COVID Transmissions for 2-25-2022

Update on BA.2, and a discussion of how to navigate the path forward

Feb 25, 2022

Greetings from an undisclosed location in my apartment. Welcome to COVID Transmissions.

It has been 802 days since the first documented human case of COVID-19. In 802, approximately, Vikings plundered Iona Abbey on the western coast of Scotland. I mention this because at this point in history, the Vikings and their raids were on the rise. They were to become quite important—and to reshape the nature of European militaries in the process, requiring flexibility and rapid responses. From this need, we saw the rise of castles and mounted knights, ready to ride out and meet raiders when they struck.

Flexibility to changes in the COVID-19 pandemic is something we need to have, too—and we’ll discuss that to a degree today.

Today covers a lot of ground—evidence of lung damage in recovered children, an update on the BA.2 variant, a discussion trying to predict CDC changes to mask guidance, and I even second-guess my statements on ivermectin from last issue, by bringing in an alternate expert opinion.

Oh, and also, because of popular demand, I describe my personal risk calculations for deciding if I think it’s safe to go to indoor events.

Have a great weekend!

Bolded terms are linked to the running newsletter glossary.

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Now, let’s talk COVID.

Lung function in recovered children

I found this image very striking and wanted to share it with you:

Image shows functional MRI of lungs in children after COVID-19. The top row shows a healthy control, then a recovered child, then a child with Long COVID. In each column, in order, we see measures of lung ventilation, blood perfusion of the lungs, and then a measure of combined defects in lung function. In that last column, green is the good color—purple, red, and blue suggest problems. The healthy child looks healthy—nice bright and even ventilation and perfusion throughout the organ, all green on the “combined defects.” The recovered child has clear reductions in ventilation and perfusion and the combined defects image shows problems abound. In the Long COVID child, the situation is even worse.

Here we see representative images suggesting that even recovery from COVID-19 in a child can lead to at least somewhat persistent lung problems. It does not take a lot of expertise to interpret this figure; the lung is about breathing in (ventilating) and providing those breaths to blood (perfusion being essential for this). When you have more ventilation and more perfusion, that’s a sign of healthy lung function. Here, the kids who recovered from COVID-19, whether they have Long COVID or not, have deficits in both key lung function measures; it’s obvious because the two scans show less signal.

Oh, and importantly? All the kids in this study were unvaccinated.

This demonstrates the dangers of treating a poorly-understood emerging disease like it is no big deal. Lung function doesn’t recover easily. Loss of lung function can be lifelong, and generally, it peaks in childhood and begins a slow decline as you age (though this can be reversed to a degree with exercise). Damaging kids’ lungs with COVID-19 sets them up for problems later. This is something to be avoided.

Image from this study: https://www.medrxiv.org/content/10.1101/2022.02.21.22270909v1.full.pdf

BA.2 subvariant update

The BA.2 Omicron subvariant, which I first mentioned here a few weeks ago, is spreading in the US and continues to spread around the world.

I continue to see claims that it is “more contagious,” but as I’ve mentioned before I think that such claims are often based on weak evidence. At this time I believe it is clear that when there is a head-to-head competition between BA.1 and BA.2 for the same group of hosts, BA.2 wins at infecting those hosts more than BA.1 does. That does not mean that BA.2 infects more of those hosts than BA.1 would have.

There is some observational data—and very limited—that it seems to spread a bit faster in some places than BA.1 might. Danish data suggest a 30% transmissibility gain, but these aren’t the only numbers out there. At this time, I do not think the numbers that are available are entirely reliable on this question—and neither does the WHO, who discuss Omicron BA.2 on page 7 of this report: https://www.who.int/publications/m/item/weekly-epidemiological-update-on-covid-19---15-february-2022

It is possible that BA.2 does have something of a transmission advantage, I wish to be clear. I just think that making that claim definitively is premature, and the fact remains: BA.2 is still a virus that causes COVID-19 and you should still avoid getting it. Vaccines and masks are the way to go if this thing is circulating widely in your area.

