WA1 is classified under lineage A, but the two defining mutations of lineage A are C8782T and T28144C and WA1 has the third mutation C18060T. Lineage B is identical to the Wuhan-Hu-1 reference genome, but WA1 has three mutations from Wuhan-Hu-1 and lineage A has two mutations. The three mutations of WA1 are ancestral in the sense that they are shared with other sarbecoviruses like BANAL-52 and RaTG13.
Almost all market samples were lineage B, apart from the environmental sample Env_0020/A20 which was taken from a glove.
WA1 is also identical with proCoV2 which Kumar et al. reconstructed as the hypothetical ancestor of known strains of SARS-CoV-2.
On GISAID there is also one sample from Guangdong which has 5 mutations from Wuhan-Hu-1, but all of them are ancestral in the sense that they are shared with RaTG13:
Much appreciated on the needed details so will reference your brilliant comment in post!
But 2-3 nucleotide difference over a 30000bp genome is trivial for a transmission study (not debating an origin study). Lineage A/B/proCoV2/WA1 strain only transmits (aka "onward transmission") in the 5 animals listed above and linked below. i.e. when the contact animal has the same viral load as the infected animal (ferrets, raccoon dogs, cats, hACE2 mice, etc don't qualify per this definition). in other words I will give Kumar et al. the Wuhan wet market, now tell us why that Wuhan wet market strain (A/B/proCoV2/WA1) transmits in RML lab animals?
the beautiful thing about a transmission study is that it can't be hidden (e.g. deer, mink) and we don't need labs to run it. Remember the sneezing Syrian hamsters in Hong Kong? Imported from Vincent Munster's old stomping grounds: the Netherlands!
The Wuhan market strain is lineage B and not A/B/proCoV2/WA1. And the paper about proCoV2 by Kumar et al. presented evidence against the market origin.
There's also a rare sublineage of proCoV2/WA1 which has a total of 5 mutations relative to Wuhan-Hu-1, which are C865T and C13694T in addition to the three mutations of proCoV2. It's shown in the top left corner of this figure by Jesse Bloom: https://academic.oup.com/view-large/figure/419264257/msab246f5.tif. I've been calling it the "Guangdong-Singapore lineage", because it's found in only 4 samples at GISAID, which are two samples from Singapore from late January and two samples from Guangdong from early February:
Even though two of the additional mutations are rare at GISAID, both of them them are found in Csabai's Antarctic samples, which is one reason why I believe the SARS2 reads in the Antarctic samples come from early COVID patients in China. There may have been early secret sequencing projects in China, because Eddie Holmes said that he heard that the plan of the Chinese authorities was to not announce the identity of the virus until the lunar new year, which fell on January 25th in 2020, and he said that Yongzhen Zhang actually got in major trouble for publishing the genome of Wuhan-Hu-1 before then: "I heard was they wanted to have - it's maybe a rumor - but I heard they wanted to have the whole thing kind of tied up by Lunar New Year, and to have one big announcement saying 'here's the virus, we've solved the problem, here it all is', you know, bow tied, post package posted - that's kind of what I heard they wanted. And we kind of like, you know, we scuppered their their plans in doing that, and like I say there has been a lot of fallout because of it. [...] Zhang was not the first person to sequence the virus, okay. I don't know about the people that have done that as well - whole set of groups were - but so, Zhengli Shi had sequenced it - actually probably before Sanger sequenced it." (https://www.youtube.com/watch?v=5u94foNmpKE&t=26m8s)
So I just had a chance to listen to your podcast on Straight Talk. Well done.
I am trying to come across to your way of thinking in that Baric was a good guy and this was all an accident.
We agree on the Made in USA and released in Wuhan, but what stops me is that Ralph accidentally sent out a bat vaccine virus to WIV designed to immunize bats, presumably after running it past Linfa in Singapore, and not knowing his brilliantly engineered virus does not infect the target bats so is useless as a Vaccine, but it is superbly adopted to humans and is very transmissible (a perfect human vaccine), yet this is only found out by a lab accident in Wuhan.
Also, you certainly are correct that this was not much of a weapon in a militarized sense (designed to kill/incapacitate), but have you considered how perfect it was for Bioterrorism ?
Ralph-2006
“If notoriety, fear and directing foreign government policies are principle objectives, then the release and subsequent discovery of a synthetically derived virus bioweapon garner tremendous media coverage, inspire fear and terrorize human populations and direct severe pressure on government officials to respond in predicted ways.”
