COVID Transmissions for 1-15-2021

Six months

Jan 15, 2021

Good morning and welcome to COVID Transmissions.

It has been 425 days since the first documented human case of COVID-19. Another weekend is upon us! Make the most of it.

Today, this newsletter is six months old.

In the headlines section, I address a recent story doubting vaccine efficacy, and a couple of stories about variants of SARS-CoV-2, our latest story arc.

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Now, let’s talk COVID.

Yes, the vaccines work.

UPDATE: When I wrote this, I was not aware that Doshi has a history of work and positions that align with the antivaccine movement. I gave him more benefit of the doubt, as a result, than I might have otherwise. I will revisit this in a newsletter issue next week but wanted to leave a note here in the online edition to flag that.

In a blog for BMJ, a pharmaceutical scientist named Peter Doshi has elected to question the efficacy of the vaccines for COVID-19: https://blogs.bmj.com/bmj/2021/01/04/peter-doshi-pfizer-and-modernas-95-effective-vaccines-we-need-more-details-and-the-raw-data/

Before you read that, I want to emphasize that Dr. Doshi is just wrong. He claims that the clinical trials for the vaccines contained a design flaw that has made them miss a large number of cases of COVID-19. Specifically, he believes it is inappropriate that they measured only confirmed cases of COVID-19 rather than looking at suspected cases of COVID-19. His argument is that if you look at suspected cases, you see a vaccine efficacy of only about 19%, where looking at confirmed cases gives an efficacy of 95%.

The thing is, this analysis is wildly flawed. Dr. Doshi conveniently ignores the fact that many of the suspected cases turned out to be negative for SARS-CoV-2 infection. So many, in fact, that it would suggest that PCR tests only correctly detect 5% of tested cases. We know this isn’t the case.

While it is probable that some positive cases were missed, it is unlikely that this is a very substantial number.

Additionally, it is not reasonable to just assume that all cases of respiratory illness in a sample of 30,000 people are due to COVID-19. This disease does not have a lot of characteristic symptoms. It is easily confused with other illnesses. Bacterial infections can cause many of the symptoms that COVID-19 causes, and there is no virus involved there even! Not to mention other viruses that can cause COVID-19-like illness. To presume without confirmation that all of these cases—even after we rule out the very many of them with negative PCR tests—are COVID-19 is, frankly, just bad science.

The question then becomes: why does someone who is a regular writer for a respected medical journal want to undercut good science on these vaccines?

Reading some of his past work, I think it is because Dr. Doshi has been consistently skeptical about the design of these trials from the beginning. He has questioned their endpoints (in an article that I happen to think made some good points), and he has questioned the quality of COVID-19 testing performed in the trials. He did this before full datasets were released, and I think that was reasonable.

Unfortunately, now that the datasets have been released, it’s quite clear that the vaccines are efficacious. The testing protocols were accurate. Yes, the trials could have been designed to tell us more about severe cases, or more about how the vaccines impact the spread of the virus, but these are studies that remain planned. The raw efficacy, as measured, is convincing. It is my feeling that Dr. Doshi has become entrenched in a position due to his past communications, and is having trouble admitting that the vaccines worked despite the criticism. Unfortunately, I think this is leading him to communicate things that fall into the realm of misinformation, which is why I chose to speak out.

It’s important to think critically and read many sources. While an article like this may appear to be convincing, it is not always clear what the author might not be telling you. It is easy for an expert to be misleading, even unintentionally. I hope to combat that, every time I sit down to write this newsletter.

Is B.1.1.7 any different in children?

The B.1.1.7 variant has been making headline after headline. We suspect that it is more contagious but I remain skeptical in the absence of clear confirmation. There are still very limited data from anywhere except the UK regarding this variant of SARS-CoV-2; I do not generally like to make conclusions based on a single country. Especially not one that has had extremely uneven lockdowns, both in terms of geography and timing.

I’ve been keeping track of how much more contagious this new variant is estimated to be. At first, it was “70%.” Then, I heard 50 to 70%. The next number was 56%. Recently, I heard “30 to 50%” more contagious (actually, in a source related to the article I am about to link). The goalposts continue to move, which I believe is more indicative of uncertainty than anything else. What is reassuring to me is that they are moving downward.

However, I have been glad to report that there are several things that we do know: it does not make disease more severe. It does not appear to interfere with preexisting immunity.

