COVID Transmissions for 4-13-2021
On the origins of SARS-CoV-2
Greetings from an undisclosed location in my apartment. Welcome to COVID Transmissions.
It has been 512 days since the first documented human case of COVID-19. 512, being a power of 2, presents us with an opportunity to talk about how things grow exponentially. 512 is the number 1 doubled just 10 times, which really goes to show you how virus outbreaks can get out of hand if each case leads to 2 or more new cases on average.
At one point, there was only one person infected with SARS-CoV-2. Today I discuss the WHO investigation of its origins.
As usual, bolded terms are linked to the running newsletter glossary.
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Now, let’s talk COVID.
UN report on the origins of SARS-CoV-2
As I reported some time ago, the World Health Organization sent some highly esteemed investigators to China to assemble evidence on the possible origins of SARS-CoV-2. I think that if you were to skim the articles about this, you would get the impression this was done to assess whether or not the Trump Administration was right to accuse the Chinese of releasing the virus from a lab, a claim which is not now and never has been supported by any evidence.
However, I want to take a minute to talk about why, conspiracy theories and international espionage aside, the question of the origins of this virus is a worthy one. Even if this virus was somehow released “from a lab,” that statement has a lot of potential meanings. If, in the scenario that we actually have evidentiary support for, it was transferred from bats to humans in the wild, either directly or through some intermediate host, that also has a lot of potential meanings.
Knowing the vague contours of the origins of a virus tells us very little that we can turn into actionable recommendations for the prevention of future pandemics. In emerging disease research, we always ask questions about origins because they help us to create changes to human behavior that prevent future outbreaks—both large and small.
The virus that was the main focus of my PhD first emerged in humans, killing many hundreds of people (40% of those sickened), due to the design of a pig farm in Malaysia. Bats were in close proximity with pigs, and pigs were sorted by the stage of life they were at, ensuring that there was a near constant supply of new hosts for the virus to infect as pigs aged out of particular enclosures. Understanding the way that mango trees planted near the farm attracted fruit bats, and the way that this constant movement of pigs helped the virus incubate in the livestock, led to a redesign of such farming facilities to reduce the chances of another outbreak. Since the initial outbreak in 1990s, Nipah virus has not returned to human populations in that same fashion again—and it has never caused such a high number of deaths, either, in subsequent outbreaks.
In other words, origins questions matter.
So that having been said, the WHO is now looking in to the origins of SARS-CoV-2. They sent a team, as I mentioned, of experienced scientists with a great track record in this area, to investigate how the virus originated in Wuhan and where it may have come from.
This was the team:
Prof. Dr. Thea Fisher, MD, DMSc(PhD) (Nordsjællands Hospital, Denmark)
Prof. John Watson (Public Health England, United Kingdom)
Prof. Dr. Marion Koopmans, DVM PhD (Erasmus MC, Netherlands)
Prof. Dr. Dominic Dwyer, MD (Westmead Hospital, Australia)
Vladimir Dedkov, Ph.D (Institute Pasteur, Russia)
Dr. Hung Nguyen-Viet, PhD (International Livestock Research Institute (ILRI), Vietnam)
PD. Dr. med vet. Fabian Leendertz (Robert Koch-Institute, Germany)
Dr. Peter Daszak, Ph.D (EcoHealth Alliance, USA)
Dr. Farag El Moubasher, Ph.D (Ministry of Public Health, Qatar)
Prof. Dr. Ken Maeda, PhD, DVM (National Institute of Infectious Diseases, Japan)
These are well-known people who are extremely experienced. In particular, Peter Daszak is a pillar of emerging disease research who has worked extensively on SARS-CoVs before and who has also collaborated with the Wuhan Institute of Virology in the past; if there were something going on there, he is exactly the type of person who would be able to figure it out.
I’ve read through the report that this group issued, and can summarize key conclusions. However, I’ll note that they aren’t exactly earthshaking:
SARS-CoV-2 likely entered humans between late September and mid-December of 2019; this is in line with the first documented human case being in November of 2019, so not a big shock, but good to know the totality of evidence still supports this idea
The virus likely did not originate in the Huanan food market in Wuhan (an open-air market with live animals that was an early suspect as the initial source of SARS-CoV-2), though there were many cases that began there
The presence of infectious virus at this market invites the question of how it got there, which is complicated because SARS-CoV-2 can infect quite a few species of animal that were sold at the market, and can persist in frozen foods that were sold there as well
They also considered several origin scenarios, and provided an estimation of the likelihood of each origin scenario (directly quoted):
direct zoonotic spillover is considered to be a possible-to-likely pathway;
introduction through an intermediate host is considered to be a likely to very likely pathway;
introduction through cold/ food chain products is considered a possible pathway;
introduction through a laboratory incident was considered to be an extremely unlikely pathway.
Obviously there is a lot more work to do here, but I’m reassured that extensive work is happening. Next steps will need to be taken to understand this better, and hopefully the Chinese government will be forthcoming and cooperative with what information it has. Getting to the bottom of the origins of SARS-CoV-2 is important for preventing future zoonoses from entering the human population.
You can read the full report here: https://www.who.int/health-topics/coronavirus/origins-of-the-virus
What am I doing to cope with the pandemic? This:
Turning the new apartment into a home
I tend to think of moving in 3 phases. Phase 1 covers the basic functions of life; sleep, being able to eat takeout, having clothes for a few days, etc. Phase 2 covers things that make you comfortable; getting your couches and chairs properly organized and clearing out all the moving trash that may be filling space. Phase 3 is getting things looking nice, and it is the hardest phase to get to. I feel like I’m finally there, now having a small bar set up in my apartment and some art on the walls:
Yes, I know, the poster is a little high on the wall here, but that’s because eventually the console table there is going to be replaced by a taller cabinet.
Anyway, the point is, I finally feel settled in, and that really helps a lot with overall mental comfort. The bar itself will do little except collect dust for a while, since we mostly own alcohol to share it with others, but to me it is a reminder of why we want to bring an end to the pandemic. One day I hope to use it again, in better times, with good friends.
Today I wanted to use this space to say how honored I am that a reader made a donation to the West Side Campaign Against Hunger in my name in recognition of the work I have been doing on this newsletter and in replying to personal messages from readers. I’m really glad to see that being paid forward and wanted to share that with you all.
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.
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No corrections since last issue.
See you all next time.
Always,
JS
Hi John, thank you for producing this newsletter. I have found it to be invaluable- most especially given the hyper-politicization of everything these days.
I’m curious to know how much the virus itself, especially in comparison to other endemic coronaviruses in the area of origin?
If the wet market isn’t the likely point of origin, where else might be an area species overlap that would produce a spillover event?
I’m also curious to get your thoughts on variants and vaccine ‘break-through’. I imagine that in the design phase of vaccine development, a highly conserved protein/epitope/antigen would be the target.
are these true break-through events by these variants or is more likely just an issue of variability of vaccine efficacy among individuals?
How much do we know about how these emerging variants differ from the OG SARS-CoV-2?
And lastly, how are viruses speciated? I know offspring viability tends to be the litmus test for organisms, but when does a variant get its own Wikipedia page?
If you’ve answered any of the above before, apologies! And thank you again for your work.
Kind regards.
About that frozen food hypothesis ... transmission by eating doesn't exist. You, IIRC, agreed with that a few days ago. So that's only possible if Wuhan citizens are in the habit of powdering frozen meat and snorting it up their noses. I am confused.