COVID Transmissions for 1-11-2021

Jan 11, 2021

Good morning and welcome to COVID Transmissions.

It has been 421 days since the first documented human case of COVID-19.

Today’s newsletter involves responses to a lot of reader questions and comments that I got over the weekend—thanks for speaking up, everyone!—as well as some headlines.

As usual, bolded terms are linked to the running newsletter glossary.

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Now, let’s talk COVID.

Does viral load correlate with disease severity?

One of the problems with treating emerging diseases is that we don’t always know what to measure in order to tell if patients are doing well or not. When a disease is poorly understood or poorly characterized, we basically are flying blind.

One possibility is that the level of virus present in a patient, the viral load, could correlate with disease severity. This is the subject of a new preprint from Dr. Akiko Iwasaki’s lab at Yale: https://www.medrxiv.org/content/10.1101/2021.01.04.21249236v1

Dr. Iwasaki’s lab looked at levels of virus RNA in nasopharyngeal (NP) swab tests; this is the deep-nose test that some of you may be intimately familiar with. They also looked at levels of virus RNA in saliva.

Their work found that saliva viral load, but not NP viral load, was positively correlated with various markers of disease severity.

So what, you ask? This means that we will have a better set of measures for patients when they first present at a clinic, to help us understand who needs the most attention. Saliva viral load is easily measured and is used in a variety of existing diagnostic workflows. This makes it something that can be directly applied in the clinic—provided these results are really true.

This is a preprint, so we need to see it get through peer review. But, I thought it was pretty interesting. It would be awfully nice to have a tool we can use to help guide care from the moment a patient first shows up at the hospital—before things get really bad.

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

Watching: Staged

Staged is a comedy about being an actor during the COVID-19 pandemic, starring and produced by David Tennant and Michael Sheen. Or is it Michael Sheen and David Tennant? You’ll understand what I mean if you watch it.

On the surface, it’s about trying to rehearse a play. Past that level, it’s about life in lockdown and how it can drive people slowly insane. It has a really star-studded guest star list, and it’s a great laugh. Check it out.

There were a LOT of comments over the weekend, which is great!

I want to start by addressing two questions that I’ve received from several anonymous people lately, regarding vaccination:

I have allergies. Should I be concerned about allergic reactions to the vaccines?
You should ask this question of your physician, first and foremost. I am a virologist; I am not qualified to practice medicine or give specific medical advice. That said, I know that the vaccines have very specific recommendations regarding allergies. The most recent estimate I heard is that serious allergic reactions occurred in only 11 out of every 1,000,000 patients to receive the vaccine. Further, the only allergies that are noted as being of concern in the vaccine emergency use authorization document are allergies to vaccine ingredients. Regardless, you should discuss this with a healthcare practitioner who knows your specific medical history and condition(s). I can only provide general commentary.
Should I be concerned about vaccination if I am pregnant or am trying to get pregnant?
You should ask this question of your physician, first and foremost. I am a virologist; I am not qualified to practice medicine or give specific medical advice. There is no specific warning against use of the vaccines in people who want to become pregnant, or people who are pregnant. Patients who are pregnant are being monitored through a registry so hopefully there will be further information regarding this situation as the vaccine is rolled out. Some animal experiments were conducted, as well, and showed no impacts on reproductive health. For those trying to become pregnant, I personally do not see how a vaccine would cause any issues with fertility. It’s not impossible for there to be some rare unforeseen consequence, but we are talking about a vaccine that is delivered into muscle in the arm and that doesn’t have any ingredients that should be transported anywhere else. I can’t say it can’t happen, but I don’t see how it could have an impact. Most important, talk to your healthcare provider if you’re in this situation.

Then, I got the following comment from Yaear BenAssa:

Hey John. Do you think vaccine distributors should check essential workers for antibodies before giving the vaccine (not wasting vaccines on healthy people that already have antibodies as it might not help)?
Also is there reason to believe there is a difference in immunity time between vaccinated people and people who had the disease?

This happens to overlap with something else I was thinking about, so this was my response:

You're asking a great question. I've addressed this to a limited extent in previous writing for this newsletter, but recently, I've been thinking about this a lot.
I do not think that natural immune responses to SARS-CoV-2 are as consistently strong as the immune responses generated by the Pfizer and Moderna vaccines. I base this on data from the Phase 2 trials where antibody levels in convalescent plasma controls were a lot more inconsistent than levels in plasma samples from fully-vaccinated patients.
For this reason, I do not think that natural immune responses are adequate protection such that a person who is antibody-positive could skip the vaccine.
I think that addresses both of your specific questions.
However, on Twitter the other day, Dr. Florian Krammer raised an intriguing possibility: do people with preexisting immunity to SARS-CoV-2 actually need 2 doses of vaccine? We would expect that anyone who tests antibody-positive would have some amount of memory B cells, ready to respond to a new infection. These memory B-cells are the same thing that the booster dose in a normal vaccination course is looking to activate, expand, and reinforce. It's possible that a person's natural infection might be a sufficient "prime" for them to only need a single, "booster" (not really a booster) dose of vaccine. This possibility is very interesting to me, because in places like NYC, almost 25% of people have already been infected with SARS-CoV-2. Giving them only one dose would free up 12.5% of our vaccine doses, and potentially help us to fully vaccinate a 6.25% larger population.
As always, I'd like to see some kind of clinical study at least showing a booster effect on patients with past infection when receiving a first dose of vaccine, but even so I think this suggestion might just work, unlike some other ideas that I'm more skeptical about.

