Thread by @PatrickSSte

1🧵Thoughts on the timing of Covid-19.
Key points to note:

First, the extraordinary stability of CoV-2 during 2020

Second, a lot can be explained if CoV-2 in Wuhan mutated to become more TRANSMISSIBLE in Oct/Nov 2019 (rather like Omicron)

2/ As @mattwridley and @Ayjchan point out in their excellent #OriginOfCovid book, this may well have started with the authorities in Wuhan deciding to cover up a small local problem.

3/ How might events have unfolded?

Covid-19 started with either a lab-leak or a zoonotic spill-over. But when?

CoV-2 was extraordinarily stable from Jan 2020 to the arrival of Alpha in Nov 2020.

4/ For example I remember a discussion in This Week in Virology where @profvrr said the various “isolates” shouldn't be considered to be “strains” because there behavior was the same (which I don't agree with, but they were very similar)

5/ A virus that has recently arrived should mutate rapidly as it adapts to its new host, which we didn’t see. This suggests (to me at least) that CoV-2 was active in humans for months before Jan 2020.

6/ Some have suggested it arrived years earlier – this seems entirely possible to me. Spring 2019 seems like the latest date for the arrival of CoV-2 in humans.

7/ BTW I don’t believe that replication in “humanized” mice could allow CoV-2 to adapt to humans so well.

8/ Let’s start with the lab-leak possibility. Say at some point in early 2019 (or before) there was a lab-leak from the Wuhan Institute of Virology (WIV). It may not have been highly transmissible at first, like SARS-1, but let’s assume that it started to spread slowly in Wuhan.

9/ This was no big deal - there have been lots of lab-leaks in China, UK, Russia, USA. But this strain seems to have come from Gain of Function research, which is controversial in the USA, so (we can speculate) WIV and the city authorities decided to hide the problem.

10/ Once this fateful decision to cover up had been taken, it would be impossible to own up to a lab-leak later on without “losing face”, which the Chinese authorities hate to do.

11/ By early August people in Wuhan started suffering from diarrhea and visits to hospitals increased, as noted by a study by Harvard Medical School that looked at internet searches and satellite images.
nrs.harvard.edu/urn-3:HUL.Inst…

12/ In September WIV scientists seem to have realised that they had a serious problem because they took their virus sequence database off-line

13/ Now let’s go back and consider the possibility of a zoonotic spill-over. Here’s the problem: if Covid-19 came from a natural spill-over, why did WIV take down its database - which they had set up specifically to deal with zoonoses?

14/ The arrival of the #MilitaryGames in Wuhan, 18-27 October 2019, seems to have created a crisis - which would be understandable if the authorities had covered up an epidemic for several months

15/ On 18 October the authorities staged a drill to test responses at Wuhan Airport to the threat of a novel coronavirus. Presumably this allowed them to deal with sick people and do testing without arousing suspicion, & to dismiss rumours of a coronavirus
dailymail.co.uk/news/article-8…

16/ The authorities seem to have locked down Wuhan during the games: a serving Canadian officer reported that Wuhan was like a ghost town during the #MilitaryGames

That should be easy to check with satellite data
jamiemetzl.com/questions-abou…

17/ In spite of precautions, many athletes, including Élodie Clouvel, Valentin Belaud, Matteo Tagliariol and a serving Canadian officer, were infected with a virus that looked like CoV-2 at the Wuhan games
en.wikipedia.org/wiki/Valentin_…

thechampionsvoice.com/la-subcampeona…

theweek.co.uk/coronavirus/10…

18/ Canadian officer jamiemetzl.com/questions-abou…

blick.ch/sport/mehr_spo…

news.com.au/world/coronavi…

19/ At this point we need to look at the timing of the arrival of the common ancestor of current CoV-2 strains

M Worobey in his Science article quotes 18 Nov as the “mean estimated date of pandemic index case”, citing his own article with co-author Pekar
doi.org/10.1126/scienc…

20/ However, this is a mis-quote by Worobey

Pekar et al. define “the period between mid-October and mid-November 2019" as "the plausible interval when the first case of SARS-CoV-2 emerged in Hubei province”

doi.org/10.1126/scienc…

21/ In other words Pekar takes us back to the period of the #MilitaryGames

So why have scientists ignored the cases among the athletes at the games?

It would be very valuable to have viral sequences from these athletes - we have a sequence of 1918 Spanish influenza

22/ Now, one puzzle is, if their illness was caused by CoV-2, why didn’t these sick athletes cause a wave of secondary CoV-2 infections in their own countries?

23/ I suggest that during the period between mid-October and mid-November a new CoV-2 variant emerged in Wuhan that was more TRANSMISSIBLE (rather like Omicron). The athletes may have been infected with earlier less-transmissible strains, which became extinct in their countries.

24/ The earlier strains may not have been less pathogenic than the new variant: several athletes seem to have suffered from long Covid.

25/ The new variant seems to have spread so rapidly in Wuhan in November and December that it became impossible to hide.

26/ If this turns out to be correct, Pekar’s period between mid-October and mid-November 2019 corresponds not to the index case of Covid-19 as a whole as they suggest, but to the index case a more-transmissible variant, which now dominates
doi.org/10.1126/scienc…

27/ The Chinese authorities now identified individuals who were hospitalized with Covid-19 in December 2019, suggesting that these were the first few cases.

28/ This included a cluster of individuals who had visited or worked in the Huanan Market. This may not be coincidental: @JuliaLBach8 and I have shown evidence that chilling can activate pre-existing dormant respiratory infections.
doi.org/10.1002/rmv.22…

28/ There are many reports during this period of mysterious viral illnesses emerging with China:

29/ For example a United Airlines pilot flying out of Beijing reported that between mid-December and mid-January, an unusually high number of passengers felt unwell on almost every flight, including two of his copilots.
viewfromthewing.com/united-airline…

30/ An individual in Ireland became sick in early December, losing their sense of smell and taste:

https://twitter.com/GroPinfo/status/1473422810273959943

31/ In January 2020 the Chinese version of events was accepted by other nations and the WHO.

Here is the abstract of Pekar, Worobey et al., discussed above⬆️

I don't understand why scientists ignore stories like this⬇️

https://twitter.com/admcollingwood/status/1477894113890553856

BTW I wrote the wrong month here. The authorities staged a drill to test responses at Wuhan Airport to the threat of a novel coronavirus on 18 SEPTEMBER

https://twitter.com/PatrickSSte/status/1477630824757743617