an hour led to a madhouse on person described as “post-apocalyptic”. https://www.denverpost.com/2021/02/07/covid-19-vaccination-denver-jeffco-teachers/. FWIW, JeffCo is the one urban county doing better on COVID-19 than Boulder.

OK, so what to watch this week? Well, given Florida is a leading hotspot for the B.1.1.7 variant and we just had big maskless crowds in the streets in Tampa Bay, might watch and see what happens https://covidactnow.org/us/metro/tampa-st-petersburg-clearwater_fl/?s=1583523—are we still vulnerable to super-spreader events? This could be a major one with the B.1.1.7 variant. Here, watch the CU numbers as students return. It would be a shock if there were not a bunch of cases upon return to campus, so it will really be late next week when we’ll see if there is to be a student-led spike in positive cases. For now, might watch the number of monitoring tests being done on the campus dashboard—its been slowly growing to near 550/weekday; if a significant number of off-campus students start getting tested regularly, that should grow a lot to several thousand/day. (Given that on-campus students have together tested, we will see numbers easily go over 1000/day).

Feb. 11. College v COVID: the spring rematch. Movein for students...and COVID?, modality rules, AstraZeneca not awful?, origins of alpha, local number, Pac-12 update.

OK, so we are in move-in week, and campus has been saying warm and fuzzy things about how much we’ve learned and how things will be better this time. Just like administrators at colleges across the country. America’s source for parents of college students, the New York Times, has taken a peek and…things look just about as bad this spring as last fall https://www.nytimes.com/2021/02/09/us/colleges-covid.html. Lots of the same failings now amplified by B.1.1.7 variant. So we here at CU have the advantage of having watched others already stumble out of the gate…will we build on that knowledge or, like others, just hope for the best?

From the campus zoom, a couple points. There seems to always be a question asking if a student who signed up for in-person could ask that that class now be taught to them remotely, and the very clear answer is that faculty are not obliged to accommodate that request (they can if they want). Another questioner said that an instructor has bailed on in-person instruction, which is a no-no as well. They also said that another instructor was going to have a class vote on modality, which is also no-no. As expected with move-in, surveillance testing jumped by nearly 1000 tests on Monday, which is probably entirely the group moving back on campus, but this dropped off the next couple of days, far below what we’d expect just from the dorms. So off-campus participation appears to still be very low. And on the call campus clarified that the wellness days only apply to students; these are not campus holidays.

Certainly the news that the AstraZeneca vaccine has been paused in South Africa has gotten a lot of attention, but as ArsTechnica points out, the study that shows no real impact of that vaccine on the B.254 (South Africa) variant is a very small one focused on healthy young adults with little or no constraint on whether that vaccine prevents serious infections. Separately, a study was published that showed how evolution in a single, immune-compromised person could produce the UK variant [later alpha]https://www.nature.com/articles/s41586-021-03291-y. On to masks, where the CDC did some work and made two suggestions for better mask wearing: on surgical masks, tie the two corners on each side together to get a snugger fit, and placing a cloth mask over a surgical mask can similarly help with fit https://www.cnn.com/2021/02/10/health/double-masking-cdc-study-escape-wellness/index.html. They point out that you do not want to double mask with [left out--cloth masks, I believe]

If you haven’t checked out the revised Buff Pass, you’ll find it now has the suggested date for weekly monitoring tests as well as a connection for results.

Well, Boulder County numbers remain pretty stagnant with about 60-65 new cases a day. As expected, the fraction due to CU has risen again (to 15% of cases), presumably as infected students are identified by entry testing. Most of the recent vaccinations have been second shot vaccinations; now about half of the 33,000 who’ve had a shot have had both. Over 60% of those 70 and older (total 30,900 people) have gotten at least one shot. As a reminder, level 1b2 covers another 27,400. This week the county got 8000 doses of vaccine; at that rate, level 1b2 will only get finished in late March. A little snippet of information is that the Pfizer vaccine is being handled by the hospitals while the Moderna is being used by Boulder County Public Health. State numbers continue a very slow decline.

Since things are a bit slow, let’s look at our Pac-12 scoreboard to get a sense of how things are changing elsewhere. Last examined 1/18, here we go: Numbers from COVIDactnow.org (last looked at 1/18):

Rank nowlast timecollegecounty case rate per 100kRt old-case rateRt new
18Stanford Santa Clara county 68.91.0310.70.76
25Washington King county 27.41.1911.00.86
34Washington State Whitman county 24.80.9111.70.69
42Oregon Lane county 22.51.0812.50.91
53CU Boulder county 23.60.9415.90.89
61Oregon State Benton county 22.01.1418.40.96
76Cal Alameda county 55.61.0619.30.82
87Utah Salt Lake county 68.01.0232.70.85
9t11tUCLA/USC LA county 139.11.0236.80.72
119Arizona Pima county 112.31.0542.50.75
1210Arizona State Maricopa county 118.71.0743.80.74

Clearly the situation has improved over the entire Pac-12 with some profound improvements (Stanford and LA county kind of stand out). Arizona, much as has been the case throughout the academic year, has been near the bottom and the Pac-12 north continues to hold on to 5 of the top 6 spots with only CU intruding.

So we’ll watch and see next week if (1) CU entices more off-campus participation in testing (looking grim right now) and (2) whether numbers start climbing as students interact.

Feb. 15. COVID^2. Reinfections, immunity and COVID Dial 2.0, endemic endgame, variants and likely responses, colleges try, COVID and public R1 schools, campus tests, returning students and rates.

One of the things many folks were counting on (e.g., Sweden, all those in favor of “natural” herd immunity) was that getting COVID would be a one-time thing. While the medical community has been struggling with the question of reinfection (versus detecting irrelevant viral fragments or a long term infection), it’s beginning to seem like we are seeing the limits of “natural” immunity. A story in the Camera had the disquieting news that resident of a long-term care facility in their 60s was reinfected recently and died. https://www.dailycamera.com/2021/02/12/boulder-county-warns-of-reinfection-reports-6-new-covid-19-deaths/. Another 21 Boulder residents have had confirmed cases of reinfection. Now out of the 18,000 who have been infected, 22 is a small fraction, but if we drop those infected since mid-November (cases of reinfection within 90 days are very rare and usually attributed to shedding of old viral fragments), then it is 22 out of 8000. The article didn’t say when the 22 were originally sickened, but if it was in the spring wave (before June), then we are talking 22 out of 1000. That is starting to get worryingly high.

The second reinfection story has been the spread of variants of the virus (mainly B.1.351 aka 501Y.v2 and P.1 aka 501Y.v3) in areas that were previously ravaged by coronavirus, which has strongly suggested that any immunity from the original virus might not carry over well to variants. While more detailed studies on reinfection are limited, the broad sweep of the numbers involved makes it seem implausible that reinfection is not a major issue.

While we still don’t know just how all this plays out with the immunity from the Pfizer and Moderna vaccines, it does underscore the need to really get the prevalence of the disease down—and down a lot. Which brings us to the ongoing tension between public health officials and elected leaders. As we’ve noted before, COVID dial 2.0 could well be a mistake, encouraging behaviors that will increase prevalence of the disease, especially in the presence of a more contagious variant. Apparently the Denver Post noticed this disconnect and ran a lengthy story on this https://www.denverpost.com/2021/02/12/colorado-restaurants-covid-transmission/. There remain still two paths forward: one is that life can be difficult and you just have to make due as best you can, the other that this is a disaster and those victims (in this case restaurant an bar owners and employees) should be kept financially afloat until the disaster has passed. We are far closer to the first path.

[In a way, this recalls the way immigrants heading west in the middle 19th century behaved. Cholera was devastating during the peak years of migration, leaving orphans and widows right and left, yet people still travelled with visions of a better life beckoning them on. No doubt many felt they were better prepared than others who fell ill and died; you get the feeling that some of the same logic lives on today.]

What is the end game? Increasingly it is that COVID-19 becomes a background threat like the flu: dangerous to some, but with impacts that can be greatly reduced by vaccines. A story in The Atlantic follows this through, pointing out that vaccinations can carry varying levels of success, from preventing serious illness through preventing symptoms to preventing transmission to preventing infection in the first place https://www.theatlantic.com/health/archive/2021/02/herd-immunity-might-be-impossible-even-vaccines/617973/. In the absence of preventing transmission, we’re probably not going to see herd immunity with this disease, so the main focus will be on preventing serious infections. There is the suggestion in this piece that infections in youths might well make COVID-19 no more than a version of the common cold for these youngsters as they grow up, whereas older folks struggle get a sufficient immune response to prevent such a transition. I think I’ve brought this up a few times before; it is hard to see COVID-19 being eradicated in a manner similar to MERS and SARS. It is just too prevalent.

