COVID Transmissions for 1-4-2021
New Year, New...sletter.
Good morning and welcome to COVID Transmissions in 2021! Happy New Year.
It has been 414 days since the first documented human case of COVID-19.
There are a few topics that I’ve chosen to address today in the headlines section. All of them are topics in areas of seriously murky scientific thought, that also happen to be areas of great public interest. In these items, I am going out on a limb in some places and offering more conjecture and opinion than I might otherwise. I have tried to make it clear where I am doing this, because I really try to provide the most accurate and least speculative information that I can here.
The two topics are this: the UK variant, and the efforts by the UK government to delay the second dose of the vaccines they have approved in a bid to vaccinate more people.
As usual, bolded terms are linked to the running newsletter glossary.
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Now, let’s talk COVID.
Towards a better understanding of the UK variant of concern
I have been working hard to better understand the situation with the new variant over the weekend/break. Several main conclusions have jumped out at me:
It appears to me that this variant does have some kind of selective advantage over other variants that compete with it
This advantage may be the result of a transmission advantage; however, I have noticed that many communications on this topic do not sort of out the transmission advantage from the D614G amino acid change vs other changes in the variant. Based on previous work, we already knew that D614G offers a selective advantage that impacts transmission. So I believe a substantial portion of the transmission benefit here may be due to this change but I am having trouble finding clear information
There no change to disease severity or mortality in this variant
It is likely that all of the disease control measures we currently have—masks, physical distancing, reducing activity, and vaccines—remain effective against this variant
I think that it is likely that if there is any transmission increase with this variant, it is less than was initially reported in the news. What I have heard most recently, via the New York Times, is that it has approximately 56% more transmissibility than the virus lineage that was originally spreading in Wuhan, China, around this time last year. This is a far cry from what was initially reported—a 70% greater transmissibility than lineages currently circulating. I think the idea that it is 56% more transmissible than the lineage that emerged last year is a reasonable and supportable claim, though it probably needs more evidence.
Let’s discuss implications. Last week, I discussed transmissibility here but I want to review it one more time. Here’s what I said before:
What this means is that in a situation where there would be some fixed chance of transmission, let’s call that chance X%, this variant may have an (X+C)% chance of transmission, where C is some constant. If, for example, there is an X=10% chance that an interaction with an infected person will infect you, then the chance with the new variant is 10+C%. This is all that “more transmissible” means. We don’t know what “C” is. C might be zero.
Now we do have a number to plug in here. This means that in a given interaction between an infected host and a new host, this variant is maybe—maybe—around 50% more likely than previous variants to infect the new host. If there was a 10% chance of spread before, there is perhaps a 15% chance now. I’m not sure when exactly “before” was vs “now,” but over the last year that change may well have happened. Those numbers, by the way, are based on some data I’ve seen out of England that I previously mentioned here as well.
This is concerning because it means as this variant becomes more prevalent, we might see a 50% increase in the number of cases. That would not be ideal and might require us to reevaluate some of our disease control measures; maybe we will need to lower the thresholds for triggering certain kinds of lockdowns. We will see as we learn more.
On an individual level, though, this doesn’t have a lot of impact. Don’t go out if you don’t have to. Don’t have people over—not anyone. If you must go out, wear a mask and stay at least 6 feet away from others. This is what I would have told you do to a month ago and it’s what I said a week ago to. It’s still good advice.
I know a lot of this repeats things I’ve said before, but what has changed is my confidence in the truth of what I’m saying. I think it’s probable that there’s a small gain in transmission here. I might not bet my savings on it, but it’s enough that I’d not risk my life flouting masking and distance restrictions.
One thing I am noticing in the overall communications on this topic, though, is that a lot of terms are getting thrown around without sufficient explanation—transmissibility, infectivity, morbidity, mortality. Later this week I will do an in-depth piece explaining these terms so that you can better understand what you may read about in the press.
The single-dose vaccine option
Another story that is making a lot of waves is the fact that the UK is delaying administration of the second dose of the vaccines available there by up to 8 weeks:
To put it mildly, I have an opinion about this. I think it is an exceptionally bad idea. Dr. Anthony Fauci is also opposed to it; I believe some folks here may be familiar with him.
In the Phase 2 trials of the mRNA vaccines, the trialists looked at levels of antibodies and immune cells generated after the first dose vs after the boost. Without exception, immune responses were weaker after the first dose than after the booster dose:
The images there are dense, but the bottom line is they show the second dose of vaccine raises levels of antibodies and T-cells, all of them key elements of the immune response.
The vaccine program was designed to use a prime-boost strategy and this is what has been tested. While it may be appealing in the near-term to try and vaccinate more people without worrying about their second dose, I fear that this will yield incomplete protection.
Incomplete protection offers the virus the opportunity to mutate to escape that protection. I think having a larger population of half-immunized people running around will not benefit us as much as people think. This is something that my former colleague, Dr. Florian Krammer, also mentioned on Twitter (I recommend reading his whole thread on this):
This is similar to how antibiotic resistance is helped along by patients who don’t finish taking their whole regimen of antibiotics. The bacteria are given a chance to evolve resistance, and then they do. It’s not the same situation, but I feel it’s analogous. If the one-dose regimen is not protective enough, we could very well see the one-dose approach lead to the emergence of a new variant that the vaccine cannot prevent. That would be catastrophe.
That said, I could be wrong. It may be possible to achieve sufficient protection with a single dose. There are prominent immunologists who are on the other side of this debate and it is a matter of a lot of scientific disagreement. I am not the definitive authority here, and I know it.