But that brings me to another point: it is not circulating widely in most areas that have already been visited by BA.1, as reported in this CNN article: https://www.cnn.com/2022/02/23/health/covid-ba2-omicron-studies-explainer/index.html

What we are seeing instead is a slow burn with BA.2 generating a bigger share of cases, but cases not spiking as they did in the original Omicron wave. This is because BA.1 and BA.2 are immunologically similar, and between vaccinations and the initial Omicron wave, there are not as many readily-accessible susceptible hosts for BA.2 as there would have been 3 months ago. Like its cousin BA.1, this virus is surviving to pass on in a smaller host pool, so there is no big spike happening.

This is corroborated by recent evidence on reinfections. Initially I had seen reports that people who recovered from BA.1 were frequently becoming sick from infections with BA.2. Additional work has demonstrated that these anecdotes are not really representative of reality, at least so far. In a study where 140,000 genomes of SARS-CoV-2 were sequenced, Danish researchers found a total of 47 cases where a person recovered from BA.1 was infected with BA.2. Reinfections of any recovered person, even if not initially infected with BA.1, were pretty rare as well. They were, reportedly, largely in unvaccinated people. So, you know what I’m going to say there. Take a look at that study here: https://www.medrxiv.org/content/10.1101/2022.02.19.22271112v1

The other question is one of severity. There were also reports—again, anecdotes—that this was causing more severe disease than BA.1. Looking at South African data, hospitalization rates with BA.2 are similar to hospitalization rates with BA.1. Only 28.9% of South Africa’s population is fully (2-dose) vaccinated, a number which has grown by only about 7 percentage points since Omicron first appeared in that country, so I think this is representative of there being little inherent difference between the two subvariants, rather than some unusual vaccine effect. In other words, BA.2 does not appear to be inherently more severe than BA.1. Study here: https://www.medrxiv.org/content/10.1101/2022.02.17.22271030v1.full

My take on this remains that BA.2 is a subvariant of Omicron SARS-CoV-2, which can cause severe disease or death in humans. We have vaccines that can protect you from these fates, and wearing masks in public in indoor spaces as much as possible is also a helpful preventive measure. Pay attention to the level of local transmission in your area and make the decision that is right for you.

The status of masks in the US

Sometime today, the CDC is expected to issue new guidance on wearing masks. I considered delaying this issue until that guidance came out, but I realize that I don’t particularly care what CDC is going to say, as much as I care about what I think they should say.

We are now in a circumstance where all but one state have lifted mask mandates, per WebMD here: https://www.webmd.com/lung/news/20220223/mask-mandates-ending-all-but-one-state. The exceptional state is, by the way, Hawaii.

I still think there is some reason to be concerned about this trend, but when I look at the numbers in, say, my home state of New York, I can’t justify saying there should be a mask mandate here. Case numbers per 100,000 have fallen precipitously, many people have been vaccinated, and there are also a large population (vaccinated and not) who have been exposed to the Omicron variant and survived with improved immunity.

I am sure there are states without mask mandates where case numbers are still concerningly high and vaccination rates concerningly low.

Which brings me back to the CDC guidance. At last report, the CDC was considering “relevant” guidance, a term that I hope means to them what it means to me. I do see some encouraging ideas in the quotes by the CDC Director here: https://www.nytimes.com/live/2022/02/16/world/covid-19-tests-cases-vaccine/as-more-states-loosen-mask-policies-the-cdc-director-says-the-agency-is-working-on-relevant-guidance

I have long felt that we should have responsive and flexible guidance on COVID-19. When cases are low and vaccination is high, we should relax protective requirements. When that changes, we should tighten requirements. CDC guidance should provide a framework that allows for this.

If the Omicron variant wave taught me anything, it is that highly vaccinated populations do very well in terms of the public health impact in the short term, at least—and there is also evidence to indicate that longer-term impacts are prevented by vaccination as well.

Right now, CDC mask guidance recommends their use by all people, vaccinated or not, in areas where transmission locally is “high,” which applies to almost everywhere in the US, even those places where the Omicron peak is gone and cases have become relatively rare. I believe this is because the criteria that CDC uses for what constitutes “high” transmission are outdated in a world where 80% or more of people in some states are vaccinated.