What might that mean for us at universities? If the recent purchase of enough vaccine to inoculate 300 million Americans by July does pan out, before the fall term all of us who want a vaccine will have it (there are fewer than 300 million Americans who say they are open to getting the vaccine, and right now it isn’t approved for those under 16 anyways). Odds are that the disease will not be gone, but the risk of death will drop down to levels like annual flu even with the variants kicking around. (Keep in mind that there is virtually no flu this year at all; if we want to avoid the flu, we’ve now demonstrated precisely how to do it). While we might get nervous if a new variant comes poking around, odds are that authorities are going to be a low slower to pull the emergency lockdown alarm given what we permit today. So I would suggest that plans for fall 2021 should be pretty normal; the balance between a far lower risk of grim outcomes pitted against over a year of living super cautiously is going to shift decisively to doing things as normally as possible. The most likely concession might well be that students will have to get a vaccine to come to college. It might seem odd to juxtapose increasing evidence that we’re not eradicating COVID-19 with an argument that we’ll return to behaving as though it didn’t happen, but that does seem to be the direction we are heading.

Meanwhile, the return of campus infections are driving some pretty strong responses at some schools: Berkeley has a lockdown enforced by police in the dorms, as does Providence College. UMass similarly has told dorm students they are not even allowed to take a walk. UC San Diego has told students that they have to stay on campus. UNC delayed return to in-person after a big post-basketball game party. UMass Amherst instituted a two-week stay-at-home order along with Villanova, Michigan and Michigan State. Clearly colleges are worried that the pile of evidence from the fall that reopening schools led to community infections might make them culpable for a recurrence. Some schools that were successful in the fall are running into headwinds this time out: Duke, for instance, has already blown past the total number of students infected in the fall https://www.chronicle.com/article/some-campuses-have-already-eclipsed-their-fall-covid-19-case-totals-whats-going-on. Frankly I am not sure how some of the draconian responses will work: most of the schools have a lot of off-campus housing, and there is no basis for college administrators to enforce a lockdown on those properties.

An in-depth article on the collision of COVID with student-funded public research universities is worth a peek https://www.chronicle.com/article/the-specter-of-semesters-past. Despite CU not being profiled, you can see all of CU’s problems and approaches illustrated, with loss of state support leading to practices from aggressive out-of-state recruiting to building new amenities to investing heavily in sports teams to shifting to recruiting internationally—all of which leads to the institution simply being unable to not have in-person education (their database has CU as #18 of 161 research publics in the country with 54% of our budget coming from students being on-campus; University of Kansas, which is profiled as facing all kinds of financial meltdowns, is still only at 38% and #84 on the list. Oregon is #4, having invested in both athletics and amenities to attract students from California).

Locally, our week of refilling the dorms led to 6625 surveillance tests and 55 positive PCR tests. This is only about 4000 or so more than testing done in mid-January, indicating that few off-campus students are participating. Now perhaps the number stayed low if dorm students arrived pre-tested; if so, we should see a big jump this coming week as regular testing is required for those in the dorms. But with campus saying they could do 20,000-25,000 tests a week, it seems that we’re failing to really get our students to buy into this. In a way, our best hope at the moment is that off-campus students had returned weeks ago and any spike from them is already baked in. If not, we could find ourselves sitting in the same position as last September. On the good side, campus launched a mobile testing facility today that will hopefully encourage more off-campus students to participate (though it is located on campus).

With the President’s Day holiday, numbers are a little screwy right now. Boulder’s numbers throughout February have been rattling around 60 new cases/day. The state as a whole continues to see slow declines in hospitalizations and new cases. Colorado has administered just under one million doses of vaccine with about 300,000 having had both shots. And yet still only 32% of those 70-79 have been vaccinated according to the state. The 2/10 regional model report shows Boulder with an Rt of 0.5 through the start of the month and one in 429 currently infectious; given the flat numbers since then, the 1 in 429 number is probably still close while Rt has probably risen. (Frankly those numbers seem too optimistic; COVIDActNow has Rt at 0.89).

We’ll learn a bit more later this week, but probably any real insight into whether the student return is going to cause trouble will not show up until next week at the earliest. Numbers this week are likely to reflect some numbers of students arriving from out of town. Whether we follow some other schools into seeing a rebound in infections (other colleges are suspecting small gatherings indoors) is the question to watch.

Feb. 18. As the COVID turns. SoCal variant, seasonality, SUper Bowl of COVID, better numbers except on campus, mental health weekend?, faculty=teachers?, declines larger elsewhere.

Awhile back I mentioned a variant out of California, B.1.426, which hasn’t gotten the publicity of the strains out of the UK, South Africa and Brazil. Maybe it can’t pay a Hollywood publicist enough. Anyways, this variant accounted for 44% of cases in LA in the first half of January and has been found across the globe (including New Zealand—but not, so far, Colorado). As with the other variants of concern, it has altered the spike protein, but much as it took time to really confirm that the UK variant was more infectious, research is still seeking to learn if this variant is more transmissible. https://www.latimes.com/science/story/2021-02-11/coronavirus-variant-first-seen-in-los-angeles-has-spread-around-the-world. Shemin has pointed me to the NY Times’s special page on COVID variants, where you can keep score https://www.nytimes.com/interactive/2021/health/coronavirus-variant-tracker.html (though this page lists the “California variant” as B.1.427 or B.1.429…seems this variant has a lot of aliases). One piece of good news is that the tests being used are not missing these variants, so at least we are not blind to this development.

It is mildly interesting that COVID cases are almost correlated with sunlight: numbers now are like mid-October, which is also true of daylight. Of course the darkest days of COVID here came before the actual darkest days; the decline has been a lot slower than the rise.

Took a peek at the data from the Tampa Bay region. COVID cases had been crashing there until 2/9 when they sharply reversed and started to slowly increase. The Super Bowl was two days earlier. Florida as a whole continued to decline over this time period. So yeah, those Super Bowl celebrations came at a price.

The Presidents Day holiday has kind of messed some with the data. Statewide numbers continue a slow decline in both cases and hospitalizations. Locally, rather surprisingly, cases might have resumed declining in Boulder County after a rather prolonged plateau while hospitalizations are still hung up in the upper 20s per day (there are some large day-to-day variations of late in case numbers, so this bears watching). The decline in cases would be even more substantial if CU was left out: CU-affiliated cases are now responsible for roughly a fifth of the cases in the county, and once again infections are highest in the 18-22 year old bracket. Right now the suspicion is that this is largely reflecting testing of returning students and so might not be of concern long-term. But so far campus’s carrots placed in front of off-campus students—things like getting entered in raffles—have not led to much engagement. With 35,000 students, you’d expect well over 20,000 on campus at some point during the week, meaning you’d hope to see that many tests. Instead last week there were just 6500 tests and so far this week levels are at a very similar number. Campus has added a mobile lab set up near the west edge of campus M-W and down by the housing by the creek on Thursday and Friday. There is some discussion going on with BCPH about off-campus group housing units. This seems like weak tea for the problem at hand.

Incidentally, the mental health day for 3/25 is looking to become a four-day weekend for many students; whether this was an official four-day weekend was actually asked at the weekly CU Zoom. Since we’ve been told no exams or homework due on the 26th, and as it turns out that the 26th is a staff holiday, students are putting two and two together and getting four days off. Look soon for missives from campus about how the 26th is not a day off and possibly encouraging faculty to emphasize that class will be run as usual on the 26th.

Another tidbit of interest from the Zoom is that campus is pursuing getting at least some faculty and staff vaccinated in the educator lane as part of a group of post-secondary schools in the state. The Polis administration has asked that the group provide numbers of student-facing employees to justify this request. As noted before, it isn’t lost on the state administration that CU has bragged about an absence of transmission in its classrooms, meaning that faculty and staff in the classroom are not at any special risk, unlike most K-12 teachers, so this might not work out for CU.

Apparently there are no plans to put the study tents back up on campus. The thought is that spring weather in the Rockies is often poor. Instead more inner study spaces are available for reservation.

Looking at the metro area, appears that Denver qualifies to go down to level blue, which is a surprise, and several other metro counties are at that level in terms of new cases. Boulder is not really making much progress (hospitalizations are actually at a level more consistent with level orange), which may well reflect the influence of CU student returns at this point. However, we are doing well at vaccinating those over 70 (now at 74% with at least one shot).

Finally, those of you teaching, undergrads in particular, you might want to emphasize that participating in the surveillance testing would be quite helpful. We really don’t need a rerun of last September (and recall that that spike came about a month after classes started).

Feb. 22. Ski COVID. Level up at resorts, declining rates here, vaccinations.

Some of you might recall that back on 2/8, I flagged Grand, Lake, and San Miguel counties as places with both high levels of COVID-19 and skiing as a mainstay. Well, that trend has largely continued to gain notice by the state public health folks and finally dribbled out to the media: the Denver Post on Saturday ran a story noting concern with growing COVID-19 infections in mountain counties, specifically noting San Miguel and Grand as having serious problems https://www.denverpost.com/2021/02/20/colorado-ski-towns-coronavirus/. While the story talks about increasing rates, over the past week actually Grand County has come down from level red sickness rates and San Miguel is at level green rates—but the two week incidence rates are far higher. The story notes that one of the variants (probably UK variant [Alpha]) has shown up in San Miguel and Summit counties, among others. Anyways, you might want to be extra cautious going up to any of the ski resorts.

