COVID Transmissions for 1-12-2022

Clarifying how to live in a post-Omicron world; masks, tests

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

It has been 757 days since the first documented human case of COVID-19. Pope Stephen II, who we only met a couple of issues ago, died in 757. He was responsible for freeing the Roman papacy from Byzantine control, and also aligned it with Pepin the Short of the Franks—these actions set the stage for an alliance between the Papacy and Charlemagne that would have influence on European affairs for quite some time afterwards.

We’ve been talking about masks and tests a lot here on this newsletter, and there have been a lot of questions. Today I want to share a couple of items that clarify two of the biggest questions, in my opinion, to help us navigate protective measures for a world where Omicron has upended the pandemic once again.

Bolded terms are linked to the running newsletter glossary.

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Now, let’s talk COVID.

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Reuse of high-filter masks

Regular readers will know I have been pretty hard-hitting on notion that we need to be using high-filtration masks like N95, KN95, KF94, or FFP2 standard respirators. these offer the highest level of possible protection, and in fact remain protective to a high degree even when not fully fit-tested. In other words, they’re what the average person should be wearing—if that average person can find them.

Limited supply is the biggest problem right now, as I understand.

Since it’s been a topic in the comment threads, I wanted to provide some expert opinion on the reuse of high filtration masks. However, I am not an expert on the reuse of high filtration masks. Fortunately, the SF Chronicle recently ran an article exploring the issue, establishing firmly that there is no firm rule, but when the condition of the mask breaks down, that’s a sign that it’s time to be done with it.

Have a look at the article here: https://www.sfchronicle.com/health/article/How-long-can-I-keep-using-the-same-N95-respirator-16765593.php

BinaxNOW rapid antigen tests continue to perform well against the Omicron variant

Normally I try not to endorse specific brands on this newsletter, but a piece of research has emerged that gives me more confidence in a specific rapid antigen test than in others.

With the emergence of the Omicron variant, there have been questions over whether these tests continue to perform well for the identification of contagious COVID-19 cases. In the pre-Omicron world, evidence suggested that rapid antigen tests on the market were able to detect 95% or more of contagious people with SARS-CoV-2 infections. I want to emphasize here that I am not saying “sick” people and I am not saying “infected people.” You can be infected without being sick or contagious. You can be sick without being contagious (at least, on certain days). These three conditions are not necessarily coexistent.¹ Some people are infected without ever being contagious. The days when a person has symptoms aren’t necessarily the days when they are contagious. As we saw with past variants, a person might be contagious before symptoms emerge or with contagious and never have any symptoms at all. Some might even have symptoms without becoming contagious.

It’s important that we understand what rapid antigen tests are really for. There is no test that can tell you with high confidence that you are safely uninfected with SARS-CoV-2. This is just a simple structural fact—the moment you took the test could have been at a point in an infection growth curve when it was undetectable, but a day or an hour later, you became contagious. Tests cannot tell you anything about the future, only about the moment in time that you take them. And even then, they are not always perfect.

With that in mind, we need to remove ourselves the illusion that you take a test to tell you that you don’t have COVID-19. A PCR can, in some cases, reasonably rule out COVID-19 (like if you’re actually sick and test negative once, or especially, twice), but for a lot of people using tests for routine purposes, the test is meant to tell them they don’t have COVID-19, and tests just aren’t so good at that.

What is more important is when a test comes back positive, at least for most people. A positive PCR cannot tell you if you are contagious. It can tell you if you were infected or recently infected; this can be useful for the treatment of disease, and that’s the context where I think that PCRs are at their best use.

A positive antigen test, on the other hand, has the feature of being able to tell you that you are contagious. To elaborate on what I mentioned before, antigen tests have a 95% or higher sensitivity for contagious cases—this means that they detect 95% or more of contagious cases, and miss 5% or fewer of them. This miss rate becomes even lower if testing is performed multiple days in a row.

In my opinion, for most people, the rapid antigen test is the most useful routine test. It takes 15 minutes and when it turns positive, you immediately know to begin isolating.