What I’d like to see from the CDC is a system that accounts for the prevalence of vaccination in considering the severity and risk assessment assigned to a given prevalence of disease. 30 cases per 100,000 per day is a lot more concerning in a 0%-vaccinated population than in an 80%-vaccinated population, because we can expect that number to grow rapidly in the unvaccinated group and quickly overwhelm the healthcare system. In the vaccinated population, it has become apparent that this number of cases per day will not necessarily become exponential spread. The impacts of this case level in a highly-vaccinated population might not be more than the typical burden of respiratory diseases.

However, even in the highly-vaccinated populations, a lot of COVID-19 cases are bad, and we need a system that also reacts to periods of high case burden. I expect new variants to emerge and I expect there to be times when even the most vaccinated communities need to don N95s in indoor public spaces and generally avoid nonessential travel.

Under these scenarios, it’s still possible to protect vulnerable populations like those with immune compromise—vaccination, prophylactic antibiotics, and high prevalence of surrounding vaccinated individuals are all measures that do help. I don’t expect people in that situation to need to stay home during the low-prevalence times in highly-vaccinated places. Some additional protective measures—like continuing to use an N95 in public spaces—might be warranted for this group, however. It depends on the individual condition, just as it always has, even before the pandemic.

What I’d like to see the CDC produce is something that takes into consideration the prevalence of immunity in a given locale alongside the prevalence of disease to produce a graduated set of recommendations for risk levels adjusted to the real experiences we had during the Omicron wave. This will help all people to understand their risk levels and help us to, as they say in public health, maximize quality of life while still minimizing the impacts of COVID-19.

Since I’m writing this before the recommendations appear, I can’t tell you if they’ve satisfied that goal, or even come close to the approach I suggest. But I hope they do; I think we need to have COVID-19 recommendations that help us navigate both the hard times and the times when things are a little bit easier.

Counterpoint: Ivermectin study

Last issue, I shared an ivermectin study that I do feel adds to a mounting body of evidence that ivermectin is not effective for COVID-19. I think when a product has consistently demonstrated no effect in a series of studies—not counting the fraudulent ones that have been identified—it means it doesn’t work.

On the other hand, there are those who disagree with me, and I don’t just mean people for whom ivermectin efficacy is an article of faith. Specifically, Gideon Meyerowitz-Katz, an epidemiologist I respect, feels the study results are not negative, but rather inconclusive.

In my opinion, even in his own article he displays a series of studies that have all shown no effect. He interprets this as inconclusive; I interpret this as meaning there is no effect.

Mr. Meyerowitz-Katz argues that there is a potential effect in the particular study I quoted, specifically with regard to the prevention of death. However, that potential effect was not statistically significant and in light of the other nonsignificant results where ivermectin was not different from placebo, the drug would be regarded as a failure immediately if it were any other product. In his perspective, it means the “jury is still out” on ivermectin—not that it is effective, but that we don’t at this time know that it is not effective.

I come to this with my own perspective as a person with pharmaceutical industry experience and thinking, while Mr. Meyerowitz-Katz has his own perspective, and I think an informed and worthy one.

Thus, despite the fact that he disagrees with me, I think you ought to go read his piece: https://gidmk.medium.com/the-jury-is-still-out-on-ivermectin-7d0a1895549

I think it’s important that this newsletter not reflect exclusively my views—when there is an opposing view with legitimate scientific reasoning, I’m going to do my best to share it and represent it.

Part of science is identifying and correcting errors. If you find a mistake, please tell me about it.

Though I can’t correct the emailed version after it has been sent, I do update the online post of the newsletter every time a mistake is brought to my attention.

No corrections since last issue.

What am I doing to cope with the pandemic? This:

Personal Risk Assessment

A few of you asked how I do my personal risk assessment for attending events like weddings.

This is very individual, but I did want to share my thought process.

Overall, in highly vaccinated areas, the infection fatality rate with COVID-19 is much, much lower than it was before the existence of vaccines. With hundreds of cases per 100,000 per day at its peak, deaths in New York County peaked around 20 per day total. Now, cases in my area are down below 20 per 100,000. The reproductive coefficient of the outbreak here is less than 1, meaning that fewer than 1 case is generated by each existing case. These numbers are despite the relaxation of mask requirements in parts of New York that are not far from where I live at all.