I am hearing that the messaging about an expectation of off-campus student participation in testing is pretty minimal; how much of this is being buried in self-congratulatory emails or laundry lists of items, I cannot say. But it remains clear that students are simply not showing up. Move in week saw 7,038 saliva tests; this past week it was only 6343 tests. Off campus students are not going elsewhere: county-wide testing has actually slowed in the past week. This is simply not going to get the job done.

For now, though, it seems that we are seeing fewer cases from CU now that all are back in Boulder; the fraction of new cases associated with CU is down to ~15% from a high of 23% and the share of cases in 18-22 year olds has declined since last week (but is still higher than any other age group). Vaccination of those over 70 is probably showing up: at New Years, per capita cases were highest in the 75+ group at about 300/100,000 per week; now they are down to nearly the lowest at ~50/100,000. (65-74 year olds have actually had a very low rate for some time, but that looks to be declining a bit too, though more in parallel with other age groups). Overall, Boulder’s numbers are declining, but in a very herky-jerky way; this week, the decline is nearly entirely in the CU cases. We are still floating above the level blue range of new cases (we’d need to average 41 new cases/day; right now we are in the low 50s). Broomfield has been dropped (raised?) to level blue and Denver and JeffCo might be close behind. Meanwhile, things are plateauing or starting to go back up in Larimer and Weld as well as some of the south-central counties. Grand and Lake counties remain the state’s hotspots. Statewide, hospitalizations are now half those at the peak last spring, just under 400 currently in the hospital. New cases though have sat at a plateau for a few days; whether a momentary hesitation in improvement or something more serious will take a few days to determine.

Looking back at the 2/3 state modeling report, we had far fewer in the hospital than they expected for 2/15 (their estimate was a median of 454, 411 were actually hospitalized). Their expectation for just over a week from now was about 340 hospitalized, and that looks pretty plausible (my exponential fit predicts 334). So for now, we remain on track for a long slow decline in cases.

But this long decline is a painfully slow process that could reverse rapidly. Vaccinations were down some this past week, but now 50,000 residents of Boulder have had at least one shot—about 15%. Just under 1.2M Coloradans have gotten at least one shot. Presumably the slowdown was related to difficulty in transporting vaccines from distribution hubs in the midst of some of the bad weather, so we might see real improvements this week.

Feb. 25, California COVID'in. SoCal variant, NYC variant, and Alpha, and their likely impacts; J&J vaccine, off-campus testing, some forecasts, vaccination update.

OK, so back in December there was a lot of suspicion that the sudden rise in cases in Southern California might have been due to a variant much as the UK saw a variant up its caseload. As recently as last week I’ve mentioned this variant (variously labeled B.1.427 and B.1.429 and I think earlier B.1.426), but overall it has gotten little national attention. That might be about to change. A paper due to be posted as a preprint shortly apparently led the LA Times to look into the results of work at UCSF, and the news isn’t encouraging https://www.latimes.com/science/story/2021-02-23/california-homegrown-coronavirus-strain-looks-increasingly-transmissible-and-dangerous. Basically, kind of like with the UK variant, there is epidemiological evidence of increased transmission as well as lab evidence. Plus there is a suspicion that it is more deadly than the more generic strains. In the lab one of the mutations (L452R) looks to improve the virus’s ability to get into human cells—this mutation is not seen in the other worrisome strains out there. It also appears to be somewhat more resistant to antibodies, thus adding to worries that the virus is getting closer to evading current vaccines. So while the country has been focused on the UK, South Africa and Brazil variants, the big one might well be this California variant. But it gets more intense: check out this paragraph from the story relating thoughts of UCSF team leader Dr. Charles Chiu:

"The U.K. and California variants are each armed with enhanced capabilities, and the likelihood that they could circulate in the same population raises the specter of a return to spiking infections and deaths, Chiu said. It also opens the door to a “nightmare scenario”: That the two viruses will meet in a single person, swap their mutations, and create an even more dangerous strain of the SARS-CoV-2 virus.”

Perhaps out of envy, New York has been apparently incubating its own new variant, presently with the catchy title of B.1.526 https://www.nytimes.com/2021/02/24/health/coronavirus-variant-nyc.html. This one has some of the traits of the South Africa and Brazil variants that suggest reduced susceptibility to vaccines and previous infection immunity as well as appearing to be growing in the population. So we just keep motoring along with mutations. Some scientists are more worried than others about these, though not really panicked … so far.

At this point I am waiting for the ads for the sports books to start hustling gambling on which variant will infect the most people or the over/under on how prevalent each variant will become.

If you want an even darker appraisal of the next few months, try Dr. Michael Osterholm, an epidemiologist from the University of Minnesota https://www.mprnews.org/episode/2021/02/18/michael-osterholm-on-how-new-covid-variants-could-change-the-pandemics-trajectory. He is expecting an even higher wave of cases in late March from the UK (B.1.1.7) [Alpha] variant than the nation saw in early January, pointing out that there will still be lots of older Americans unvaccinated and that the increased transmissibility will blow things up. Additionally, he points out that we are still at a high level of infections and that the decline in cases appears to have stalled. Personally, I am not so sure this is that bleak: the Colorado group has tried including B.1.1.7 in their models and unless we regress on behavior, it doesn’t look to blow up. If we do regress some (which has happened before), then the risk appears. [In the event, there was an 'alpha bump' but it was perhaps a third the size of the winter bump]

Now it is worth pointing out that cases have dropped dramatically in California even as that variant increases its share of cases, so we’re not looking at Armageddon here (cases in LA metro are now less common than here in Colorado); even if the variant accounts for 90% of California cases by the end of March, as is posited in the article, that would appear to be 90% of a much smaller number than the 45% of cases at the late December peak: in December in LA there were 64 cases of the variant per 100,000 per week; but with the curve still going down below 17 total cases per 100,000, clearly this variant isn’t blowing up at the moment. This underscores how well the business of masks and distancing and whatnot can be even with these more troublesome variants. This variant is now present in Colorado (described locally as the L452 variant); it and the UK variant amount to 122 known cases in the state, but the South Africa variant has not yet been seen. [The SoCal variant did indeed peter out]

For us, though, recall that 10% of our students are from California; it seems highly likely some of them have brought the California variant back to Boulder. Whether that will matter or not, only time can tell.

Speaking of those California students, I asked at the campus zoom on Tuesday what efforts would be forthcoming to battle the clear absence of off-campus students from any testing. The answer was that we’re doing a wonderful job of reaching those students and the proof is that we gave away some Apple products in our raffle. Um, sorry, no, unless we have almost no in-person classes, the numbers of tests aren’t consistent with a lot of off-campus students being tested. Ask your students if they’ve gotten the message that they are expected to participate if coming on campus and let me know….A quick aside: the plan for the summer was just announced this week (mostly more of the same) and the fall will be in a couple of weeks.

If you want to compare with other schools, the New York Times tracker has been updated to show how things have gone so far this year https://www.nytimes.com/interactive/2021/us/college-covid-tracker.html. (But the number listed for CU Boulder (437) is higher than that from campus’s testing (326) but is lower than the county’s estimate (488) and happens to be identical to CSU’s number in the NY Times list. So might take these numbers with a grain of salt). Kind of funny that a Science News piece on how five campuses dealt with COVID has a lead photo from CU…which is not one of the five campuses in the article https://www.sciencenews.org/article/coronavirus-covid-19-college-university-campus-cases-testing.

OK, trending a little dark today, but you’ve probably already noticed the good vaccine news, with Johnson and Johnson *finally* moving forward and both Moderna and Pfizer promising a big increase in vaccine production such that a third of Americans could be fully vaccinated by the end of March. The long-awaited Johnson and Johnson vaccine is 86% effective against severe COVID-19, which is below the 95% level for the other two approved vaccines but still very good (and just one shot). In addition to ramping up further, Moderna has already developed a new version of their vaccine to specifically address the South African (B.1.351) [beta] variant that has been send in to the FDA.

As for the future with variants in Colorado, supposedly the B.1.1.7 [Alpha] variant doubles over ~10 day periods; reportedly that is kind of what the state is seeing https://www.cpr.org/2021/02/24/covid-variant-mutations-vaccine-colorado/. If that continues, we have a problem that will become terribly clear no later than early April when daily cases from B.1.1.7 would start rocketing up to hundreds of cases a day. Of course if we have a third of the state immunized by then and maybe another 10-20% with some level of immunity from having had COVID-19, the impact might be significantly diminished. Uncertainty lies in not knowing what fraction of the B.1.1.7 cases are being identified at present. We’ll apparently be getting a new study from the state modeling board shortly (the last was in early February); it will be interesting to see how they project possible outcomes with B.1.1.7 and other variants now circulating. [ This is about how it played out, with the peak of Alpha cases coming in April with statewide levels of ~1700/day].

