“Where did the 🦠 come from?” is one of the most asked questions. First, I don’t like unsupported conspiracy theories, but it’s a lingering question. @sciencemagazine examined this based on Lancet article. Nobody knows, but seafood market isn’t whole story sciencemag.org/news/2020/01/w…
2. Again, no outright conspiracy theories please. Here is another explanation: The new #coronavirus is an RNA virus—that is, viruses that have RNA as their genetic material rather than DNA—which have a “high mutation rate,” which allows it to “change properties very quickly.”
3. The RNA sequences of the #coronavirus isolated from 6 patients from the same household are different from each other (Lancet), sign of the virus evolving. This may not be so good to the ear; it suggests the difficulty of containing this virus”. (from m.theepochtimes.com/china-underrep…)
4. DEEPER DIVE into #coronavirus RNA genome 🧬, here goes... “it came from bats 🦇” is often heard, but it’s trickier. The 🦠 has similarities to bat coronavirus, but this new paper REJECTS there was recent recombination. There is something discordant too:
biorxiv.org/content/10.110…
biorxiv.org/content/10.110…
5. (Continued from above)... “A BLAST search of 2019-nCoV middle fragment revealed no considerable similarity with any of the previously characterized corona viruses (figure 2)” —> it’s a sequence entirely new to any known #coronavirus. What does this mean? We don’t know yet.
6. “Notably, the new coronavirus provides a new lineage for almost half of its genome, with no close genetic relationships to other viruses within the subgenus of sarbecovirus.” —> basically it’s saying it’s completely brand new to #coronavirus subgenus.
7. Very strange: So what is in this new mystery middle segment that has no #coronavirus history? The study authors continue: “This genomic part comprises also half of the spike region encoding a multifunctional protein responsible also for virus entry into host cells[30,31]”.🤔
8. Continuing: “Our study rejects the hypothesis of emergence as a result of a recent recombination event.”—> I.e. the authors also conclude that the new #coronavirus did not originate from random recent admixture between different coronaviruses. Other possibilities of course.
9. BOTTOMLINE: 1) Seafood market not the source. 2) This RNA #coronavirus mutates really fast. 3) 🧬 has unusual middle segment never seen before in any coronavirus. 4) Not from recent mixing. 5) That mystery middle segment encodes protein responsible for entry into host cells.
10. TO BE CLEAR: I am absolutely not saying it’s bioengineering, nor am I supporting any conspiracy theories with no evidence. I’m simply saying scientists need to do more research + get more data. And finding the origin of the virus is an important research priority. Goodnight😴
11. Dubbing this the [GENETIC THREAD] 🧬 thread, let’s delve back into the genetic similarities of the new 🦠 with SARS and bat #coronaviruses. Study in Lancet says ~88% related to closest bat coronavirus, 79% to SARS (which is more than humans-elephants) marlin-prod.literatumonline.com/pb-assets/Lanc… 
12. ...As you can see, the new nCOV is a branch off the bat coronavirus subgenus. It is too distant from SARS (79%) or MERS (only 50% related)
13. For the most part, the new #coronavirus shares 87-88% overlap with bat coronavirus. But there are parts of it like the “S” gene 🧬 region where I drops to ~70%, and even 68% in lowest point. But other gene regions share 🧬 consensus as high as 95%.
14. What is in the “S” 🧬 region of the #coronavirus? According to the Lancet piece (link 🧵 above), it encodes the virus envelop spike protein of the 🦠 for binding receptors of host cells - “crucial for host tropism” — which basically identifies how to target 🎯 host tissue.
15. One source or many sources? The mutation rate suggests the 2019-nCoV came from just one recent source in single jump (as opposed to several mutation sources). This doesn’t mean much other than it wasn’t several strains that started outbreak. Don’t over-interpret. Just FYI.
30) Dear friends, after learning that the original authors have formally retracted yesterday’s “uncanny” titled pre-print article, I believe it is prudent to delete the earlier posts 16-24 pertaining to it. Public health science has never been challenged by both such a fast...
31) ...moving epidemic + combined with instant un-peer-reviewed pre-print open publishing of science before. Science is all about cross-checking each other’s experiments, analyses, calculations (nobody is perfect) until a stable theory is reached and we move further forward...
32) This is why it is important to never rush to conclusions and judgement on pre-print articles that aren’t peer reviewed. Even peer reviewed papers are sometimes flawed too, but hence why the need for replication of work by others to further confirm/refute. Normally all this...
33) ...is done in the realm of universities and academic conferences. But with such a fast moving 🦠#coronavirus, the normal pace of science is suddenly upturned and the public thirst for information like the R0 or 🧬 of a virus outpaces the time to properly vet all studies.
34) Same way I also made mistake with my off the cuff “holy mother of God” one night last week, among other things like misreading a paper detail about a SARS’s R0 (that was too low). It’s a valuable lesson learned as someone who once only had a modest Twitter of 2k friends...
35) As they say, “To err is human; to correct, divine.” What we do to correct shows the world what we stand for. And I have indeed stood for science + facts my entire career, even challenging big pharma on a billion-dollar drug. It landed me in hot water 14 years ago doing so...
36) ...but worth the effort because fighting for science and the pursuit of evidence-based public health is important. That is why, during this challenging multi-country epidemic these next few weeks (hopefully not too much longer), we all refocus on sound thoughtful data and...
37) ...and use thoughtful evaluation of the gushing torrent of 🦠outbreak data that’ll continue pouring out to help stop the epidemic. So let’s all not rush to judge/run with the pre-print too much, and let’s not rush to conspiracy theories, and let’s all be kinder to each other.
38) As for the unexpected ‘fortuitous’ sudden Twitter fans out there - I hope you will all stay tuned + mindful of all the data/facts, keep open mind that research data will often conflict, and keep a level mindset to not panic or incite fear. And to fellow scientists out there:
39) ...I am here ready to retweet if you ever have good informative insights and thoughtful in presenting them. @trvrb and @MackayIM and @mlipsitch (inventor of the modern R0 formula) are great follows. I don’t know everything, I’m just a “general Harvard epidemiologist”🤷🏻♂️😀...
40) I have a doctorate in Epidemiology (and an in nutrition) and taught courses on it at Harvard+elsewhere, but I’m not an infectious disease/virologist. However, nobody’s a genius who knows everything in the world-we need the whole scientific community’s hands on deck as a team.
41) In a time of global 🦠crisis like this, the whole world’s better off if we work together to communicate our expertise to the wider public. Let’s stop infighting, and instead focus on the greater good to educate the public. Thanks everyone. Now let’s do this 💪🏼
42) p.s. it seems the thread got disjointed. Here is the link to the earlier post with a good article debunking the ‘uncanny HIV’ paper that has been retracted.