You are about where I was early last year, I can't understand how Baric is talking to the press in 2020-21 and carefree about his obvious creation (BsaXI, UGGUCGC, ENaC, etc). But I take their <2020 interviews as gospel and Baric was on record that my hACE2 mice are safe. They don't sneeze, don't transmit, and "the process of adapting these viruses to mice actually makes the germs less able to infect human cells." He's adamant in this interview he doesn't do transmission studies, and I've never found one, it's all infection studies.
And then in 2022, the 'virus' spilled into deer and I quickly became suspicious of RML taking Baric's creation and turning it into a contagious bat vaccine. They also have deer mice, mink, EFB bats, and Syrian hamsters, the only 5 transmission models for a Wuhan wet market strain (WA1) that I've found. Let me know if you find others?
And we may disagree but SARS2 doesn't infect lab mice, but it does transmit in Munster's hamsters, which aren't found in WIV
I've reread that creepy 2006 "dual use" Baric paper, and now interpret: I, Ralph Baric can create any genome on the planet, used for any purpose, but I will use it for 'benevolent' purposes like animal vaccines.
Baric's only done 1 interview since Defuse leaked, and it was basically to throw Munster under the bus for his "edgy" transmission work. Munster and Linfa and Dani were close bat colleagues (I don't think Baric had ever held a live bat).
Engineer Sars-Cov-2 and not know he created the Munster Virus he was trying to create a Vaccine for, before sending it to Shi Zheng Li , knowing she did most of her work in a BSL-2
WA1 is classified under lineage A, but the two defining mutations of lineage A are C8782T and T28144C and WA1 has the third mutation C18060T. Lineage B is identical to the Wuhan-Hu-1 reference genome, but WA1 has three mutations from Wuhan-Hu-1 and lineage A has two mutations. The three mutations of WA1 are ancestral in the sense that they are shared with other sarbecoviruses like BANAL-52 and RaTG13.
Almost all market samples were lineage B, apart from the environmental sample Env_0020/A20 which was taken from a glove.
WA1 is also identical with proCoV2 which Kumar et al. reconstructed as the hypothetical ancestor of known strains of SARS-CoV-2.
On GISAID there is also one sample from Guangdong which has 5 mutations from Wuhan-Hu-1, but all of them are ancestral in the sense that they are shared with RaTG13:
$ curl https://mongol-fi.github.io/f/gisaid2020.tsv.xz|xz -dc>gisaid2020.tsv;grep RaTG13 gisaid2020.tsv|cut -f12|tr , \\n|awk -F\\t 'NR==FNR{a[$0];next}$11<10{split($12,b,",");n=0;for(i in b)n+=b[i]in a?1:-1;print n FS$0}' - early.comb|awk '$1>=3'|sort -rn|cut -f1-8,12-13|tr \\t \||head -n1
5|EPI_ISL_413892|hCoV-19/Guangdong/FS-S30-P0052/2020|2020-03-09|2020-02-28|A|China|Guangdong|5|C8782T,C18060T,C21711T,C24382T,T28144C
Much appreciated on the needed details so will reference your brilliant comment in post!
But 2-3 nucleotide difference over a 30000bp genome is trivial for a transmission study (not debating an origin study). Lineage A/B/proCoV2/WA1 strain only transmits (aka "onward transmission") in the 5 animals listed above and linked below. i.e. when the contact animal has the same viral load as the infected animal (ferrets, raccoon dogs, cats, hACE2 mice, etc don't qualify per this definition). in other words I will give Kumar et al. the Wuhan wet market, now tell us why that Wuhan wet market strain (A/B/proCoV2/WA1) transmits in RML lab animals?
https://www.ecdc.europa.eu/en/publications-data/sars-cov-2-animals-susceptibility-animal-species-risk-animal-and-public-health
the beautiful thing about a transmission study is that it can't be hidden (e.g. deer, mink) and we don't need labs to run it. Remember the sneezing Syrian hamsters in Hong Kong? Imported from Vincent Munster's old stomping grounds: the Netherlands!
https://www.bbc.com/news/business-64170999
Please let me know if you find a 6th animal on the planet?
The Wuhan market strain is lineage B and not A/B/proCoV2/WA1. And the paper about proCoV2 by Kumar et al. presented evidence against the market origin.
