[BostonCard]

Yeah, see, I viewed this tweet as an example of someone who seems vested in the late January start date and simply declares it to be so (though I have no doubt author bases it on data).  And I believe that is very, very likely true.  However, I'm just wondering why it is completely beyond the realm of possibility that people had it prior to that, thinking it was 'worst flu ever,' but never went to hospital and recovered.  Is it because there absolutely would had to have been deaths (at abnormal levels), which would have led to earlier discovery?  That makes intuitive sense, certainly. But is it possible that bad cases, even if they go into the hospital, are never properly diagnosed?  Or is that not possible?

It's because the data strongly argues against it.  I have already quote the Stanford study, where they looked at stored respiratory samples collected between Jan 1 and Feb 29, that were collected looking for viruses, but which tested negative for conventional viruses (influenza, RSV, etc.).  They looked at like 2000 samples, and only 2 were positive, both from the second to last week in February.  You'd expect that if the virus was circulating in the Bay Area for longer some of those samples would have been positive.

https://jamanetwork.com/journals/jama/fu...ultClick=1

Another study looked at viral samples collected throughout the world to look at genetic variation.  Basically, random mutations serve as a "clock" since the mutation rate is more or less constant, so you can trace the virus back to its entry into humans.

https://www.statnews.com/2020/01/24/dna-...mutations/

By comparing the two dozen genomes, scientists can address the “when did this start” question. The 24 available samples, including from Thailand and Shenzhen as well as Wuhan, show “very limited genetic variation,” Rambaut concluded on an online discussion forum where virologists have been sharing data and analyses. “This is indicative of a relatively recent common ancestor for all these viruses.”

Given what’s known about the pace at which viral genomes mutate, if nCoV had been circulating in humans since significantly before the first case was reported on Dec. 8, the 24 genomes would differ more. Applying ballpark rates of viral evolution, Rambaut estimates that the Adam (or Eve) virus from which all others are descended first appeared no earlier than Oct. 30, 2019, and no later than Nov. 29.

It doesn't answer the question of how long it has been in the Bay Area, but does answer the question of how long the virus has been in humans, and the thing seems to have made the jump in November. If the virus only made it into humans in November, it is very unlikely to have been circulating in the Bay Area in the fall.

BC

[BostonCard]

Yeah, see, I viewed this tweet as an example of someone who seems vested in the late January start date and simply declares it to be so (though I have no doubt author bases it on data).  And I believe that is very, very likely true.  However, I'm just wondering why it is completely beyond the realm of possibility that people had it prior to that, thinking it was 'worst flu ever,' but never went to hospital and recovered.  Is it because there absolutely would had to have been deaths (at abnormal levels), which would have led to earlier discovery?  That makes intuitive sense, certainly. But is it possible that bad cases, even if they go into the hospital, are never properly diagnosed?  Or is that not possible?

It's because the data strongly argues against it.  I have already quote the Stanford study, where they looked at stored respiratory samples collected between Jan 1 and Feb 29, that were collected looking for viruses, but which tested negative for conventional viruses (influenza, RSV, etc.).  They looked at like 2000 samples, and only 2 were positive, both from the second to last week in February.  You'd expect that if the virus was circulating in the Bay Area for longer some of those samples would have been positive.

https://jamanetwork.com/journals/jama/fu...ultClick=1

Another study looked at viral samples collected throughout the world to look at genetic variation.  Basically, random mutations serve as a "clock" since the mutation rate is more or less constant, so you can trace the virus back to its entry into humans.

https://www.statnews.com/2020/01/24/dna-...mutations/

By comparing the two dozen genomes, scientists can address the “when did this start” question. The 24 available samples, including from Thailand and Shenzhen as well as Wuhan, show “very limited genetic variation,” Rambaut concluded on an online discussion forum where virologists have been sharing data and analyses. “This is indicative of a relatively recent common ancestor for all these viruses.”

Given what’s known about the pace at which viral genomes mutate, if nCoV had been circulating in humans since significantly before the first case was reported on Dec. 8, the 24 genomes would differ more. Applying ballpark rates of viral evolution, Rambaut estimates that the Adam (or Eve) virus from which all others are descended first appeared no earlier than Oct. 30, 2019, and no later than Nov. 29.

It doesn't answer the question of how long it has been in the Bay Area, but does answer the question of how long the virus has been in humans, and the thing seems to have made the jump in November. If the virus only made it into humans in November, it is very unlikely to have been circulating in the Bay Area in the fall.

BC