A few tidbits from the county’s Zoom presentation. Vaccinations of those in group 1B1 (70+ and medical personnel) still have 8500 to go. About 80% of those over 70 have gotten at least one shot and nearly half have two; 33% of those 65-69 have gotten a shot as well. While group 1B3 is to open up next Friday (3/5)—that’s those with 2 medical conditions + essential workers—the governor is to speak tomorrow and might revise the order of battle much as he has a few times before. Even if it does go forward as planned, odds are that the county will still be finishing off group 1B1 and probably be focused on 1B2 when 1B3 folks start getting in the queue. Vaccine shipments did slip a bit because of weather (so some 2nd injections were delayed), but those vaccines are on their way. The county is prepared to ramp up in a big way; currently about 7-8,000 vaccines are administered each week, but if more vaccines come in, plans are in place to have a larger vaccine site at the county fairground, which could administer 15,000 more.

As for the local numbers, well, things feel pretty flat, though the last four days have seen some smaller numbers of new cases in the county; we are almost asymptotically approaching level blue numbers (today the state’s page claims we are down to level blue case levels, but the erratic changes in new cases day-to-day makes it likely that we’ll hop back up in a day or two). Maybe in early March we’ll cross that threshold. County hospitalizations are stagnant near 25, as they have been all month (we are doing worse on this than nearly the rest of the state, which is curious and might keep us from level blue). Somewhat surprisingly, positivity numbers have dropped sharply to below 3% after hanging out a long time nearer 3-4%. CU cases are down to under ~15% of the county’s cases, and the 18-22 demographic has retreated to be near levels of other age groups, so any CU-induced spike isn’t evident at this point. Statewide, case numbers actually rose back up some this week; hopefully just a blip rather than a turn for the worse. These seem to be coming from Weld, Adams, and El Paso counties. Statewide hospitalizations continue a slow decline.

Have a good last weekend of February as this “cruelest month” wanders off…see you in March.

March 1. Bipolar COVID. Cases not declining (alpha? laziness?), vaccine progress, paternalistic misguided PSAs, masks still on, local declines to blue?, anniversary of the Colorado start to pandemic life, worst hit states.

Is the news good or bad? Honestly, on the one hand, vaccines. On the other, variants. I will presume you all have digested the latest revision to the vaccine parade in Colorado (60-64? Congrats, Friday you can sign up. Over 50 or a college face-to-face educator? You’ve been bumped up to a new level that might start in a couple of weeks).

Trivia question: which were the five states with the highest mortality from COVID (per million) since July 1? How about overall? Answers at the end.

Well, my dour missive from last week seems to have been matched nationally as COVID numbers are not only refusing to decline further in Colorado, this is also happening nationally, to the dismay of national authorities https://www.nytimes.com/2021/02/26/us/politics/coronavirus-infection-rates.html. Is this like kids on Christmas Eve demanding to open at least one present before they really should? Or is this a somewhat early appearance by our zoo of variants, kicking their heels up? Or are we seeing hiccups from the cold blast that froze Texas and delayed vaccine shipments as well as a lot of testing? Looking state by state, there is certainly a glitch from Texas, where there was a sharp decrease in cases starting ~2/15 and then a rapid recovery by a couple days ago. Places like California and New York continued to see declines while Georgia and New Jersey saw steady rates much like Colorado; Arkansas kind of mirrored Texas. So maybe as yet we aren’t hitting bottom nationally. But then there are indications that 10% of cases are the UK variant (B.1.1.7 later Alpha) and rising, so maybe that is in play https://arstechnica.com/science/2021/03/b-1-1-7-variant-now-10-of-us-cases-and-cases-are-once-again-ticking-up/. Are folks whooping it up prematurely? Well, maybe, but it is just as likely people are being careful as you don’t want to be the one to die of COVID with a vaccine heading your way.

On the good news side, vaccine distribution seems to be accelerating; something like a third of the country should be fully vaccinated near month’s end and everybody in July https://www.cnn.com/2021/03/01/health/covid-vaccines-coming-when-trnd/index.html. The CDC suggested that the second shot of Moderna or Pfizer does improve your odds with the known variants. You’ll know a vaccine surge reached us when you hear of Boulder County Pubic Health opening a big vaccination clinic at the fairgrounds. Phase 1B3 opens on Friday and is expected to include about one million Coloradans; phase 1B4 might open a couple weeks later with another 2.5 million Coloradans eligible. That would get us well over halfway to immunizing everybody sometime in April.

In Colorado, the state modeling group estimates that transmission control (aka social distancing) has declined from 83% to 76%, which has pushed Rt to nearly 1, which is of course the boundary between growth and reduction. While it sounds like reducing transmission control is the kids on Christmas Eve scenario, as this is based on hospitalization numbers, it could also reflect an unrecognized circulation of a variant, too. And as it is based on hospitalizations, this was what was happening a couple weeks ago, infection-wise. So we are once again balanced on a knife-edge; small changes up or down will lead to very different outcomes. Combining revised estimates of the impact of the B.1.1.7 variant with vaccination projections shows that even at our current level of transmission control and even with vaccination proceeding, cases will resume rising in March. At any lower level of transmission control, things start to go bad quickly even with a pretty aggressive vaccination campaign. What will start working in our favor (that isn’t accounted for in these projections) is that the weather will improve, and that might help us some. You might wonder how cases would increase if we are in essence vaccinating everyone who wants one by June, and the answer simply is that they are assuming there will be a population that won’t get the vaccine (plus some cases in those vaccinated).

A novelty in the latest report is an estimate of what fraction of the population is currently immune; they are estimating 22% (and this is considering immunity wearing off over time). If we get another 15% immunized in March and 20% in April, we’ll be knocking on the door of herd immunity in May.

In The Atlantic, Zeynep Tufekci writes about some of the misguided messaging that public health officials, scientists, politicians and the media have put out that may well be counter-productive https://www.theatlantic.com/ideas/archive/2021/02/how-public-health-messaging-backfired/618147/. Paternalistic lecturing by health officials is one (recall the “don’t use a mask” routine, and now the “you’ve got to continue to do everything else even after you are vaccinated"). Kind of related were the rather ridiculously precise rules: stand 6 feet apart was interpreted by some as “I can stand here all day 7 feet away from you and we are OK” which is of course nonsense. Precise wording leads to doing stuff just outside the limits. (The author prefers avoiding the "three C’s—closed spaces, crowded places, and close contact”). Shaming is also frequently misdirected and usually counterproductive. Another oopsie is failing to recognize that there are many risks, and they need to balance, not to be suppressed by the best COVID rules. Perhaps the final one is something we as scientists sometimes fall into: stating that something is unproven when what we mean is that we haven’t tried to prove it yet. An example from the story: "Thus, on January 14, 2020, the WHO stated that there was “no clear evidence of human-to-human transmission.” It should have said, “There is increasing likelihood that human-to-human transmission is taking place, but we haven’t yet proven this, because we have no access to Wuhan, China.” (Cases were already popping up around the world at that point.) Acting as if there was human-to-human transmission during the early weeks of the pandemic would have been wise and preventive.” The current version is “There is no evidence that vaccines work on new variants or stop transmission”—which strictly speaking might be true (though less true each day as there are some studies popping up), but this is more because of the time it takes to do the studies. The expectation is that they will be at least somewhat effective against the variants and they probably will reduce transmission, maybe by a lot. But the effect of that negative statement is to discourage people from getting the vaccine—something the anti-vax crowd recognizes and so spreads those statements around.

So with a lot of advice flying around, just what is reasonable once you are vaccinated and cleared the two weeks after the last shot? Really, it can be a bit hard. Your personal risk will be way down, especially if you are older, so going places you wouldn’t risk earlier is probably the main plus for now. But because you could become an asymptomatic carrier, health officials would kind of like you to still wear the mask and keep your distance. But even there, the risk of transmitting the disease is far lower than prior to vaccination. The hope is that as infection numbers drop, we’ll get to a point where we can drop masks because transmission is very rare. Of course the wrinkle at the moment are the variants circulating: presumably we’ll want to see if we see spread of any variants in vaccinated populations.

OK, well at least in Boulder, cases resumed dropping and we fell into level blue kind of numbers. A lot of this is the rapid decline in CU-related cases to about 7% of new cases; similarly, 18-22 year old case incidence is similar to other age groups. Non-CU cases haven’t really improved much; it kind of looks both in the county and the state like there was a small President’s Day/Valentines Day bump in cases. Boulder stands out from the rest of the Front Range as numbers are gently moving back up nearly across the board; of the Front Range counties, only Boulder and Pueblo (and Gilpin and Clear Creek, though not really Front Range) are lower than level yellow in case numbers. This will be a test of the state’s claim that this new system was to react more quickly: will Broomfield and JeffCo be kicked back to level yellow while Boulder gets promoted to level blue? Statewide case numbers are wobbling around a plateau value a bit over 1000 new cases/day while hospitalizations are very slowly declining. Positivity remains low (3.4% statewide) even though testing has come down from high levels in late fall. Interestingly, while infections are about 3.5x summer levels and hospitalizations are still about triple summer values, deaths have dropped down to closer to double the summer rate: are we seeing some benefit from vaccinations? It seems plausible at this point.

