COVID Transmissions for 12-29-2021

New--and questionable--guidance from CDC

Dec 29, 2021

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

It has been 743 days since the first documented human case of COVID-19. It has been 7 days since I became a human case of COVID-19.

I am still testing positive by rapid antigen tests, and have not yet gotten my PCR result for the test taken last Thursday. My symptoms are largely resolved, though I have been experiencing new fatigue, which I don’t love. Hopefully this will be transient, but there’s always a chance it won’t—Long COVID is real. Though, I do think vaccination substantially reduces the chances of it.

In today’s issue we are going to talk about two new items out of the CDC that are pretty concerning to me—in terms of how much we ought to be relying upon the CDC.

Bolded terms are linked to the running newsletter glossary.

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Now, let’s talk COVID.

US CDC now believes that Omicron cases were less prevalent last week, but highly prevalent this week

Last week I shared news with you that Omicron cases had surged to 73% of all cases in the US, according to a CDC estimate. Yesterday, the CDC revised that estimate to 22%, saying that by this week, Omicron variant cases had surged to 59% of all cases in the US. Details here: https://www.reuters.com/world/us/omicron-estimated-be-586-coronavirus-variants-us-cdc-2021-12-28/

What??—> this was my initial reaction. Ecological studies can be difficult, and this one requires sequencing too, but to be off by 51 percentage points in one estimate is a major error. I understand of course that the situation with Omicron is rapidly changing, but I have to say I am disappointed.

However, let’s try to understand how this can happen at least. To begin with, we need to keep in mind that data indicate the Omicron variant’s spread in the US has been pretty uneven. As of 4 days ago, only 25 of 50 states had even reported cases of infection from this variant: https://www.cidrap.umn.edu/news-perspective/2021/12/25-states-report-omicron-covid-19-most-cases-mild

At the same time, 6 days ago, the CDC estimated that the Omicron variant was responsible for 90% of cases in the NYC metro area: https://www.nbcnewyork.com/news/coronavirus/omicron-surge-cdc-estimates-more-than-90-of-current-ny-area-cases-are-new-variant/3463603/

If there was overrepresentation of places like New York City in the CDC population used to estimate country-wide prevalence, this could well have been the source of the error. I can see how that might have happened, considering that case growth in East Coast urban areas has been truly alarming, and the US has just reached all-time highs for daily new cases. Perhaps the rapid change in overall geographic distribution of cases of different variants distorted whatever model the CDC was previously using.

It doesn’t really instill a lot of confidence, though, does it? I hope to see the CDC get its act a little more together, and not repeat this error. However, I’m also glad they took responsibility for it and corrected the record. Mistakes do happen, and there are those who might have let this go uncorrected.

US CDC guidance changes: isolation for COVID-19 positive individuals

Now for the bigger issue. Recently, the CDC has been revising its guidelines for isolation for people in various settings who have tested positive for COVID-19.

First, they made changes to the guidance for isolation of healthcare workers, which considered those workers’ vaccination status and whether or not they were symptomatic. This made sense to me; it didn’t seem reasonable that in the middle of a pandemic emergency, we could be sidelining staff at hospitals who are vaccinated and asymptomatic, but have trace amounts of RNA by PCR. The guidelines considered more situations than that, and included not only provisions for testing but also a variety of different scenarios where the rules might be laxened. Specifically, under more emergent, dire conditions, the protocols could be made a bit less restrictive. It’s in these less-restrictive scenarios that some uncomfortable suggestions were made, and I think in some cases these new guidelines might ask contagious healthcare workers to put on N95s and keep working. Not ideal, but since our healthcare system is extremely strained, I think they had a hard call to make.

Where I begin to strongly object is to the update that was released yesterday: https://www.cdc.gov/media/releases/2021/s1227-isolation-quarantine-guidance.html

This guidance applies to the general public. It says that members of the general public, regardless of vaccination status, only need to isolate for 5 days if they are COVID-19 positive, provided that they meet these criteria1:

If you have no symptoms or your symptoms are resolving after 5 days, you can leave your house.
Continue to wear a mask around others for 5 additional days.

I have a number of problems with this. First, I don’t think the guidance is good communication, because several parts are unclear or subjective. “No symptoms or your symptoms are resolving” —> what does this mean? What is a “resolving” symptom? My symptoms have been getting consistently better, but if they’re still present, are they “resolving?” It is not clear.

“Continue to wear a mask around others” —> Indoors? Outdoors? Since masks are recommended indoors in public spaces, is this actually new guidance? Or are they saying you need to wear a mask outside, too? I think they are saying you need to wear a mask in any setting where others are present, which seems to suggest they think even people who fit these criteria might be more contagious than others after just 5 days.

In that regard, I think they are correct. This 5-day cutoff requirement is a problem, and in fact, it’s the main problem that I have. While it is clear that there is a limit to the number of contagious days in COVID-19 infection on average, using the average contagious period as the barrier creates a problem that is common with averages. That is, many people experience conditions that are above-average. Often about half of people.

