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1. 2021-03-14 13:41 Robert F. Garry
   So - I am obviously struggling to get this straight - grate data ([high levels of virus in the sewer] suggests that lineageB SC2 infected raccoon dog or dogs and perhaps other animals were in the Market. These lineage B viruses spreadto 30 or more ppl who were linked to the market and were already accumulating mutations. Lineage A virus differsfrom lineage B at positions 8,782 in ORF1ab and 28,144 in ORF8. Lineage A is more like bat viruses and had infected several other ppl in Wuhan, but not linked to this market - one of those ppl flew to Seattle and started theWA1 lineage. WA1 lineage died out in the US. WA1 is lineage A and has bat-like T8782 and C28144 plus another bat-like snp and therefore may be even closer to the MCRA than the other early sequenced lineage A viruses from Wuhan. WA2 (also lineage A) was introduced separately. WA1 did not give rise to WA2.
2. 2021-03-14 13:53 Robert F. Garry open
   Lots of questions. 1. How different were the lineage B SC2s from the humans and environmental samples at the market? Market lineage B SC2s had apparently accumulated some mutations (the Chen paper says 14). 2. Did the SC2s from the environmental samples give rise to the samples in the early Wuhan patients linked to the market orperhaps is it the other way around or perhaps no way to tell? 3. Is it fair to say that lineage A likely gave rise tolineage B?
3. 2021-03-14 14:09 Robert F. Garry open
   Seems to me - given the smoking raccoon dog - low Cts from the grate indicating the animals were infected that it isa LOT more likely that the animal or animals infected the humans in the market instead of the other way around. Most likely scenario for the 30 cases linked to the market is a human-to-human super-spreader type event. Just can't really see multiple ppl individually getting infected from a few caged animals.
4. 2021-03-14 14:28 Robert F. Garry open
   Assuming a. human to animal transmission is an unlikely explanation for the smoking raccoon dog and b. that lineage A gave rise to lineage B, this suggests that the 2 or 3 snps that converted lineage A to B happened via animal-to-animal transmission in a batch of animals that includes some animals that ended up in the Hubai market and some animals that ended up elsewhere. The Hubai market animal initiated the lineage B human-to-human transmissions. The hypothetical group of other animals initiated the lineage A human-to-human transmission. The animal-to-animal transmissions that created the 2 or 3 snps that converted lineage A to B could have been completely in the wild or after the animals were trapped and hauled to market. If in the wild it means that lineage Aand B viruses are circulating and it just happened that a lineage A and a lineage B animal were both were trapped atabout the same time initiating separate SC2 outbreaks within weeks of each other. On the other hand I can easily see one infected animal infecting another during transport and separate distribution to a couple of markets inWuhan.
5. 2021-03-14 14:33 Robert F. Garry open
   Either this or the nefarious virologists at the WIV engineered two lineages of SC2 and in a moment of inspiration tocover up their genocidal plan decided to infect a bunch of animals in the Hubai market with lineage B SC2 and abunch of other unsuspecting civilians in Wuhan with lineage A SC2.

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