Another try by @tgof137 at explaining that since the Wuhan outbreak began in a market it must have involved a double spillover where an evolutionarily derived virus emerged first & its ancestral sibling jumped later.

Is there a better, non-circular, alternative explanation?
1/🧵

https://twitter.com/tgof137/status/1759743322154058188

Peter's favorite visualization of early genomes (green=lineage A, blue=lin.B) immediately reminded me of an old thread in which I dissected a similar figure from Tang et al. 2020, a pioneering analysis of the 2 early lineages (red=lin.A, blue=lin.B).

2/🧵 academic.oup.com/nsr/article/7/…

Stoyan/Chiu's takedown of Worobey et al, followed by the publication of an early draft of DEFUSE (disclosing even more clearly the 2018 project to screen & tweak SARS2-like viruses in Wuhan) have outranked news that SC2's genome was known in Beijing way earlier than thought. 1/🧵 The news that SC2's genome was known 2 weeks before China acknowledged the "novel coronavirus" was broken by the @WSJ () building on a @HouseCommerce investigation (see ), and analysis by
@jbloom_lab ()

2/🧵archive.is/LPFBk
energycommerce.house.gov/posts/e-and-c-…
github.com/jbloom/SARS2_2…

Building on an earlier thread (quoted below by @niemasd) let me elaborate on some of the explicit & implicit assumptions that in my view permeate the recent Pekar et al. preprint, how they influence their conclusions, and why I think those assumptions might be unwarranted.

1/🧵

https://twitter.com/niemasd/status/1503512847615086592

Let's start with "the observed viral diversity" that guided their simulations. I note that "observed" here actually translates to "published".

However, publication on origin-related research was (and still is) severely restricted in China.

edition.cnn.com/2020/04/12/asi…

2/🧵

A lot has been written already about four recent preprints that look into the origins of the Wuhan outbreak from various perspectives.

A thread with some additional thoughts.

1/🧵 Gao et al reported additional data from the environmental & animal sampling led by China's CDC at Huanan market in Jan/Feb 2020. Part of these data were presented in the China/WHO report over a year ago, so one might expect final results by now? Nope

researchsquare.com/article/rs-137…
2/🧵

A commendable attempt by @MichaelWorobey to dissect the early COVID-19 cases in Wuhan, in order to try and elucidate the origin of the pandemic.

Some comments:

1/🧵

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

It's a Lapalisse truth that to elucidate the origin of the pandemic we need to understand where & how the Wuhan outbreak started.

Having previously looked at phylogenetic data in Pekar et al. 2021, Worobey now focuses on epidemiological information.

science.org/doi/10.1126/sc…
2/🧵

Because of his late arrival to the origins debate & near exclusive reliance on quotes from hard core zoonati, @hiltzikm's writings on Covid origins are arguably irrelevant.

Here, however, he proclaims "more debunking of the lab-leak theory for COVID" so I gave it a read...

1/🧵

https://twitter.com/hiltzikm/status/1443047893699481601

@Hiltzikm's opinion is clear from the start: he sees the lab-leak hypothesis as an unsupported assertion that should be branded as pseudoscience.

But is the difference between science and pseudoscience as clearcut as the difference between journalism and pseudojournalism?

2/🧵

Many questions remain with regard to the two early genomic lineages of SARS-CoV-2 that were circulating in Wuhan around the time the virus was first reported.

Thread about lineages S and L (also called lineages A and B) and their relevance for the origins debate.

1/🧵 SARS-CoV-2 lineages were first defined by Tang et al. 2020 according to differences in genomic positions 8782 and 28144.

Lineage S (like seen in related bat CoVs) has 8782T/28144C whereas 8782C/28144T defines lineage L, now fully dominant in humans.

academic.oup.com/nsr/article/7/…
2/🧵

@BillyBostickson @SharriMarkson I'm preparing a short thread on this topic. @BillyBostickson @SharriMarkson 🧵 on some specifics about the WIV bat cage patent.

This 2018 patent (full version available as a PDF at patents.google.com/patent/CN20831…) was recently reported in connection with a WIV promo video released by the Chinese Academy of Sciences in 2017: zmkxj.cas.cn/zpzs/whfy/2017…

1/🧵

@stgoldst Following on @CNN's poor coverage of the debate around COVID-19's origins, @npwcnn also fails to do justice to the amount of "coincidences" that definitely point to a lab scenario.

Illustrated thread.

1/🧵 @stgoldst @CNN @npwcnn The piece starts with three "massive coincidences":

1) A bat coronavirus (CoV) started an outbreak on the doorstep of a lab (in the Wuhan Institute of Virology or WIV) that specializes on bat CoV research, the lab where SARS-CoV-2's closest known relative was sequenced.

2/🧵

@gsgs2 @franciscodeasis @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen Questions/hypotheses about SARS-CoV-2 origin mustn't distract us from established facts. Sequential recap:

1/ A bat-derived coronavirus (CoV) starts an outbreak near a bat CoV research center, the Wuhan Institute of Virology (WIV)
2/ WIV's virus database is noticed to be offline @gsgs2 @franciscodeasis @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen 3/ In a February 2020 paper, WIV admits having possession (since 2013) of one close relative of the outbreak virus, but fails to cite its own 2016 paper where it had been published as RaBtCoV/4991

@Rossana38510044 @jhouse678 @franciscodeasis @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen 1/ Here's some takeaways from Zhou et al's Addendum.

First, some background:

• The authors' earlier version of the Tongguan mine sampling (Ge et al. 2016) says "we conducted a surveillance of coronaviruses in bats in an abandoned mineshaft (...) from 2012–2013." @Rossana38510044 @jhouse678 @franciscodeasis @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen 2/
• The 2016 paper reports a total of 276 bat samples, where the authors detected "150 sequences homologous to alphacoronaviruses" and "two sequences (HiBtCoV/3740-2 and RaBtCoV/4991) homologous to betacoronaviruses"
• Only one of those beta CoVs was said to be SARS-related.

1/ Re-upping this thread on the origins of #COVID-19. It makes a compelling case for a possible lab escape.

Magnitudes more plausible that SARS-CoV-2 emerged from a lab in Wuhan (known to be lacking in safety protocols) than from a 100% natural zoonosis.

https://twitter.com/TheSeeker268/status/1313858771064512517?s=20

2/ How do the experts rationalize these facts surrounding SARS-CoV-2 origins?

@firefoxx66 @BallouxFrancois @jonny_polonsky @DrMikeRyan @OWMorgan @_katusche @SCBriand @ChungongStella @mtosterholm @llborio @celinegounder @ZekeEmanuel @doctorsoumya @HelenBranswell @ProfVolkerThiel

1. While awaiting @shingheizhan reassembling of RaTG13, here's a thread with some odd features reported by authors who made use of its GenBank sequence. Most of them used the sequence for other research goals, rather than assessing it, so its anomalies are mentioned incidentally. 2. This Feb 2020 preprint found that synonymous mutations "are dramatically elevated between SARS-CoV-2 and RaTG13" and "enriched in T:C transition."

Since some RNA mutagens "could induce the same mutation pattern", authors suggest further investigation.
biorxiv.org/content/10.110…