So here we have the CDC recommending that a cutoff be placed where we are not certain that 100% of the people it applies to will stop being contagious. That all of these people are supposed to wear masks after 5 days still is not being as well communicated as the idea that isolation can end early. Effectively, this guidance could well be sending contagious people back out into the world.

In the UK, a totally different approach is used. Patients are expected to isolate for 5 days, and then continue to isolate while they perform a Day 6 antigen test. If that is negative, they take another test on Day 7, and if that is negative, isolation can end. This test-out approach is based on good science that demonstrates rapid antigen test negativity relates well to contagiousness. You can read an example study showing that here, but it has been shown in many places: https://academic.oup.com/cid/article/73/9/e2861/6105729

It’s possible to be contagious for about a day before you initially test positive by rapid antigen tests, but if you have converted from positive to negative, especially over two consecutive tests, it is fairly well-assured that you are no longer contagious. This approach is, in fact, the criterion I’ve been using for my own isolation. My 3 month- old daughter is still not at home because my wife and I continue to return positive antigen test results, for her own safety. We’re going to go to the full 10-day isolation, or negative tests, whichever happens first. The reason we’ll be stopping at 10 days is that it may be possible for leftover “junk” from the virus to cause us to continue to test positive. I am waiting for more science on that, though. If I hear that Omicron variant infections have a longer contagious period, I might adjust my thinking on this.

I don’t think the decision that CDC has made here is very good. I would urge you to modify it by using rapid antigen tests, with negatives for two consecutive days, before leaving isolation early—just as I am doing. If you don’t get those negative tests, stick to the old 10-day guidance, which was pretty reliable so far.

I have additional questions about this guidance. Quarantine guidance was adjusted as well, and people who are “fully vaccinated” under the old definition of that (2 doses of an mRNA vaccine or 1 dose of the J&J vaccine) will now need to stay home for 5 days after exposure, and wear a mask around others for 5 additional days (provided those 2 mRNA doses were received more than 6 months ago without a booster, or that dose of J&J was received more than 2 months ago without a booster). The same instruction also applies to unvaccinated people. In other words, the quarantine rules are now the same for unvaccinated people, and people who have gone more than the recommended amount of time without a booster. The definition of fully vaccinated has, in a way, been silently updated. That is probably a good thing.

However, it isn’t all good. This guidance now says “If you can’t quarantine you must wear a mask for 10 days.” Unvaccinated people should always be wearing masks. They should quarantine if exposed. This guidance now sends them back out in public, without quarantine?

The guidance also recommends testing on Day 5, which I think is good, at least.

People who are within the appropriate number of months of their primary vaccination series, or who have received a booster dose, are told to wear a mask around others for 10 days after an exposure, now, and asked to test on Day 5. This is also new. Before, such people would have been told simply that they do not need to isolate. One problem here is that the J&J vaccine, which may be less effective against the Omicron variant than a boosted mRNA series in terms of preventing infection, is treated as the same as that mRNA series. That is on top of the “wear a mask around others” guidance being relatively unclear.

In both quarantine cases, regardless of vaccination status, the guidelines instruct that “If you develop symptoms,” you should “get a test and stay home.” Presumably you can leave to go to the hospital. Would be good if they stated that outright, though.

Look, I think the CDC really messed up here. Had I written these guidelines, I would have said the following:

Individuals who are within 6 months of their primary mRNA series, have received the J&J vaccine with an mRNA vaccine booster,2 or who have received a 3rd dose booster do not need to quarantine, but should wear a mask around others in indoor public settings or in outdoor settings where they cannot maintain distance, for a period of 10 days. After this they may return to wearing a mask only in indoor public settings.
Individuals who are unvaccinated, have received the J&J vaccine without an mRNA vaccine booster, or have received only 2 doses of an mRNA vaccine more than 6 months ago should quarantine, with a test on the 5th day of quarantine. If this test is negative, they can leave quarantine early and continue to wear a mask according to normal CDC recommendations. If this test is positive, they should isolate according to guidelines for COVID-19 positive individuals.
Regardless of vaccination status, if you develop symptoms of COVID-19, assume that you have it, get a test, and stay home except to receive essential medical care for your illness.

This is just a rough draft, and already I think it is superior to what the CDC put out today. I have a lot of concerns about this new guidance. I hope they clarify it substantially. And by clarify it, I mean revise it to be evidence-based in a way that lets them save face at least a little.

I’m disappointed.

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

Painting with Black 3.0

I don’t know if you’ve heard of it or not, but Black 3.0 is an incredibly black paint. Most black paints don’t manage to absorb as substantial a fraction of visual light as you’d think, and as a result, don’t always look quite as black as they ought to.

Some years ago, an artist named Stuart Semple started playing around with ways of making an exceptionally black pigment, and developed a series of paints, now in their third iteration (3.0), that absorb more than 95% of visible light. They are…wildly…dark.

