1/16 I recently gave a public lecture about SARS-CoV-2 origins that touched on some of the myths & misinformation promoted by some proponents of a lab leak origin (below).
But I'd like to discuss a couple others here that I didn't have time to get into.
2/16 First, there is the talking point you've probably heard many times that there is something inexplicable about a new SARS-like coronavirus emerging in Wuhan because it is *so* far away from where the ultimate progenitor in bats existed.
3/16 But recombinant viruses related to SARS2 have been found in Hubei province, where Wuhan is.
And, leaving that aside, the fragment of the SARS2 genome most closely related to a known bat virus shares an ancestor with it only a few years before 2019...
4/16 (See "non-recombinant region" 3 in the above figure, from the virological.org post below from my colleagues and me.)
And it turns out the most closely related fragment is from a bat virus sampled in Yunnan province in southern China...
So those who had shifted their goalposts for a lab origin to WIV-imported viruses from Laos will now need to shift them back to southern China I guess.
At least until the next scientific finding necessitates digging the goalposts up yet again.
6/16 Anyway, the key point: the distance travelled, potentially via the wildlife trade, between a possible Yunnan reservoir and Hubei, for SARS2, is no more remarkable than the distance travelled between Yunnan and Guangzhou for SARS1.
7/16 No sensible person claims on these grounds that SARS1 was due to a lab leak. So judge this argument for the origin of SARS2 - and the people promoting it - with that in mind.
Big h/t to @MilesFujimoto for the figure above and all the following graphics.
8/16 Second, there is the assertion that it would be a crazy coincidence if SARS2 had emerged in Wuhan, of all places, if it *hadn't* come from a lab.
It is true that the Wuhan Institute of Virology is a major center of coronavirus study.
9/16 I can identify with anyone who thinks this is a crazy coincidence. I never quite thought it was crazy, but at one time I thought it was very provocative. But two things I've learned about this have altered my views completely.
10/16 The first is that SARS2 wasn't going to emerge just anywhere in China. Research I helped conduct, led by Joel Wertheim and @jepekar, showed that about 99% of the time a virus with the transmission properties of early SARS2 would jump into a human...
11/16 in a rural location, it would fizzle out. It really takes a city to allow a virus like this to take hold.
12/16 And, cities in China with a lab (or even 3 or 4 labs), which you could point to after the fact as the source of a pandemic that emerged there, are a dime a dozen.
Here's a map of (by one count) mainland China's ten most populous cities.
13/16 Turns out most major cities (Hong Kong too) have sites that could & would be blamed, after the fact, for a pandemic. There's even a lab in Beijing that collected bat virus samples from the 'Mojiang mine' and worked with @PeterDaszak and EcoHealth Alliance. A few examples:
14/16 I think that many of us have fallen into a cognitive trap by positing that an outbreak in Wuhan - whose epicenter was some 15 km from the Wuhan Institute of Virology - started at the WIV...because otherwise there would be some crazy coincidence to explain.
15/16 Perfectly fine idea. But one that kind of falls apart when new analyses, and knowledge beyond the spotlight on the WIV, are taken into consideration.
16/16 It's a shame, but understandable, that Christopher Wray, the FBI, the 'Z Division' and the DOE, among others, appear not to understand this.
*Guangdong, I meant.
• • •
Missing some Tweet in this thread? You can try to
force a refresh
We need to talk about that human case of H5N1 in Texas...
Here is a bootstrapped (NJ) tree showing how the closest realtive of H5N1 sampled in cattle is a virus the infected an male individual who reportedly worked on a farm with cattle (dairy, I believe).
I used all-8-genome-segment concatenated sequences for this analysis, with the help of @evogytis, for this, for maximum signal. Bootstrap values show strong support for the (human + cattle) grouping.
@PeacockFlu was the first person I know of who homed in on how interesting this human's virus was, in the context of the cattle H5N1 outbreak, in this piece by @HelenBranswell.
Important update on metadata of H5N1 in cattle (and back to birds):
Thanks to the extraordinary detective skills of @flodebarre, we are pleased to be able to share this table containing locations and dates for several H5N1 cases in cattle and birds:
We have pseudomized specific location data relating to individual farms/herd/operations, and are only sharing location to state.
We are now incorporating this important metadata into our phylogeographic analyses, which will allow us to do things like use "local molecular clocks" of the sort that Andrew Rambaut and I previously used to resolve the deep history of influenza A virus:
One reason it is particularly frustrating that full metadata has not been shared for genome sequences my colleagues and I have assembled from raw sequence read data released by @USDA / @USDA_APHIS, is that without those dates...
it is not possible to test some really important hypotheses.
Years ago, staring long enough (weeks) at evolutionary trees of all 8 flu A genomes segments that stored on my kitchen table, it finally occurred to my brain that you can't just assume that these viruses evolve...
at the same rate in each host species. Andrew Rambaut and I devised a "local molecular clock" to allow the virus molecular clock to tick at a different rates in each host species.
A few thoughts on the role of pigs in the emergence of influenza A virus in mammals.
1. It is simply not the case that movement of flu viruses into non-swine mammal species requires pigs as a "mixing vessel".
2. Here is a list of mammalian influenza A lineages that *did not* require the involvement of pigs:
Canine flu
Equine flu
Phocine flu
Now bovine flu.
I'll save you a google search: "phocine" = seals/sea lions.
3. Pigs are tested routinely for flu in the US and it is likely that H5N1 would have been detected by now if it was circulating in pigs (h/t @swientist).
4. A big push to screen asymptomatic cattle, and those who work in close contact with them, is important right now.
So, *preliminary* molecular clock analyses indicate that the time of the most recent common ancestor (TMRCA) of the US cattle flu clade was late December.
TMRCA of that clade and the closest relatives in birds, mid-December.
If single intro, likely between those rough dates.
Team effort:
@xrayfoo @flodebarre Kristian Andersen @LouiseHMoncla @swientist @meera_chand @MOUGK @EvolveDotZoo @stgoldst @stuartjdneil @PeacockFlu Andrew Rambaut @angie_rasmussen David Robertson @suchard_group @LemeyLab @jepekar @josh__levy Joel Wertheim @LrnM9
@xrayfoo @flodebarre @LouiseHMoncla @swientist @meera_chand @MOUGK @EvolveDotZoo @stgoldst @stuartjdneil @PeacockFlu @angie_rasmussen @suchard_group @LemeyLab @jepekar @josh__levy @LrnM9 More details to follow, but sincere thanks to scientists @USDA and contributors to @GISAID for making this possible.
OK, I think we're close to decisive evidence that US bovine H5N1 had a single origin from birds, and that when related viruses from birds *have* been found, they are jumps from cattle back into birds.
Grackles, blackbirds, chickens all show mammalian adaptation like PB2 M631L.
My understanding is that these bird (and cat) viruses within the "bovine" clade were sampled from farms that had bovine H5N1.
So, are the birds on these farms giving this virus to the cattle, or are the cattle giving it to the birds? It is cattle to birds very likely.
There is just no good reason to think there's an epizootic of mammalian adapted H5N1 in birds.