Meanwhile, hospitalization rates in our high-vaccinated (I want to be clear I mean more than 80% of people here are vaccinated) area were lower during the Omicron wave than with past waves. Estimates came in around a third as many hospitalizations as would have been expected based on case loads.

Back in the summer, there were about 3 cases per 100,000 and mask mandates were being lifted in my city—despite lower vaccination rates and apparently a higher risk of hospitalization. Now, we see at least 6 times that number of cases per day, but more people are vaccinated, more people are recovered, and the hospitalization rates per infection are definitely lower.

All of these make me think that as long as we stay below about 30 cases per 100,000 per day, I feel relatively safe attending fully vaccinated events that verify vaccination status and where I occasionally remove my mask indoors.

Part of the reason I feel safe doing this is that I am also 3x vaccinated and have recovered from the Omicron variant. These two facts mean I have the most protection possible, with both blood-based and mucosal immunity being possibilities for me.

So, based on the numbers, I think there is a relatively low chance I will encounter the virus in public, but it’s still not zero. Based on my personal circumstances I think I have really robust immunity. Taken together, I feel safe going to occasional events with other fully-vaccinated people. The thinking is this: My chances of getting infected are, right now, well below 1 in 100, considering where I am and my immunity. If that happens, my chances of getting ill are also quite low—perhaps 1 in 5, at worst. My changes of becoming severely ill if I get sick at all, again because of my vaccine-assisted immunity, are probably well lower than that, maybe 1 in 500. So I estimate, going to my friend’s wedding, I was looking at what I considered to be an aggressive estimate of a 1 in 250,000 chance of severe illness, and maybe a 1 in 500 chance of getting sick again. I decided, to attend their wedding, I was OK with that risk. But I went in very well aware that despite being small, those numbers are more than zero.

There was also a chance that the car I rode into to the wedding would get into a terrible accident—I accepted that, too, and I think in the present circumstances it was more likely than severe COVID-19 for me. All of life involves balancing risks, and if you’ll forgive me the Tolkien quotation, “It’s a dangerous business, Frodo, going out of your door.” I try to take on that danger as deliberately as possible, knowing what I’m getting into as much as I can.

I don’t feel comfortable doing this particular type of thing—a wedding with more than 10 people—very frequently because there is an unvaccinated person1 in my home to whom I could be a silent carrier of infection, but I do think it is acceptable for special occasions like weddings. If everyone in my household was vaccinated, I might be more comfortable doing this frequently.

Even when I do attend an event like this, I mask as much as possible. More time masked means less time exposed. Even if you removed your mask to eat a meal, putting it back on lowers your risk. Do not assume that just because you had your mask off at one point, it’s already too late for you. You don’t know if you’re infected until you have definitive evidence, so putting that mask back on could mean protecting yourself even if you had it off for a little while.

This is my own story. Yours should consider your personal risk assessment, prevalence in your local area, and the protective measures you have taken. Vaccination is the best protection we have available, but continuing to mask, ideally with a high-filtration mask like an N95 or similar, as much as you can in indoor public spaces makes a big difference too. I hope my perspective on this is helpful, but please—consider that I am a different person from you, with different circumstances and different risk factors, and I choose to accept risk of exposure to COVID-19 based on my personal tolerance for it.

Do not do something because John Skylar says, “I did that.” Do something because you evaluated your own risk-benefit for it and made a choice with which you’re personally comfortable. Remember, no matter what the numbers are, if they’re above zero, someone out there is getting COVID-19. Think about the rates, and decide what they mean for you personally—and whether you’d be OK being one of those people.

Pandemic life, and the headlines section, addressed all of the comments on last issue. But, feel free to go back and read them if you would like.

You might have some questions or comments! Join the conversation, and what you say will impact what I talk about in the next issue. You can also email me if you have a comment that you don’t want to share with the whole group, or if you are unable to comment due to a paywall.

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