As some may be aware, I sometimes paint miniatures from the X-wing Miniatures Game as a way to relax. I picked up some Black 3.0 and tried it out on a TIE fighter, as a base coat, to see what the material does. Have a look:

Image shows two models of TIE fighters. The one in left is painted in the traditional blue-grey scheme, while the one in the right has been entirely coated in a completely black paint.

Looks pretty dark to me! I used my airbrush for this, because it creates nice, even coats. But the pigment is just so thick that I had to dilute it a lot, which meant the paint flowed in certain spots while drying. Not ideal for a 3D model, but you can’t really see it, because you’re staring into a void whenever you look at this.

On the whole I found this paint to be incredibly cool. I am going to play around with it some more—maybe I’ll share a photo of the finished model.

Reader Karen left the following comment about my new feelings on mask quality (which actually aren’t so new):

I'm so sorry you have COVID!
Last issue you said you no longer thought cloth masks were sufficient. Could you explain that a little more?

My reply:

Hi Karen! Thank you for your question.
Several studies at this point have demonstrated meaningfully better protection with N95 or even surgical masks. The filtration offered by a cloth mask just doesn't cut it anymore. this recent opinion piece by an aerosol filtration expert attempts to make the case and also includes some links to studies: https://www.theguardian.com/commentisfree/2021/dec/27/best-masks-covid-tests-cloth-surgical-respirators
When we think about it, this makes sense. Cloth masks were initially a stopgap measure intended to provide some protection against the D614G variety of virus, very close to the original Wuhan isolate, but we have seen a ramping up both of the contagiousness of the circulating virus as well as the ability of global manufacturing to provide high-filtration masks. It's time to move away from this emergency measure of cloth masks to options that are better at protecting people.

Reader Sam had the following comment about Omicron-specific vaccines:

Relevant to the vaccine discussion -- first evidence that Omicron infection confers cross-immunity to Delta:
Alex Sigal @sigallab
We have submitted new results to medRxiv: Omicron infection enhances neutralizing immunity against the Delta variant The preprint can be found here: sigallab.net
9:48 PM ∙ Dec 27, 2021
8,014Likes2,686Retweets
. This suggests that perhaps that we wouldn't need a multi-valent vaccine to take on both Omicron and Delta. Scott Gottlieb had expressed the worry that it would be otherwise.
We still need to ask if it's really worth it to roll out a variant-specific vaccine, of course. But it should be pointed out that the primary endpoint of the original trials was prevention of symptomatic infection -- not just severe disease. Whether that goal now needs to change is a conversation scientists, government officials, and the public can have, but it won't do to just move the goalposts and hope no one notices.
That's not to suggest that preventing mild illness is *as important* as preventing hospitalization, or to diminish the hugely important role vaccination is still playing in saving people's lives. But it leaves a lot to be desired in terms of democratic accountability, not to mention respect for people's intelligence, to alter policy and messaging without even acknowledging that it is, in fact, being altered.

Here are my thoughts in reply:

I think it is worth it to roll out a variant-specific vaccine, for people who have not yet been boosted, or for people who are aging into vaccine eligibility. In the latter case, a multivalent vaccine might be appropriate in the event that Delta is not totally displaced by Omicron. I think it is important that we improve the breadth of the immune response going forward, to reflect the viruses that are actually circulating. I don't know that I, as someone almost certainly recovering from Omicron, would require this specific booster, but I think there will still be quite a few people out there who might benefit from it. I did not enjoy getting Omicron, and wouldn't recommend it to others.

Reader Sally felt that I did not mention Long COVID-19 sufficiently in my description of the Omicron variant situation emerging in the US:

I realize we don't know much yet about LongCovid but to suggest that there are two options - mild Covid or into-the-hospital-with-you Covid does ignore that very real third scenerio, that even people with few or no symptoms can be badly affected longterm.

I must point out here that just because I did not discuss Long COVID in particular in the last issue, does not mean I am suggesting it does not exist. It has been covered regularly in this newsletter. I believe in recent data that the use of vaccination strongly reduces the risk of Long COVID, as we discussed here recently—even if some of that vaccination series is given after disease. At least, I believe this with regard to non-Omicron variants.

We do not know anything about the Omicron variant with regard to Long COVID, and there is not any protective action I can endorse in that regard, so in my Omicron-focused comments, I did not speculate about it. I have to reserve comment until we know more about any long-term sequelae in this Omicron-dominated wave. I try not to comment on phenomena in a vacuum of data, and I think it’s very important that there be communications on the immediate danger that Omicron poses. When there is information about the rate at which Long COVID occurs with this variant, I will communicate about it.

As you can imagine, since I am someone who has become infected with the Omicron variant and is still recovering, the prospect of developing a long-term illness that science does not understand how to treat has very much been on my mind.

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.

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