Next up, I had a comment from Madeline Morrison:

Lee, can you speak to this Twitter thread from the other day? I found it...alarming. https://twitter.com/drericding/status/1346899021621813249?s=21

This links to a very alarmist thread from Dr. Eric Feigl-Ding on Twitter. Some of your have emailed me privately in the past with things from Dr. Feigl-Ding, and I’ll be honest, I’m not really a fan of his style. I think he is overly alarmist and doesn’t always take the most holistic approach. I’ll say this for him: he does a good job getting people concerned about COVID-19, and COVID-19 is concerning. Still, I think this thread goes too far. Here are my thoughts:

Well, I'm going to start by saying that this isn't the first sensationalist Twitter thread from Eric Feigl-Ding that has crossed my radar. I don't follow him and it's because I think he tends to blow things out of proportion readily, often by emphasizing only part of the evidence or communicating in a way that sounds impressively technical but that is only telling half the story. In this thread there is at least one example--he says that the B.1.1.7 variant will come to "dominate" virus populations around the globe, without really explaining that this means less than it sounds like it means. It just means that eventually this virus variant will be a bigger share of the virus population than other variants. And we've known that for quite some time--it definitely has some kind of fitness advantage.
However, I think that he is touching on some important points--this variant is probably more transmissible. I don't think it is obviously 40 to 80% more transmissible, as he claims--this appears to be exaggeration. As of the day that he wrote that thread, data from Denmark indicated that the spread of the epidemic there was actually slowing, not accelerating. This is probably the result of aggressive lockdown measures that the country took in December, though. The effects of the B.1.1.7 variant are probably not yet realized in the data, even as of the time that Dr. Feigl-Ding wrote this thread.
The most recent high estimate for transmissibility for it is that it's around 50% more transmissible, as far as I have heard, and it may be substantially less than that. This news story provides a more honest view of the situation in Denmark as of the time of that writing: https://www.thelocal.dk/20210104/how-widespread-is-more-contagious-variant-of-covid-19-in-denmark
Now, 50% more transmissible is still concerning, but I think we don't have great data on this right now. The WHO still calls any of the evidence that it is more transmissible "preliminary," and I remain skeptical of a finding that is largely confined to the UK. The Danish experience is going to be informative in this respect, but Denmark has very low numbers overall for incidence as well.
Yes, it is concerning that there is an apparently more contagious variant running around certain countries, but we need to be realistic that every country is different.
The UK has had an extremely inconsistent response to COVID-19, and has suffered for it. Their approach has involved short lockdowns followed by a euphoric public response when those restrictions were lifted--only to see cases spike and the restrictions be put in place again. This has made it somewhat more difficult for me to have faith in the data on transmissibility of this variant, because the best of it comes out of the UK.
Denmark had rather limited disease control measures in place until mid-December, because COVID-19 was still pretty uncommon there. I believe there are still around only 1500 new cases a day in Denmark lately, and about 26,000 total cases in the country. They have about half as many cases per million population as the US, and a quarter as many deaths per million population. For Denmark, getting COVID-19 back down to vanishingly small levels is a goal that is possible in the near term and this virus variant stands in the way of that. If I were Danish, I would find this quite alarming.
In the US, where I know you live, we have very few localities where disease control measures are taken seriously at all. New York City seems to be one of the few places that is managing well in the face of a massive upswing in cases. It is not realistic to compare the US to Denmark or even the UK, because the US has not widely made use of lockdowns or really any disease control measures at all. COVID-19 is out of control in this country. Frankly, I don't know what B.1.1.7 could be doing in the US right now. We don't have adequate surveillance to detect it and we don't have adequate measures to control any form of COVID-19. We need to place COVID-19 in general at a higher level of priority. Once we have some control over the uncontrolled generalized pandemic we should begin to concern ourselves with uncharacterized variants like B.1.1.7.
What Dr. Feigl-Ding most distinctly ignores in his thread is that masking, physical distancing, and staying home definitely still work against B.1.1.7. He provides a great deal of alarmist rhetoric in his thread but not a lot of practical, solutions-minded points about what we should be doing about this. What we should be doing about this is what we always should have been doing--we need a national mask mandate. We need another set of national lockdowns. We need real, tangible support for people affected by those measures. And we need to have a surveillance network in place that can detect variant spread. Even if B.1.1.7 turns out to be only slightly more transmissible, this is true. It was true a month ago and it's true now. If you're personally always masking, avoiding other people, and staying home, you're already doing everything that you can be doing, and everything you're doing will help against whatever variant is spreading locally to you.
I can't say whether you should be alarmed or not; Dr. Feigl-Ding's rhetoric is always alarming, but most people in the US are insufficiently alarmed at the pandemic, so maybe he's doing something good here. The numbers run together and we start to forget the massive scale at which this has grown in our country. COVID-19 is the only thing the government should have been concerning itself with for the entirety of 2020. We continue to ignore it at our peril.
In other words, what I'm trying to say is this: Should you be alarmed? Yes, but you should have been alarmed for months now.

You might have some questions or comments! Send them in. As several folks have figured out, you can also email me if you have a comment that you don’t want to share with the whole group.

Join the conversation, and what you say will impact what I talk about in the next issue.

Also, let me know any other thoughts you might have about the newsletter. I’d like to make sure you’re getting what you want out of this.

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