The problem is, I don’t know who is right, either. This delayed-boost approach was never tested. No clinical trial examined the amount of protection that can be achieved with a single dose in a well-designed fashion. We just don’t have the data. What we do have are data showing that 2 doses, given around a month apart, will achieve more than 90% protection for both mRNA vaccines. We know that with confidence.
In the choice between “maybe” and “for sure,” I like the sure thing. There are too many unknowns and we have already, globally, taken far too many risks that have allowed this virus to dominate us.
One thing that could change my mind would be clinical trial data. Recently, in The New York Times, Dr. Michael Mina ran an op-ed arguing that a single-dose regimen may be viable. His op-ed has been used to support the way the UK is doing things, but I think this does a disservice to his argument. Instead, he called for clinical trials of the single-dose regimen: https://www.nytimes.com/2020/12/18/opinion/coronavirus-vaccine-doses.html
I disagree with certain aspects of Dr. Mina’s proposal. I think it may take vaccination doses and resources that are desperately needed and divert them to generate evidence supporting a concept that doesn’t actually work. I took these concerns to Dr. Mina and had an extensive conversation with him on Twitter about it last night, and he kindly helped me to see where he is coming from. I understand him to believe that the potential benefits of this approach are much higher than the costs; this may be true.
What I will say is this: Dr. Mina’s approach, where clinical trials are conducted, is a hell of a lot better than the open-air experiment that the UK is conducting on all vaccinees. Since the UK is barreling forward with this approach, I think it could save lives to know for sure whether a single-dose regimen is effective or not. In other words, let’s do the clinical trial.
I’m going to revisit my conversation with Dr. Mina on this topic in a future issue, once I’ve processed it a little more. That said, faced with the idea of his plan vs what the UK is doing, I think he’s doing things in a much more scientific way that doesn’t stand to leave a lot more people vulnerable.
Letter from a pissed-off virologist
Synthesizing both of the topics I covered today, there is an anonymous letter circulating written by a virologist who is clearly angry about how some countries have approached the pandemic. The letter appears to specifically target the UK, but it could be applied to the US as well. You should read it. Found here:
The letter highlights the various ways that our incompetent government responses make it easier for the virus to thrive and escape our attempts to control it.
What am I doing to cope with the pandemic? This:
Thinking about what to write next
It has been some years since I published any short fiction. Over the break, I have been giving a lot of attention to what I’ve written in that time and finding that it’s not…wholly terrible. I think the pause in my output has actually been good; I think my skills have improved because I wrote a lot of things that I didn’t intend to publish that gave me some practice. One thing that I would really like to explore is the feeling of our long isolation this year, and what it will feel like to eventually emerge. It reminds me of a long voyage—perhaps a journey through space or on the sea in ages past. I wonder where we will be when we arrive at the end of this journey.
Before the break, I had shared an old piece that I wrote years ago, about epidemic intelligence and surveillance, and compared it to the current state of the art. Carl Fink, one of the more interactive members of our newsletter community, had some thoughts to share:
Hi, John. By now you've noticed that I am a frequent commenter by nature. Hope it isn't getting obnoxious ... because I am, sometimes, and I know it.
In the Medium article, you wrote, "We now live in a world where news of a disease travels faster than the disease itself ... Really, we’ve lived in that world for more than fifty years now." Yes, in the sense that 200 is more than 50. The "semaphore telegraph" is darn fast (as Larry Niven mentioned in a side comment in Ringworld).
Have a happy new year, John.
I certainly don’t find Carl’s comments obnoxious. I like to discuss ideas. We are talking about ideas here, and that’s great. Here’s what I said in reply:
A happy new year to you too, Carl!
I think we need to be mindful here of the speed at which we learn about new diseases, though. Sure, the telegraph may have been invented in the 19th century, but that telegraph is useless without an electron microscope and sequencing technology to actually be able to detect new viruses. Let's look to the most recent pre-genomics era pandemic to understand how far we've come. AIDS emerged in the 1920s or 1930s. It went unnoticed largely until the late 1970s/early 1980s, when puzzling deaths among gay men were on the rise. It took until 1983 to identify the causative agent, HIV. The disease was spreading for at least 40 years before anyone even knew it existed, and for 53 years before they determined a virus was the causative agent.
Compare this with COVID-19. The first known human case occurred in November 2019. The disease was identified in December 2019. The virus was identified and sequenced a week later. That's a blinding pace by comparison.
Yes, AIDS has a slower progression of disease, but not sufficiently so to explain the sheer difference in scale here. We've come a very long way in our disease intelligence capabilities, allowing us to discover and publicize the emergence of new diseases faster than those diseases can spread. It's not just a matter of communications technology. It's a matter of discovery technology.
Anyway, I thought that Carl’s comment offered a fun opportunity to expand upon what I mean when I say things have really changed, and I am thankful for that opportunity. I think he was making a slightly less expansive point, but I still appreciate the conversation.
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.
After reading responses about the frequency of the newsletter, I’ve decided that I won’t be making major modifications to the schedule. In January, I may be changing the schedule such that the Wednesday issue is sent to paid subscribers only, to recognize their support for this project. The other 4 issues a week will continue to go to everyone. Whether I make this change or not, I plan to continue to write this newsletter 5 days a week.
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.
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.
Correction: In the 12-31-2020 issue, due to a misunderstanding about the name of the clinic, I said that the clinic where vaccine was intentionally spoiled was in Colorado when it is in fact in Grafton, Wisconsin. This has been corrected in the online edition; thank you to those who pointed out the error!
See you all next time. Happy New Year everyone!
Always,
JS
I'm not usually a conspiracy theorist, but part of me is sure the new UK strain is not actually more transmissible, but the BoJo government needs an excuse for the current out-of-control outbreak in the UK that isn't, "We let it happen."