Welcome to March. Spring is coming. A year ago today was when the American Physical Society cancelled their meeting to be held on 3/2/20; that was the start of a crazy two weeks where the roof caved in on all of us. Now at least the pace of change is a lot slower; I’ve been reviewing my emails and notes from a year ago and will send out a kind of memorial around the 12th, which was really the day everything went topsy-turvy.

And the five states with the worst mortality since 1 July: In increasing order of deaths: North Dakota, Alabama, Mississippi, Arizona, and South Dakota (whose governor, you might have heard, has been patting herself on the back for doing a fine job of having 99.8% of the population not die of COVID on her watch). (Colorado is ninth fewest in that time). Even with the big spikes this fall, the top five overall were mainly clobbered last spring when standards of care were in flux: Mississippi, Massachusetts, Rhode Island, New York and, taking the crown for most deaths, New Jersey, where 2.6 out of 1000 have perished. (South Dakota was eighth in the end, but 16th fewest on 7/1; Colorado was 14th most on 7/1 but 11th fewest overall). Finally, if you are wondering, the five states doing the best overall, in improving order, are Utah, Oregon, Alaska, Vermont and Hawaii, where only 307 out of one million have perished, roughly a ninth of what New Jersey saw.

March 4. COVID variables. Cases stable, parties back, vaccines in Boulder, hospital admissions down, Polis update on vaccinations, pandemic over in Texas?, masking to end?, variants, Astra-Zeneca stumbles (again), CAL variant not really a problem?, alpha and different states.

I’m going to put numbers up front and then a couple pertinent items before a rather lengthy digression on variants that may or may not be worth your time.

So this week local case numbers were slowly drifting downward before reversing some the last couple of days. Around us, other counties seem to see-saw more; lately a few have resumed going down while some (like Broomfield) seem to continue to grow. If you want to dig into that fairly easily, there are useful plots for the Front Range at https://www.denverpublichealth.org/clinics-services/infectious-disease-clinic/coronavirus-disease-2019/denver-metro-covid19-data-summary. We were briefly at level blue levels of new cases before returning to level yellow. Oh well, maybe next week, though the 5-star restaurants can now operate at level blue levels. Hospitalizations dropped significantly the last couple of days to a number last seen in late September; hopefully that won’t be a fluke.

And if you forgot that students had returned to campus, well, the big party that Boulder police broke up is that wake-up call to remind us how things went last fall. Recall that COVID levels were low at first, but then we saw a big spike in mid-September that led BCPH to quarantine all 18-22 year olds. We’ll see if campus’s refusal to demand participation in surveillance testing leads to another run-up in cases. For now, it is the 10-17 year old group that is seeing case numbers rise, not the college age crowd.

A bit over 90,000 shots given in Boulder County, so 30,000 have had all their shots and 30,000 more have had one. I guess this will get a bit more complex once the J&J vaccine is here. So probably a bit more than 10% of adults are done and another 10% are well on their way.

Statewide numbers are basically stable but in detail back to slowly falling, though case numbers are still a bit higher than a couple of weeks ago. To give you an idea, the magnitude of the decline in hospitalizations over the ten days before today (from 392 to 341, a decline of 51) is less than the two day increase back on October 18-20 (from 348 to 417, an increase of 69). A number I haven’t been tracking is the number of hospital admissions for COVID. This is less noisy than some other signals, and it has been on a steady decline for many weeks to levels from early October. As for vaccines, nearly a million Coloradans have had one shot, so getting over 20% of the adult population.

On Tuesday Governor Polis led off his news conference with (after an actual drum roll) the news that 70% of those 70 and up have gotten at least one shot, which was his goal for the end of February. He went on to share what he is expecting in terms of vaccine numbers. After a first run of the Johnson & Johnson vaccine this week, there will be a lull in those but they hope to see ~100,000 doses per week in April. The other two vaccines are ramping up from a total of ~250,000/week shortly to 300,000/week in early April. The state is preparing six “pods” for mass vaccination around the state for when we see higher numbers of vaccines coming in; these will be opening later in the month. The governor suggests going through cocovidvaccine.org to find a local vaccination clinic and notes that as the clinics usually only have one type of vaccine, so that if you are picky, you will want to choose your site based on the vaccine they are handling (although he said you would be able to tell from the state website which vaccine a given site had, my poking about failed to locate that information). While doctors keep saying that the best vaccine is the one you can get, a number of Catholic bishops made the statement that the Johnson and Johnson vaccine should be avoided if possible https://www.npr.org/2021/03/03/973486060/church-leaders-say-johnson-johnson-vaccine-should-be-avoided-if-possible. Whether that might slow things remains to be seen.

Elsewhere we have Texas announcing that everything can reopen and all mask mandates are gone https://www.cnn.com/2021/03/02/us/texas-governor-mask-mandate/index.html. The pandemic is over! Um, ’scuz me, governor, but you do know that cases are increasing as you do this, that you are well behind on vaccinating your citizens, that your positivity rate is unacceptably high, and that your overall case numbers are, at the moment, among the worst in the nation? Well, occasionally actions like these have not directly led to disaster, and we’ll hope that the people of Texas will manage to stay safe (recall that 80% or so of good COVID behavior is keyed on local experience and not state mandates), but if this goes off the rails, please, Texans, don’t take your spring break vacation here in Colorado. President Biden wasn’t impressed, labeling this “Neanderthal thinking,” which might just be insulting Neanderthals. Some speculation is that Texas's governor saw how South Dakota’s governor spun her abysmal record in South Dakota into gold at CPAC and he wants in, but this also is to put all that electricity stuff in the rear view mirror. Ain’t politics fun?

For what it is worth, at this writing Gov. Polis has apparently not decided on extending our mask mandate beyond Saturday. Passing on the chance on Tuesday at his press conference, presumably he’s going to let the statewide mandate lapse. Probably urban counties will then declare their own mandates.

Last time we discussed what the rules should or will be once you are vaccinated. The CDC has been working on their suggested rules and, no surprise, about the only activity they see changing in the near term is socializing with other fully vaccinated people https://arstechnica.com/science/2021/03/cdc-to-release-guide-for-life-after-vaccination-with-normalcy-still-far-off/.

OK on to variants, which is more speculation than a recap, so feel free to move on to the latest missive from campus leaders:

We’ve been deluged (well, at minimum you’ve been deluged by me) with info on variants. Keep in mind the majority of evidence we’re working with: changes in the dominant strain of SARS-COV2 measured by sequencing studies, epidemiological calculations on changes in transmissibility, and lab work on how effective different strains are at entering human cells or evading antibodies. Some of this is kind of contradictory: the UK variant [Alpha] that has gotten the most press apparently dominates UK cases, yet those cases have fallen precipitously since the first week of the year (fallen from about 70,000 to ~6000 cases). Similarly, the California variant has become dominant in the Golden State as cases have plummeted. Estimates of Rt and transmission control are based on cases that emerge, not on observations of behavior changes; Rt could go up even as actual “transmission control” actions stay constant. Something I still haven’t puzzled out are statements that these variants are twice as infectious, which I believe means that Rt doubles in the absence of any other change. Given that Rt has rarely even gotten close to 0.5, how is it possible that rates have declined at all in the face of these variants? California certainly didn’t lock down, though the UK did. When you look at mobility data (e.g., https://covid19.apple.com/mobility), you see mobility went up a lot in the UK late in 2020, fueling the surge there, and then a precipitous decline, so it is reasonable to assume that behaviors were an important factor in the UK surge and subsequent decline—perhaps as much or more than the appearance of the variant (to be sure, there have been studies addressing this that determined that B.1.1.7 is in fact more transmissible). In California, you don’t see any similar change in mobility to explain the large late December-early January spike—in fact, mobility had slowly been declining for months into the spike, and since then has been increasing as cases have plummeted. You almost get the feeling that the California variant somehow outcompetes other strains but is somehow a lot less infectious (how would that even be possible?). (Or, of course, there is something about the California lifestyle that makes you more isolated the more you are traveling about—time spent in traffic is time not getting COVID?). In short, separating underlying characteristics of a variant from the environment in which it emerges is tricky; when combined with a tendency for caution, just how bad these things are might well be overstated.

