> I've never found anyone able to explain in their own words why "two lineages" definitely implies two zoonoses despite the tiny genetic distance between them. I strongly suspect that most people making that claim are simply repeating it, and aren't able to understand the paper, and that the reason none of us can understand is that it's nonsense. If anyone believes otherwise then I'd love to hear, though.

Plenty of us understand - even Bloom, who I generally respect (aside from some sloppy work at the beginning of the pandemic) understands but thinks it's slightly less likely than the theory you're implying. I (and many others!) disagree.

Pekar does a lot of complicated testing and statistics to shore up his case, but "in my own words", it all comes down to timing. We know in which direction the genetic drift of SC2 occurs, which lets us know that Lineage A is the closer than Lineage B to the ancestral bat coronavirus. So Lineage A could mutate into Lineage B, but the opposite is very unlikely.

However, the very first cases reported to the Chinese government - e.g. the very first patients actually were infected with Lineage B. It was several days later until patients began showing up with Lineage A infections. They've reconstructed the phylo trees to the extent possible with the genomes from those first patients and they just don't leave any real possibility that B came from A. The timing just doesn't work. Pekar estimates that Lineage B infections precede Lineage A ones by ~7 days.

This is further buoyed by the rate of divergence in both Lineages being almost exactly the same even though the basic characteristics of each virus are identical. For that to be true, Lineage A. would've had to quietly spread without being IDed, would need to quickly mutate to Lineage B in order for the first sicknesses to be IDed as Lineage B, and then greatly slow down the rate of mutation to maintain the same divergence as B.

This doesn't "disprove" that a single infection could have sparked both lineages - though it's extremely unlikely to have caused two viable viruses and left no trail whatsoever before them in the genetics. It's all a matter or probabilities and IMO, this shows it's far more likely to have had two jumps (similar to how SARS1 and MERS spread) than some hidden ancestor that was extremely similar to SC2 but wasn't noticeably pathogenic.

At very least, this greatly narrows the timeframe and the location of the very first infection. If various vendors at the market were infected with viruses of different lineage within a handful of days of each other, it's completely obvious that this was the site of the first spread. That may seem like an anodyne observation but unfortunately there are still a lot of people who dispute even that much.

I think Bloom is missing something here that would further change his odds in favor of the multiple zoonosis;

https://mobile.twitter.com/jbloom_lab/status/153466370506077...

> Agreed & one scenario under "not seeded by lineage B at market" is seeded by lineage A at market which then evolved into lineage B in humans. Alternatively could have been seeded by lineage A elsewhere & superspreading of derived lineage B at market.

Guo found environmental samples of both Lineage A and Lineage B at the market -- so both were present there -- his second hypothetical would then be highly unlikely.