Thread by @macroliter

There’s been some back & forth of late between Worobey & Bloom about early SARS-CoV-2 genome sequences from China, focusing on the meaning of deleted SRA files. Anyone else notice that none of this debate concerns what the existing data say about the #OriginOfCovid ? 🧵

Jesse’s main argument is “because the early viral genome data from China is incomplete, we can’t make strong conclusions about the #OriginOfCovid.” This assertion has some serious flaws..

https://twitter.com/jbloom_lab/status/1534406872337350657

Let’s not let the innuendo distract us: Jesse does not provide an alternative interpretation of the existing data. He merely states that Worobey et al’s conclusions are too strong.. Between the lines though, he is obviously implying a lab leak *might* still be plausible

As far as the data being “incomplete,” remember: this isn’t a tidy lab experiment. It’s a pandemic. By analogy: the fossil record is likewise quite incomplete. Does this mean we must hold evolutionary theory in doubt and continue to debate the merits of creationism?

Whatever China’s motives for not helping us get a more complete set of viral genome data from the first human infections in Wuhan, their govt was unable to control the early outbreak. Hence, we ended up with a pandemic, right?

But viral genome sequences from the early phase of the pandemic were determined from all over the world. China cannot hide these. Scientists have analyzed the global 🧬 data to infer when the pandemic started. These data also help shed light on if the virus is “natural” or not.

There are 2 clear viral lineages that seeded the pandemic: Lineages A & B. No one disputes this. We now know that both A & B lineages were in the Huanan seafood market. nature.com/articles/d4158…

Jesse seems unconvinced that there’s enough data to say A is ancestral to B. But I don’t know of any viral genomic epidemiologists who are still debating this. And he leaps from this “uncertainly” about is A was the “root” to whether there was one or two spillover events.. 🧐

https://twitter.com/jbloom_lab/status/1534406925579743232

The closest natural (bat viruses) relatives to SARS-CoV-2 match A-lineage at two key nucleotides that differentiate A-lineage viruses from B-lineage viruses.. virological.org/t/early-appear…

So again, we have a distraction.. Jesse is no doubt sympathetic to the possibility of a lab leak origin to the pandemic. But he won’t come out and say that in this thread.. (Why not?). All that he says is there still isn’t enough data yet and we have to keep investigating.

Plenty of people are still investigating, but the preponderance of data point to the illegal wildlife trade & highlight the Huanan market as the likely place where two spillover events seeded the pandemic. Responsible scientists acknowledge when colleagues make progress.

IMO, it’s long past time to give credit where it’s due. Work from @MichaelWorobey @K_G_Andersen @acritschristoph @stgoldst @robertson_lab @angie_rasmussen @SpyrosLytras & others points to 2 spillover events at Huanan wet market. Innuendo without new evidence just isn’t helpful.

Wherein Worobey deconstructs @jbloom_lab’s sloppy & disingenuous claims. Quite notable because Jesse Bloom is a cautious, brilliant & well regarded scientist who —for whatever reasons, is pushing specious arguments about what the data do & don’t say regarding COVID origins

https://twitter.com/MichaelWorobey/status/1534898063134732288

Also, h/t @jepekar & @edwardcholmes and several others whose handles I don't have handy I should have also acknowledged above). Incredible team worked very hard to put this beautiful pre-print together.. look forward to seeing it in peer reviewed form.. zenodo.org/record/6291628

and though I hope anyone reading this thread already read this pre-print, too.. if not, please consider it essential reading alongside Pekar et al.. zenodo.org/record/6299600