Obviously this is all amateur sleuthing, but the point is that there are a lot of moving parts, and generally researchers will focus on their part of the elephant. So if the lab says the variant can enter cells more easily and the sequencing says a variant is responsible for more of the cases, we add one and one and maybe are getting three. Recall that there was some panic that immunity was going to fade away based on some early antibody work, but then T-cell work suggested immunity is much longer lived. We might be seeing something similar now, as a preprint indicates that T cells don’t really care which variant they face https://www.biorxiv.org/content/10.1101/2021.02.27.433180v1. Now this is another lab study of one facet of this whole thing, but it does suggest that the variants might not have quite as severe an impact.

Now keep in mind that what matters are effects on the ground. Sometimes things aren’t what they seem. The “failure” of the Astra-Zeneca vaccine in South Africa might be more an issue with inadequate test design than actual failure (their subjects were mostly young adults least likely to yield a clear signal about protection from severe disease, which was the main goal of these studies). Frankly, from top to bottom, Astra-Zeneca/Oxford has been one of the more amateurish efforts out there, starting with their bizarre mistake in initial doses of the vaccine to a subset of subjects, continuing with the very low numbers of older adults in their studies, which led the French to not recommend the vaccine for those over 65 until recently, to this South African blunder. Hopefully their vaccine is better than their testing capability: the massive use of the vaccine in the UK suggests it is in fact proving effective https://www.nytimes.com/2021/02/22/world/europe/vaccine-studies-UK-hospital.html. And there is talk that the lower success rate of the J&J vaccine is actually because it was tested later, when these variants were starting to cruise around. So it can be hard to identify the signal you care about (how good was the vaccine) from the surrounding noise (how well was the study done, and were the conditions comparable). Beginning to sound like a theme, no?

On the other hand, the rise in cases of a city in Brazil (Manaus) by the P.1 variant [later gamma], which appears to be reinfecting significant numbers of people, does point to very real hazards, but there is a lot odd about the original widespread infections in Manaus https://www.nytimes.com/2021/03/01/health/covid-19-coronavirus-brazil-variant.html. So while the Brazilian situation bears watching, it isn’t yet clear it is the disaster it might seem to be.

So are worries about the variants utterly overblown? Well, it is hard to know. Researchers in California argue that their variant (B.1.457/459 or CAL.20C) is more infectious because it outcompetes the previously dominant strains, but this is largely happening statewide as cases plummet. Did Californians really improve behavior that much? Even as indoor church services were restarted after a Supreme Court ruling? Even as health officials were resigning out of frustration that their advice was falling on deaf ears? The California variant has had fewer studies than the UK one, so maybe it is just luck of the draw, but it does suggest that outcompeting may not be the same as being far more contagious.

At this point, we’ll probably start to get more robust answers as differences between states permit more natural experiments to occur. Nearly everything right now suggests that infections should be receding: vaccinations are taking place, weather is improving, family gathering holidays are behind us, colleges that are returning students to campus have done so, messaging about masks and social distancing is more coherent (e.g., OSHA has put out workplace rules). So if we see rising numbers of cases in places where a variant is widespread while cases continue to decline in other areas, it will get crystal clear how dangerous that variant is. If hospitalizations increase even as the most vulnerable are vaccinated, we’ll learn either that a variant does get around a vaccine (if the vaccinated are falling ill) or that it is a more serious form of the disease (if the unvaccinated are ending up in hospitals more frequently). So are the higher number of cases in Texas, Georgia, Florida and New York proof of the potency of the B.1.1.7 virus, which has been seen in more than 100 cases in each state? Maybe, but California and Michigan and Colorado also have seen that variant in those numbers without case numbers quite as high, and California in particular is decreasing a lot. Guess we’ll be watching; so far cases are not rising in any of these states (well, maybe Texas).

OK, sorry, just was one of those things I’ve been noodling on...

March 7. Year of living COVIDly. Special recap of events a year before.

A usual update tomorrow (with some details on vaccines you might find helpful), but it was a year ago this coming week when all the wheels came off the wagon; here are the main milestones here in CU…

A year ago, campus abruptly came to a screeching stop as worries about the novel coronavirus finally took hold. While the pandemic seemed to be raging back then, we have grown numb to levels far higher than what shut campus down in March of 2020. Of course part of the reason is ignorance back then—we weren’t sure how bad things could get, we weren’t sure where the virus was hiding, and advice on preventative measures was largely guesswork. So a quick peek back at the start of this year of living with coronavirus. It is quite something to see just how compressed the timing was between “we’re planning in case of trouble” and near-panic.

CU’s first official missives on coronavirus came on 29 January 2020 https://www.colorado.edu/today/2020/01/29/cu-boulder-monitoring-coronavirus-updates. At the time, travel to China was being restricted, but otherwise no special changes were in the offing. February was largely spent in recalling study abroad students; planning was underway to consider having to adjust for the virus; Dan Jones sent an email to campus on 2/26/20 saying "Our university has specific plans to guide our response to infectious disease outbreaks. Plans include procedures to allow for continued operations in the event that any cases are confirmed locally. Additional guidelines are being developed for situations where remote work or teaching may become necessary.” As we know, that last sentence proved to be ominous. But at the time, there were no known cases in Colorado (though in hindsight, it was likely circulating in some of the ski towns at this point). Still, February ended with little change to all our lives.

March 1, though, made clear that the landscape was shifting under our feet. The American Physical Society abruptly cancelled its meeting in Denver a mere 24 hours before it was to start. Emails were circulating speculating on how a spring break field trip would be run. The possibility of teaching remotely was now openly part of departmental discussions on 3/2. Advice at the time looks kind of awful in retrospect; an article from the Colorado Sun shared with faculty ended with a do’s and don’ts list: 'DO Wash your hands. DON’T Wear a mask, unless you’re sick. “They really are not going to help you,” University of Colorado Hospital Dr. Michelle Barron said of face masks. The reason? “The basic principle of respiratory viruses is that they are spread by your hands,” she said.’ This following an article talking about negative pressure rooms and mask usage in the hospital; this was certainly misguided advice that was widespread at the time. Prospective grad student trips started to be cancelled.

The first Colorado cases were announced on 5 March; campus activated its emergency response team. University sponsored international travel was shut down. Wardenburg finally ended the practice of providing doctor’s notes to excuse an absence on 3/7. Campus was advising those planning to travel to check the CDC’s website. By March 9, 9 cases were in Colorado and testing of some suspected CU employees had started. Campus started allowing for remote instruction. TP was vanishing from stores.

On March 11, the boom was lowered both at CU and nationally. As the NBA shut down its season, Chancellor DiStefano announced that on Monday, 16 March campus would go to fully remote instruction (although there was allowance for classes that needed more time to transition to the 30th—it wasn’t clear if the extra time would have no instruction or continued in-person instruction). All university-sponsored travel was banned. We didn’t even make it to the 16th: on March 12 campus had its first positive case of COVID-19, and campus preemptively shut down all in-person classes for Friday the 13th, announcing this at 10:45 pm on the 12th. The 13th also saw the first COVID death in Colorado. Our year of living COVIDly had begun less than two weeks after it was clearly on the horizon.

The following day, Gov. Polis shut down the ski resorts; two days later, all restaurants and bars were closed. Nine days later, on the 25th, Polis issued a stay at home order for the whole state. Hospitalizations would actually peak just over a week later, though those numbers stayed high into late April.

In a way it is hard to remember, a year out, just how stunningly abrupt all this was. The nation was watching the impeachment of President Trump into the first week of February, so there was barely a month from really starting to pay some attention to COVID to being under its thumb. It is a reminder just how fast things can turn on you with a fairly communicable disease, and this might be a good time to remember this in case one of the variants circulating really does get out from under our control.

We’ve made it this far; whether we emerge to our old normal or something akin to it should occur over the summer, judging from vaccine numbers and the general decline of COVID transmission in the summer last year. Unlike the start, that transition will be many small steps—first sit-down indoor restaurant meal, first movie in a theater, first concert or ball game. First meal with friends without masks. In a way it is too bad there won’t be a magic moment when we can all run into the streets and celebrate, ala V-E day. The New York Times estimated that one in three Americans has lost someone dear to them to COVID. We need to use this costly lesson to avoid even direr outcomes from climate change and other threats. This pandemic was foreseen in many ways; Dr. Fauci had described it nearly to a tee some years ago when asked what kept him up at night. Science can give us foresight into events we might otherwise fail to anticipate: plagues, ozone holes, droughts, tsunamis, earthquakes, volcanoes, floods. It can also arm us to be resilient in the face of threats. Most of you reading this know this, but maybe now would be a good time to make sure others know it as well.

Daylight Savings is a week away and spring a week later. We’ve come most of the way through this storm; enjoy the signs of softening weather and lessening worries.

March 8. Picky, picky: COVID vaccines. Cases still stable, more vaccinations, COVID in vacation spots, Alpha and Gamma in Colorado, masks still on, Alpha spike, student party/riot an outdoor spreader event?, a day off of COVID deaths, probing vaccine numbers (deep dive), vaccine pickers, real-world Pfizer data, calculating the odds, comparing with flu.

