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Alina Chan Profile picture
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8 Dec, 5 tweets, 2 min read
Estimated 76% Manaus and 29% São Paulo population infected by covid by October.

"These results confirm that, when poorly controlled, COVID-19 can infect a high fraction of the population causing high mortality."

science.sciencemag.org/content/early/…
In Manaus, the >70% attack rate is "above the theoretical herd immunity threshold.. Monitoring.. new cases and.. ratio of local versus imported cases.. vital to understand (how) population immunity might prevent future transmission and the potential need for booster vaccinations"
US has 15M confirmed cases, "probably, at best, diagnosing 1 in 5 cases" - former FDA commissioner Scott Gottlieb, Nov '20.

Rough calculation ~23% US population infected with covid by now + doubling time ~50 days according to @OurWorldInData + Xmas/NYE..

cnbc.com/2020/11/06/dr-…
Possible that some parts of US will attain >70% herd immunity by natural covid infection before vaccines are widely distributed in April 2021 or later. nytimes.com/interactive/20…
This is not a desirable outcome. Would be better to slow the spread to avoid increased fatalities & suffering. I'm just not optimistic Americans are capable of not travelling for Xmas+New Years. Thanksgiving vehicle travel was only ~5% less than in 2019.
globalnews.ca/news/7501416/c…

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More from @Ayjchan

Alina Chan Profile picture
9 Dec
I was recently asked what I would like to see come out of SARS-CoV-2/covid origins investigations.

I would like to know that, the next time a pandemic like this occurs, the world is better prepared, better informed as to how to determine its origins and prevent future outbreaks.
I'm going to break down 3 key publications that I think relate to covid origins. What were the questions they asked to determine whether SARS-CoV-2 came from nature vs from a lab?

Are these approaches sufficient to prepare us for the next mysterious pandemic?
The 1st is the widely-read Proximal Origins article - a correspondence published in @NatureMedicine on March 17, 2020. How did the authors determine that "SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus"?
nature.com/articles/s4159…
Read 23 tweets
Alina Chan Profile picture
8 Dec
New perspectives piece in ⁦@NatureComms
Wonder what all these scientists could be talking about...
⁩“actors may be incentivized to be reckless if they believe they are unlikely to be held accountable for any accidents arising from their actions.” nature.com/articles/s4146…
"A key security challenge involves attribution: determining, in the wake of a human-caused biological event, who was responsible."

Any chance this is about COVID?

nature.com/articles/s4146…
"if an incident occurs.. near laboratories working on the causative agent, there is a greater chance of it being attributed to an accidental release."

Wonder which recent incident occurred near a lab working on the causative agent. nature.com/articles/s4146…
Read 20 tweets
Alina Chan Profile picture
8 Dec
Different CDC, different covid test kit blunders. Except China already had the SARS-CoV-2 on Jan 3, 2020. apnews.com/article/china-…
*SARS-CoV-2 genome
Also, this was ~2 weeks before China told the WHO that the virus could transmit between humans, but they were already handing out contracts to buddies for test kit development & sinopharm started developing a covid vaccine once they got the SARS-CoV-2 genome.
From the AP article: “We did a brilliant job, we worked so hard,” said Gao Fu, the head of China CDC, in a videoconference in July. “Unluckily, unfortunately, this virus we are facing, it’s so special.”
Read 4 tweets
Alina Chan Profile picture
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 17 tweets
Alina Chan Profile picture
5 Dec
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)?
Read 5 tweets
Alina Chan Profile picture
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

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