Thread by @jbloom_lab

I wanted to add to renewed discussion of early Wuhan #SARSCoV2 triggered by @MichaelWorobey's recent perspective (

https://twitter.com/MichaelWorobey/status/1461417259600023556

). Although some the Twitter discussion has deteriorated into lab leak vs zoonosis yelling, there's some interesting scientific substance (1/n)

First to clear up point of confusion, there isn't new data about patient zero. As @BallouxFrancois explains (

https://twitter.com/BallouxFrancois/status/1462173229070618627

), patient zero was infected probably at least ~1 month before mid-Dec cases @MichaelWorobey is discussing, possibly substantially earlier. (2/n)

Note this misunderstanding about patient zero comes from newspaper headlines, and isn't fault of @MichaelWorobey. In fact, he's done work suggesting patient zero was infected between mid-Oct to mid-Nov (science.org/doi/10.1126/sc…), although there's still a lot of uncertainty (3/n)

However, even if there is no new data about patient zero, the perspective piece pursues some interesting lines of inquiry. Most of these boil down to: What if anything can we guess about earliest December cases for which we do have details? (4/n)

One valuable thing @MichaelWorobey does is dig into details of earliest cases described in joint WHO-China report. He provides evidence that the "earliest case" in the report, who is described as having symptom onset on Dec 8, actually didn't have onset until Dec 16. (5/n)

As I said in NY Times article on topic, I find this mind-boggling. Most important part of an outbreak investigation is tracing earliest patients, & joint WHO-China report was multi-week study by combined team of over two-dozen prominent international & Chinese scientists... (6/n)

But despite interviewing Dec 8 "earliest" patient, joint WHO-China team missed fact he didn't become symptomatic until Dec 16. Fortunately @MichaelWorobey & two other sleuths @franciscodeasis @Drinkwater5Reed found these facts in publicly available info on internet (7/n)

I haven't followed minutia of early patients to same extent the three of them have, but I highly recommend reading through two Twitter threads that detail their discussions and interpretations:

https://twitter.com/flodebarre/status/1461477807498964999

and

https://twitter.com/MichaelWorobey/status/1461829914634571779

(8/n)

They seem optimistic about examining these early cases more. @MichaelWorobey writes in his perspective that "conclusive evidence... may nonetheless be obtainable" & @franciscodeasis suggests (see below) we may be just 2-3 steps from finding source:

https://twitter.com/franciscodeasis/status/1461665574191255553

(9/n)

I hope they're right, but must confess I'm more pessimistic. Normally in an outbreak investigation you trace the contacts of known patients backward in time to find earlier cases. But for #SARSCoV2 investigations in Wuhan, it's going in the opposite direction! (10/n)

In early 2020 newspaper articles described confirmed cases in Nov (scmp.com/news/china/soc…, docs.google.com/document/d/e/2…), Lancet published confirmed Dec 1 case (thelancet.com/journals/lance…), and preprint w China CDC authors (medrxiv.org/content/10.110…) had supp fig w early Dec cases (11/n)

Then pre-print was withdrawn with unconsummated promise it would be published in revised form later (medrxiv.org/content/10.110…), and joint WHO-China report asserted w little detail that all previously reported confirmed cases from before Dec 8 "earliest" case weren't real. (12/n)

Now it appears Dec 8 case isn't accurate either & earliest acknowledged case becomes female seafood vendor at Huanan Market w symptom onset Dec 11. Not much can be concluded from this fact alone, because Dec 11 is clearly at least multiple weeks after patient zero. (13/n)

Nonetheless, @MichaelWorobey suggests we can try to learn about true early cases from distribution of acknowledged Dec ones, some (but not all) of which cluster around Huanan Market. He also argues there wasn't strong ascertainment bias towards market until late Dec. (14/n)

I agree these directions worth pursuing, but given gap between patient zero & earliest acknowledged cases, I doubt it will be possible to conclude anything w high or even moderate confidence about where virus originated unless we get direct data on earlier cases. (15/n)

For instance, here in Seattle many of first cases occurred over a 3-4 week span at a nursing home in Kirkland (seattletimes.com/seattle-news/t…). It's still not clear how virus got into nursing home, but it's considered unlikely that it was the site of WA state's patient zero. (16/n)

Another origins-tracing approach to keep in mind if there isn't better data on earlier patients is "rooting" of the #SARSCoV2 phylogenetic tree based on viral sequences. This rooting question is nicely explained in this thread by @trvrb:

https://twitter.com/trvrb/status/1408080693091991558

(17/n)

The basic idea is that if #SARSCoV2 is ultimately derived from a bat CoV (which I believe is clearly true), then the first #SARSCoV2 sequences to infect humans should be more similar to bat CoV sequences than later sequences that have evolved in new directions in humans. (18/n)

Currently, the two most similar bat CoV to #SARSCoV2 at full-genome level (~96-97% identity are BANAL-20-52 (from Laos) and RaTG13 (from Yunnan via Wuhan Inst of Virology). (Others are more similar in some genome regions but not full genome.) (19/n)

Neither of these viruses are close enough to be the direct progenitor of #SARSCoV2, but they are close enough to allow us to identify which human #SARSCoV2 sequences are most similar to this progenitor. (20/n)

Importantly, viral sequences from Huanan Market (Wuhan-Hu-1) are *not* closest to bat CoV. Two other sequences are more similar to bat CoV at sites 8782, 28144, and 18060 or 29095. See papers by @sergeilkp et al (academic.oup.com/mbe/article/38…) and me (academic.oup.com/mbe/advance-ar…). (21/n)

These sequences often described in "lineage A vs B" terminology that confuses people. Easier way to think about it: for these viruses to be descended from known market viruses, first 3 mutations would have had to all make sequence more similar to both RaTG13 & BANAL-20-52. (22/n)

Since only a small fraction of mutations make #SARSCoV2 more similar to RaTG13 and BANAL-20-52, it's extremely unlikely a virus would get just 3 mutations and they'd all do this. So the known market viruses can't be the ancestor of all human #SARSCoV2. (23/n)

Instead, there were clearly other early human infections evolutionarily upstream from the mid-Dec market cases. Where did these occur? A bat cave in Yunnan? A lab in Wuhan? The Huanan market before anything we know about? Another market? There is no dispositive evidence. (24/n)

So clearly we should dig into whatever can be accessed about mid-Dec cases. But without substantially earlier case data, we're not going to be able to reach a confident answer just using epidemiological approaches, and we need to remember that too. (25/n)