Again, numbers first and then another bonus blurb recounting a deeper dive I’ve made into the statistics on the vaccines we have in the U.S.

As a county, we keep flirting with Level Blue illness numbers, which is saying we’re kind of sitting on a plateau. Today we’d be level blue. So a slight decrease in cases was accompanied by an increase in CU cases, back to about 15% of new cases—not a good look with the party this weekend. While hospitalizations finally took a turn for the better, falling to numbers last seen in mid-September, statewide numbers are only very slowly dropping, though new cases finally dropped below the mid-February low point and hospitalizations briefly fell to under 300. Meanwhile, other Front Range counties are wobbling around in new cases, with Douglas, Adams and JeffCo rising up of late. It feels like we’re getting close to a bottom; whether it turns up or kind of stays at these levels or finds a way down remains to be seen. National numbers continue their slow decline (8000-9000 fewer daily cases/week), and the reversal a week or so ago is more clearly an artifact of the winter storm that hit.

Vaccinations proceed. Over 66,000 Boulderites (20% of total population, 24% of those who can get vaccinated) have gotten at least one shot and 11,000 more doses were in the county last week (you’d expect more this week). 87% of those over 70 have gotten at least one shot in Boulder (highest percentage in the Front Range). 37,000 are done with shots. Statewide, more than one million have gotten a shot.

With spring break coming for some out of state, we might be seeing visitors over the coming month, so let’s check in with our local canary in the coal mine, Estes Park. The last week of February was brutal: from 2/22 to 3/2 there were 25 new cases in Estes, compared to 34 from 2/1 to 2/21 (2.8 vs 1.6/day). Is this a harbinger of trouble to come? We’ve got something of a baseline and now we watch. Another spot we can watch (though not as closely) is Vail. Eagle County has been seeing about 20 new cases/day for awhile now. However, unlike any other time in the pandemic, cases are pretty similar across the country at the moment.

It took awhile longer than I’d have expected, but the South African variant (B.1.351) [later Gamma] has made it to Colorado https://www.denverpost.com/2021/03/07/colorado-south-african-covid-variant/. The CDC is keeping track of variant case numbers reported to them: https://www.cdc.gov/coronavirus/2019-ncov/transmission/variant-cases.html. Colorado is #4 in B.1.1.7 [Alpha] cases behind only Florida (motto: number one again in things only Florida Man would think cool), Michigan and California. Of course these numbers are strongly dependent on the level of sequencing of samples, which varies a lot state-to-state https://www.sciencemag.org/news/2021/02/us-rushes-fill-void-viral-sequencing-worrisome-coronavirus-variants-spread—but Colorado isn’t particularly high on the list, and our population is smaller than these other states, so that count might be a worry.

Gov. Polis waited until the last minute to decide to continue the statewide mask mandate. You do have to wonder how much of that decision was driven by the firestorm aimed at Texas (including having the president call it “Neanderthal thinking”) and how much was waiting to see…what, a rapid plunge in new cases? And the CDC has given guidance on what those fully vaccinated should and should not do https://www.cnn.com/2021/03/08/health/covid-19-vaccine-cdc-guidelines-fully-vaccinated/index.html; this seems pretty reasonable given the current situation.

Some folks are expecting a spike in COVID in Texas because of Gov. Abbott’s declarations. Frankly, I doubt we’ll see too much different that can be attributed to that move given the usual delay in a spike after changes in behavior, issues from the recent cold snap as well as the rest of the U.S. potentially seeing a spike as B.1.1.7 grows exponentially https://www.nytimes.com/interactive/2021/03/06/us/coronavirus-variant-sequencing.html. In fact some European countries are getting slammed as B.1.1.7 rises up, so a fourth spike is definitely a worry https://apnews.com/article/europe-england-coronavirus-pandemic-france-milan-2b4e8c5092db92c38194884a4b8049e4. It could be we might see a return to more stringent rules if the B.1.1.7 rises faster than vaccinations damp it down. Anyways, what happened last summer was that some states removed restrictions and the public responded quite cautiously; it took well over a month before everybody thought it was safe to go into businesses again and cases finally ramped up. With vaccines chugging along and weather improving, a decent chance we’ll see little special in Texas. Although their rule change has inspired the Colorado tourism folks to make ads aimed at Texans traveling on spring break to make sure they know we still have a mask mandate.

And as long as we are considering potential means of spreading COVID, how about inviting about 800 students to 10th and Pennsylvania on Saturday night? You’ll recall The Atlantic piece I linked to last time that argued that there haven’t been any superspreader events outdoors. This event certainly seemed to be trying its best, and of course we don’t know what the scene was indoors, so maybe little will come of it (well, other than a few suspensions or expellations and an arrest or two). BCPH will be watching closely over the next week. If you thought students had learned good behavior from the fall…well, optimism dies hard. It might well be more concerning that students felt this was an appropriate behavior than the actual event: potentially more damaging behavior might be going on indoors (this is probably part of the reason it is so hard to call an outdoor event a superspreader, for like Trump’s Rose Garden intro of his Supreme Court pick, there were elements both outdoors and indoors, and we know indoors is worse). So we’ll watch the numbers closely in the next couple of weeks to see if trouble is brewing… and this is a reminder that testing those off campus students would be a really, really good idea. But CU Boulder Chief Operating Officer Patrick O’Rourke "asked anyone in the campus community who attended to immediately quarantine and participate in monitoring testing” https://www.dailycamera.com/2021/03/07/cu-students-clean-damage-after-university-hill-out-of-control-party/. Um, yeah, folks who participated in a party with several hundred folks, most unmasked, certainly understanding the risks in a pandemic will be first in line for monitoring testing…(And yes, this adventure made some national news sites, e.g. ABC News https://abcnews.go.com/US/hundreds-rowdy-revelers-throw-control-street-party-university/story?id=76307613 and CNN https://www.cnn.com/2021/03/07/us/boulder-colorado-large-party-officers-injured/index.html).

Although it is a bit of a fluke, Saturday the state announced no new COVID-related deaths, which is a first for a very long time. Even if a fluke (three more deaths were announced Sunday but only 1 Monday), deaths are down to ~6/day after hovering well over 65/day back in early December; that factor of 10 decrease is better than the factor of 5 decrease in new cases and the factor of six decrease in hospitalizations; it is possible that this reflects vaccinations of those over 70 filtering through the system.

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OK, on to vaccine numbers. You all have seen “95% effective” and “72% effective”—but what are those numbers really saying? Effective against…what, exactly? And you’ve also heard health authorities say the vaccines are all great—which should make you wonder if this is health authority speak for “We know they are different, but as we really think you should get one of them ASAP, we’re going to say out loud that they are all equally good.” Evidently I’m not the only one wondering, as a story in The Atlantic also tackled this https://www.theatlantic.com/health/archive/2021/03/pfizer-moderna-and-johnson-johnson-vaccines-compared/618226/. We now have three vaccines, and while the first two were so similar, both in technology used and efficacy, that there was little reason to pick one over the other, the Johnson and Johnson vaccine has opened up several cans of worms. Should it be prioritized for those who will have difficulty arranging a second shot (e.g., far from hospitals, homeless, etc.)? Or those living where the super cold freezers for the other vaccines are absent? Or is that ghettoizing certain groups? (The mayor of Detroit sent back a J&J vaccine package kind of viewing it that way). Is Johnson and Johnson a lot worse? So let’s actually dig through the most relevant numbers, namely the reports of the phase 3 trials, and then see what else we know.

First up, what were the trials testing? The decision was made to test for symptomatic COVID. Other things like hospitalizations and deaths were auxiliary data not likely to reach a level of significance in the desired time frame. Basically, time was short and looking for sick participants was the quickest way to learn something. Interestingly, landing in a hospital was not something most of the trials looked at, so several of the reports lack that information. What was usually reported was severe COVID-19—which need not have put somebody in the hospital (conversely some with milder cases might enter the hospital as a precaution). Got that? OK, here we go.

Moderna was reported in the New England Journal of Medicine in early February https://www.nejm.org/doi/full/10.1056/NEJMoa2035389. All the trials were in the U.S.. Just over 15,000 received the vaccine and an equal number a placebo. 185 in the placebo group developed COVID with symptoms. Only 11 of those receiving the vaccine did. Thirty people got severe COVID and one died: all in the placebo group. So if you are keeping track, your odds of developing symptoms drop by about 174/185 or 94%; your odds of getting severe COVID are effectively zero (30/30), but given the numbers could be only reduced by something less [one vaccinated person did end up with severe COVID that was not included in the NEJM report]. The population’s demographics had 25% of the participants over 65. Roughly half of those getting the vaccine reported side effects, especially after the second shot, with headaches, fatigue, myalgia (muscle pain); a bit under a quarter of those getting the placebo reported similar side effects (though with lower grades).