The problem is, there have been some reports that these tests do not perform as well with the Omicron variant as they have in the past. I’m pleased to share a large study (N=731) conducted at UCSF with funding from the SF Department of Public Health that has provided good evidence that the BinaxNOW test from Abbott Laboratories continues to perform very well for this purpose. The full preprint paper on this can be found here: https://www.medrxiv.org/content/10.1101/2022.01.08.22268954v1

If you don’t want to navigate the full paper, read this take by Dr. Michael Mina, who has been one of the most vocal champions of rapid antigen testing throughout the pandemic:

Michael Mina @michaelmina_lab

New #OMICRON Research Rapid Ag Tests work w omicron This data cannot be refuted @AbbottNews BinaxNOW working As Well for Omicron as prior variants See the line at 30? Above is NON-infectious virus. Below is likely infectious virus 95% sensitivity! medrxiv.org/content/10.110…

January 10th 2022

457 Retweets1,414 Likes

As Dr. Mina explains, the figure he shows compares rapid antigen testing to PCR, using the “Ct,” or cycle threshold value. This is for a set of cases that were 97% due to the Omicron variant. Each of these cases had a BinaxNOW rapid antigen test and also had a PCR conducted, and the dots are graphed according to increasing Ct.

For a PCR, the higher the Ct, the less virus genome is actually present in the sample. A Ct above 30 almost never represents a contagious case; there is a line in the figure demarcating the Ct=30 threshold. In the figure, we see the difference between rapid antigen positive tests and rapid antigen negative tests represented by blue vs yellow dots, respectively. Yellow, negative dots cluster above the Ct=30 line in each figure, and blue, positive dots cluster below.

This evidence recapitulates what was seen in surges of past variants, and suggests strongly that the BinaxNOW test continues to accurately detect contagious cases, successfully finding about 95% of them.

I feel very reassured by this. I’m sure more data will come out for other tests, but for the time being, it’s good to know that we can rely on the BinaxNOW test.

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

Considering a reward for those who financially support this newsletter

As many of you will be aware, I do not require money to subscribe to this newsletter. That is, of course, purposeful, because I think that good information can save lives in this emergency, and I also remain very grateful to have received my PhD training for free on the taxpayer time.

However, many of you do choose to provide some subscription money, and I am very grateful for that. It helps justify the hours that I spend, and I appreciate it.

However, every time I have thought about adding some kind of paid-only content, I’ve received pushback from paid subscribers that they want all the information here to continue to be free. That’s great to hear too, but it’s meant I haven’t been able to find a way to show my appreciation.

To that end, I am thinking of creating a gift for those paid subscribers who would like it. Right now, my thought is that I would create custom challenge coins² with graphics from COVID Transmissions, and send them to those subscribers who:

1. Want them (it’ll be totally opt-in)

2. Are paid subscribers or who would be willing to buy the challenge coin (it’ll be around $10, maximum, depending on the mold fees and per-unit fees—this is not an attempt to make a profit, I’m good)

I’ve selected challenge coins because I think they’re fun, and also because a couple of times readers have contacted me to say that they were in the process of recommending this newsletter to one friend or another when that person told them they’re already a reader. Showing a challenge coin would be a perfect response in a situation like this!

I haven’t created a design yet, but I’m curious to hear what people think of this idea. Would you like to have one? Imagine that it will feature the newsletter logo design on it, and will likely use full color on at least one side.

Let me know what you think! Email and comments are open.

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There were some great comments on the last issue, but I think they mostly cover territory that we’ve discussed here already. For deeper enrichment on the topics we discussed today, go back to last issue and read the comments there.

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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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.

See you all next time. And don’t forget to share the newsletter if you liked it.

Always,

JS

1. The one combination that I would except is that you cannot be sick with COVID-19 if you’re not also infected with SARS-CoV-2; that said, you can be sick for other reasons, and it can easily be confused with COVID-19.

2. If you’re not familiar with challenge coins, here’s a link to explain them: https://en.wikipedia.org/wiki/Challenge_coin