I'm hoping that one effect of the pandemic is that journals will start publishing peer reviews so that readers can quickly grasp the strengths and weaknesses of each paper.

Without published peer reviews, we need to rely on experts critiquing papers on twitter every weekend.
Peer reviews are performed by other experts in the same or similar fields, who spend hours to days reading and critiquing a paper.

This is real work. By highly skilled experts. That is also unpaid, no tangible incentives. Yet, not published unless a journal has open peer review.
It costs next to nothing to publish peer reviews online or as a supplementary file. But the value! Even people outside the field can see what questions the experts asked, were these addressed in the revisions? Were reviews fair, totally overboard, or negligent (just publish it)?
I'm really looking forward to peer reviews of preprints. I get requests every couple of days to comment on preprints or peer-reviewed papers - but this realistically is a time sink and I only choose to do it when I think the paper is genuinely interesting or especially important.
Otherwise I won't have time to do actual peer reviews and write my own papers.

This is why I believe that peer reviews (all that hard work and expertise) should all be published. Authors should also have the option to take peer reviews with them to the next journal if rejected.

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More from @Ayjchan

6 Dec
On the pangolin story that is still drawing breath, "(Shi Zhengli, WIV) said that if the intermediate host was the pangolin.. it’s possible the virus jumped from bats to pangolins outside China.. smuggled in from other Asian nations, including India."
theguardian.com/world/2020/dec…
Thankfully, before scientists go on a wild goose chase to sample pangolins in India, David Robertson (U of Glasgow), who was also interviewed, said, “We’re fairly confident the pangolins have picked up their virus, presumably from horseshoe bats, after being imported into China.”
If any pangolins need to be investigated, I recommend starting with the Guangdong pangolins confiscated in March, 2019. This is the only batch of pangolins with a CoV that has a SARS2-like Spike RBD. Many questions remain re: the sample histories and data. biorxiv.org/content/10.110…
Read 7 tweets
4 Dec
"You may disagree with their unconventional approach, but the truth is that these people behave, to all intents and purposes, like a small scientific community: they search and analyze data, they share and discuss their findings and, more importantly, they make discoveries."
Timely piece by @emmecola on how a coalition of twitter users, several anonymous, have been at the front of investigating the origins and sample history of RaTG13 + connection to SARS-like cases among miners from a Yunnan mine full of bats in 2012. mygenomix.medium.com/the-origin-of-…
Their work and fringe (I say this positively) influence on scientists & journalists has led to measurable outcomes. Namely, this @Nature addendum, confirming that RaTG13=4991; was seq'ed in 2018, not post-covid; linked to severe respiratory cases in 2012.
nature.com/articles/s4158…
Read 9 tweets
3 Dec
Are these the 8 other SARS viruses from the Mojiang mine? Where can the sequences and metadata be accessed?

The partial RdRp sequence for Ra7896 can be found here: ncbi.nlm.nih.gov/nuccore/MN3126…

Associated with this May 31 preprint, later in Nature Comm: biorxiv.org/content/10.110…
Latinne et al. (EcoHealth, WIV et al.) say "Our host datasets included.. 528 β-CoV sequences (273 new sequences, including 97 new SARSr-CoV sequences (Sarbecovirus) from 31 bat species"

Could be helpful to post the 97 SARSr-CoV sequences in one dataset.
nature.com/articles/s4146…
Also good to note that this manuscript was

Received by Nature Communications on 6 October 2019

Preprinted on bioRxiv on 31 May 2020

Accepted by Nat Comm on 6 July 2020
Read 7 tweets
1 Dec
@shingheizhan and I just submitted for peer review our rewritten pangolin CoV manuscript within a mini-review of what we currently know about RaTG13 and the chances of natural spillover in Wuhan. We are hopeful that it gets through this time and will be published in early 2021.
The story about the possible intermediate host and how SARS-CoV-2 spilled over into humans has changed so much over the past year. We were told in Jan that the virus came from wild animals sold at the market. And then in Feb that it was likely pangolins...
All of these trails have fizzled out... leaving no trace of an intermediate host, no clear evidence of natural spillover, while the closest virus relatives are from bats in Yunnan, a thousand miles away from Wuhan city.
Read 5 tweets
1 Dec
Thread breaking down the newest peer-reviewed study suggesting that COVID was on the West Coast in mid December, 2019.
It's not impossible that SARS-CoV-2 arrived in Europe and the US in Dec 2019, but consider that out of 640 throat swabs from Wuhan patients w influenza-like illness, Oct 2019-Jan 2020, only (9) samples in January tested positive for SARS-CoV-2. nature.com/articles/s4156…
Even in the city where cases were detected in Nov 2019, even when only patients with influenza-like illness are considered (not random blood donors), the virus could only be detected in January 2020 patient samples.
Read 4 tweets
30 Nov
Nothing really surprising in the new Wuhan leaked documents shared by CNN, but I find this sobering:

"The documents show health care officials had no comprehension as to the magnitude of the impending disaster."

cnn.com/2020/11/30/asi…
A month before, one of the first whistleblowers was made to sign a letter on Jan 3, 2020 confessing to spreading rumors and violating the law.
"In the future, doctors will be more afraid to issue early warnings when they find signs of infectious diseases." bbc.com/news/world-asi…
The day after Dr. Li signed the letter, a leading Chinese vaccine developer Sinopharm kicked into high gear manufacturing a covid vaccine on Jan 4; 2 weeks before China confirmed human-to-human transmission.
Thanks @norman7177 @dktatlow for sources.
Read 6 tweets

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