Pfizer was also reported in the NEJM in late December https://www.nejm.org/doi/full/10.1056/NEJMoa2034577. Trials were mainly in the US (about 3/4 of test subjects) but also some trials were in Turkey, Germany, South Africa and Brazil. Just under 22,000 received the vaccine and another 22,000 the placebo. 42% were 55 or older. Interestingly, the incidence of COVID for those receiving the vaccine slowed greatly about 11 days after the *first* dose, so while you don’t get the full benefit of the vaccine until after the second dose, you are a *lot* better off just under 2 weeks from the first one. Side effects were split into the younger and older subjects; older folks had somewhat lower levels of side effects, but again roughly half of the participants saw fatigue, headaches, or muscle aches (though this might be a bit lower than the Moderna vaccine). Of those who had no indication of infection prior to the trial (a bit over 18,000 participants in each side), there were 162 who developed COVID symptoms on the placebo leg but only 8 on the vaccine leg. Only 10 severe cases of COVID appeared, 9 in the placebo group, one in the vaccine group (who developed the disease more than a week after the second shot). No deaths were reported in the trial. So we’re in the land of small numbers with only 10 severe cases (vs. the 30 in the Moderna trial). The most robust number, the improvement in symptomatic COVID, was essentially identical.

OK, Johnson and Johnson. As this was more recently approved (more than 2 months after the first two), we don’t quite have the same documentation. So I’m looking at the NIH’s interim analysis https://www.nih.gov/news-events/news-releases/janssen-investigational-covid-19-vaccine-interim-analysis-phase-3-clinical-data-released and J&J’s press release https://www.jnj.com/johnson-johnson-covid-19-vaccine-authorized-by-u-s-fda-for-emergency-usefirst-single-shot-vaccine-in-fight-against-global-pandemic and a website compiled by Hilda Bastian (author of the Atlantic story) http://hildabastian.net/index.php/107. This was a far more internationally based trial with about 44,000 total participants again split into two legs, with 34% over age 60. In the U.S. (where 44% of participants were), the vaccine was 72% effective in preventing moderate or severe COVID-19 but only 57% effective in South Africa, which may well reflect the South African variant coming into play. Overall it was reported to be 67% effective, with 65 ill on the vaccine side and 193 on the control side. It was 85% effective against severe COVID across the full study (5 vs. 34). Nobody who got the vaccine died of COVID-19, but 5 on the placebo side did. And NBC News reports says that nobody who was vaccinated was even hospitalized https://www.nbcnews.com/health/health-news/how-effective-johnson-johnson-vaccine-what-know-n1259652, though this is a mild distortion (2 vaccinated landed in the hospital between 2 and 4 weeks after vaccination, compared to 8 with the placebo; after four weeks the numbers drop to 0 and 5). The NBC News report also claims that this vaccine’s success rate gradually increases with time to 90% effective a couple months out from the shot. It also claims that side effects are reduced with this vaccine compared to the others. The tougher question is, why 72% when the others hit 95% on preventing symptomatic COVID? Is it just having faced a broader array of variants? (They really were not circulating in the US at that time). Or maybe this vaccine does require more time to become fully effective such that starting to count at 4 weeks from the shot is a bit too soon? Or maybe it is indeed a bit less successful? Realistically, we don’t know. Could be J&J out more than a month is about equal to the others once you are dealing with the same variants and other issues. Presumably there will be efforts to track this in the population at large.

Should you get picky about the vaccine you are offered? Well, probably not at this point, but it is worth noting that the numbers on hospitalizations and deaths are way too low to accept any probability (certainly not 100% effective at preventing death, as stated in some stories). J&J looked at illness four weeks from injection, which works out to the same time period as Pfizer (3 weeks between shots and then efficacy a week after second shot) while Moderna’s calculations start 6 weeks after the first injection (4 weeks between shots and two weeks after the second to consider efficacy). If you are really worried about the side effects of the shots, Johnson and Johnson will make you happier (significant side effects were far lower than the other two). If you are wanting to play what seem the best odds at the moment, Moderna looks a bit better simply because there were a few more cases in the control group. And if you want to use an mRNA vaccine and be “immunized” sooner, Pfizer buys you a couple of weeks relative to Moderna. If you are worried that mRNA technology is still pretty much on trial, the J&J vaccine uses a technology previously fully approved for an Ebola vaccine. These are relatively petty concerns, but I hope that the numbers here help you get a handle on these claims that bounce around.

Now there is some real-world data coming in. The Pfizer vaccine has been in use in Israel, where a study looked at a *million* histories, half vaccinated, half not https://www.nejm.org/doi/10.1056/NEJMoa2101765. There is a lot here, but basically the infection rate for those given the Pfizer vaccine diverged from that of unvaccinated people at about 14 days after the first shot. If we look at the first two weeks of the period after the vaccine is considered fully effective (i.e., four weeks-six weeks after the first shot), we get these splits: 325 unvaccinated people were diagnosed with COVID, 55 of those vaccinated were (this includes some asymptomatic cases). Mild symptomatic COVID: 274 vs 16, 94% improvement. Hospitalization: 15 vs 2 (87%). Severe COVID 17 vs 3 (82%). Death: 5 vs 2. This might be biased low as the authors noted that the matched unvaccinated people were on average younger, and we know bad outcomes are less common among the young. It also appears that the numbers continue to improve into the last week the study had data. A somewhat similar study in Scotland found that the Astra-Zeneca vaccine was reducing hospital visits by 94% and Pfizer 85% four weeks after the first shot, though the methodology was far more primitive than the Israeli study and not set up to properly compare the two vaccines . So even with B.1.1.7 prevalent in both Israel and Scotland, these vaccines are knocking down infections a lot. These numbers are probably being updated frequently somewhere, but I’m not seeing them.

But I think those numbers are also revealing why we sort of get this split messaging from public health authorities along the lines of “these are all great, but you’ll still be wearing face masks, etc., for some time to come.” A reduction in hospitalizations of 85% means that if you were facing a 6% chance of landing in a hospital should you have gotten COVID [probably about the number for early 70s], now your odds are a hair under 1%. So while your odds have improved, is it worth sitting in a crowded theater? Presumably what will do that is seeing the prevalence of the disease drop. Say today that one in a hundred are contagious, so if you go to a restaurant twice a week and a movie theater once, you might be sharing the air with 200 people, 2 of whom might be contagious. Let’s say your odds are one in twenty of catching COVID in these environments, so say in that week you have a 5% chance of catching COVID living as usual. Odds of going to the hospital pre-vaccination are about 0.3% for numbers used here [your numbers will be quite different]. Your immunization gets you down to about 0.045% chance of going to the hospital, or one in over 2000. Doesn’t sound too bad. Repeat weekly and your chances keep inching up; after three months (14 weeks) your odds start to look poorer—maybe 1 in 150. But if the prevalence of the disease drops to a level Dr. Fauci suggested (10,000 daily cases nationally, so if contagious for 10 days, 100,000 out of 330,000,000 or 1 in 3300 contagious at a time), your odds now drop to 1 in 5000 of ending up in the hospital after three months of getting out and about. Probably in the first case you might opt for being cautious (masks, minimizing indoor with non-household/non-vaccinated folks), but in the second you might feel OK with things.

[If you are wondering, in Colorado, on average, of the 410,000 who have had a confirmed case of COVID, 24,000 have entered the hospital and 6000 have died. Since we know there were far more cases than confirmed, the state estimated there have been 1.5M infections, so odds of going to a hospital once you’ve contracted COVID overall are 1 in 62 or 1.6%, and of death 0.4%. This is obviously far higher for older adults and lower for younger ones; my numbers above might be for somebody near 72].

How does this compare with flu? CDC’s guess for 2019-2020 (which was sort of cut off as COVID came about) was ~40M illnesses, something over half a million hospitalizations, and over 40,000 dead of flu in a somewhat above average year, and somewhat like COVID, this is skewed heavily towards older adults (mortality over 65 is 49/100,000 compared to 12/100,000 overall). The flu vaccine generally reduces the severity of the disease if you get it (estimated to reduce doctor visits by 50% and ICU visits by 82%). Generally most of us view this as a nuisance despite that chance of death in the range of 1 in 8000 (0.0125%). With the COVID vaccines reducing the chance of hospitalization and death by perhaps a factor of 10-20, had the vaccine been around from the start we might have had fewer than 50,000 dead from COVID instead of half a million. So in a sense, once you are vaccinated, you are probably playing with roughly the same kind of odds you take during flu season if COVID incidence is down in the 1 in 1000 range or better. (Yes, it is more complicated; this is just an order-of-magnitude napkin calculation to help place this in context).

OK, that’s quite enough. Hopefully the vaccine fairy will visit you soon and bless you with the vaccine your heart desires.


Please send mail to cjones@colorado.edu if you encounter any problems or have suggestions.

C. H. Jones | CIRES | Dept. of Geological Sciences | Univ. of Colorado at Boulder

Last modified at December 27, 2021 2:57 PM