Now, I can report that it does not seem to cause disease that is any different in children, nor does it appear to be any more transmissible in children than in adults. Both of these were concerns, previously. Apoorva Mandavilli of The New York Times reports on recent work demonstrating that neither of these concerns is the case: nytimes.com/2021/01/14/health/coronavirus-variant-schools.html

Children are about half as likely to transmit this variant than adults; this is the same as for other variants of SARS-CoV-2. There also don’t seem to have been reports of any kind of enhanced disease severity.

I will note that there was an apparent gain in contagiousness, though again the exact magnitude of this gain is not entirely clear in a broader context. However, we can be reassured in the fact that tried and true methods like distancing, masking, and isolation were effective in younger populations being studied here.

It comes back to what I’ve said before: there may be a modest increase in transmissibility for this variant, but it is not a doomsday scenario and it can be managed if we take disease control measures seriously.

The B.1.1.7 variant was first found in the UK. There are other variants appearing in the US.

Another thing we’ve talked about here is that viruses mutate frequently. I’ve expressed concern that the longer we go with inadequate vaccination and uncontrolled spread, the more of these variants we are going to see. This was underscored for me, today, in the following very technical Twitter thread (click through for the full thing):

Trevor Bedford @trvrb

After ~10 months of relative quiescence we've started to see some striking evolution of SARS-CoV-2 with a repeated evolutionary pattern in the SARS-CoV-2 variants of concern emerging from the UK, South Africa and Brazil. 1/19

It’s a cool explanation of virus evolutionary biology, but what I really liked most was the takeaway:

Trevor Bedford @trvrb

Again, this hypothesis is highly speculative at this point, but separately, the fact that we've observed 3 variants of concern emerge since September suggests that there are likely more to come. 19/19

And, indeed, today, I was tipped off about a report of new variants in the US: https://www.forbes.com/sites/williamhaseltine/2021/01/14/researchers-identify-new-covid-19-variant-in-ohio/?sh=2185701f6cd4

This Forbes article details a report of two variants that appear to be native to Columbus, Ohio, and may have some interesting, or even concerning, mutations. I think the authors amps up the concern level a little much, but I do think he’s right about one thing: we’re finding these things now because we’ve started looking in earnest. This is a sign that US surveillance of SARS-CoV-2 sequences is ramping up, which is what I was calling for yesterday. I hope we don’t find anything too dangerous. That said, if we do find something dangerous, I’ll be glad that we found it. You can’t fight a variant that you didn’t know existed in the first place.

The Johnson and Johnson vaccine is safe and generates an immune response

Per a company announcement yesterday, the Johnson and Johnson company vaccine has succeeded in its Phase 1/2 trial: https://www.cnbc.com/2021/01/13/covid-vaccine-johnson-johnson-one-shot-safe-generates-immune-response.html

I will cover these results in detail next week, but I want to note they’re quite promising.

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

An anniversary

Today is actually two anniversaries. The first is the fourth year of marriage for my wife and I, and of course the first year that we’ve been married during a pandemic. Last year we went to a local jazz club for the occasion. This year we went to a local apartment that we live in. We ordered sushi, drank something bubbly, and also ordered in gourmet cookies. It’s a different sort of life, this pandemic, isn’t it?

The other anniversary is of this newsletter. It has now been six months since I started doing this. When I began, I thought that it would be for the sake of friends and family, but it grown beyond that. I thought that it would provide information on a somewhat local day-to-day of the pandemic, and it has certainly grown beyond that.

I’ve faced a lot of challenges in this writing. It’s not easy to keep up with a pandemic, with its global nature, from a local apartment that I live in. When we set out, I knew very little about this virus, because everyone knew very little. We have learned a lot together, really, because I have learned with you while information has revealed itself.

When this began, I knew that it would have a natural time limit on its existence. The pandemic will, eventually, end. I wasn’t sure that I would still be doing this today, at the six month mark, but here I am. As much as I enjoy communicating with all of you, I must say this: it is my hope that six months from now, we are all safe enough that I can shut this newsletter down.

Carl Fink left me the following comment yesterday:

You saw the reports that Johnson and Johnson can't produce their vaccine until April, even if it shows great effectiveness when they report on their Phase 3 trial this month? Apparently, they are having trouble getting manufacturing set up. Not that surprising, commercializing these processes is hard, but disappointing.

Thanks for calling this to my attention, Carl. My reply:

I had not actually heard this. Yesterday they reported Phase 1/2 results, and as you mention, Phase 3 results are expected. However, I see this reported here: https://www.politico.com/news/2021/01/13/johnson-johnson-vaccine-production-458941
It does, in fact, look like they're about two months behind their original manufacturing plans. That's unfortunate, but...really, better late than never.

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