Pekar et al.'s modeling paper needed to invoke the double spillover hypothesis to explain why the market strain was not the ancestral strain, but their paper was destroyed by nizzaneela: https://gillesdemaneuf.medium.com/backstage-story-the-oct-2023-correction-to-pekar-et-al-e167080e957d.
All three mutations of proCoV2/WA1 are also featured in the Antarctic reads that were analyzed by Csabai et al: https://media.discordapp.net/attachments/1096166927174483968/1129115132333666395/antarctic-small-heat.png. But I believe the Antarctic reads contain a mixture of samples from different early COVID patients in China, so all three mutations were not necessarily featured in the same sample.
There's also a rare sublineage of proCoV2/WA1 which has a total of 5 mutations relative to Wuhan-Hu-1, which are C865T and C13694T in addition to the three mutations of proCoV2. It's shown in the top left corner of this figure by Jesse Bloom: https://academic.oup.com/view-large/figure/419264257/msab246f5.tif. I've been calling it the "Guangdong-Singapore lineage", because it's found in only 4 samples at GISAID, which are two samples from Singapore from late January and two samples from Guangdong from early February:
$ curl https://mongol-fi.github.io/f/gisaid2020.tsv.xz|xz -dc>gisaid2020.tsv
$ grep C13694T gisaid2020.tsv|grep C865T|cut -f1,3,4,6-8,11-12|tr \\t \|
EPI_ISL_536447|2020-09-16|2020-01-25|Singapore|||5|C865T,C8782T,C13694T,C18060T,T28144C
EPI_ISL_418993|2020-04-01|2020-01-29|Singapore|||5|C865T,C8782T,C13694T,C18060T,T28144C
EPI_ISL_413862|2020-03-09|2020-02-01|China|Guangdong||5|C865T,C8782T,C13694T,C18060T,T28144C
EPI_ISL_413855|2020-03-09|2020-02-07|China|Guangdong||5|C865T,C8782T,C13694T,C18060T,T28144C
Even though two of the additional mutations are rare at GISAID, both of them them are found in Csabai's Antarctic samples, which is one reason why I believe the SARS2 reads in the Antarctic samples come from early COVID patients in China. There may have been early secret sequencing projects in China, because Eddie Holmes said that he heard that the plan of the Chinese authorities was to not announce the identity of the virus until the lunar new year, which fell on January 25th in 2020, and he said that Yongzhen Zhang actually got in major trouble for publishing the genome of Wuhan-Hu-1 before then: "I heard was they wanted to have - it's maybe a rumor - but I heard they wanted to have the whole thing kind of tied up by Lunar New Year, and to have one big announcement saying 'here's the virus, we've solved the problem, here it all is', you know, bow tied, post package posted - that's kind of what I heard they wanted. And we kind of like, you know, we scuppered their their plans in doing that, and like I say there has been a lot of fallout because of it. [...] Zhang was not the first person to sequence the virus, okay. I don't know about the people that have done that as well - whole set of groups were - but so, Zhengli Shi had sequenced it - actually probably before Sanger sequenced it." (https://www.youtube.com/watch?v=5u94foNmpKE&t=26m8s)
noted and understood since lineage B = wet market. I talked about the infamous "glove" in post #2
https://jimhaslam.substack.com/p/2-why-did-the-batman-fly-into-wuhan
so Jesse Bloom basically claims WA1 is the best known "progenitor" of SARS2 in that paper?
So I just had a chance to listen to your podcast on Straight Talk. Well done.
I am trying to come across to your way of thinking in that Baric was a good guy and this was all an accident.
We agree on the Made in USA and released in Wuhan, but what stops me is that Ralph accidentally sent out a bat vaccine virus to WIV designed to immunize bats, presumably after running it past Linfa in Singapore, and not knowing his brilliantly engineered virus does not infect the target bats so is useless as a Vaccine, but it is superbly adopted to humans and is very transmissible (a perfect human vaccine), yet this is only found out by a lab accident in Wuhan.
Also, you certainly are correct that this was not much of a weapon in a militarized sense (designed to kill/incapacitate), but have you considered how perfect it was for Bioterrorism ?
Ralph-2006
“If notoriety, fear and directing foreign government policies are principle objectives, then the release and subsequent discovery of a synthetically derived virus bioweapon garner tremendous media coverage, inspire fear and terrorize human populations and direct severe pressure on government officials to respond in predicted ways.”
https://www.jcvi.org/sites/default/files/assets/projects/synthetic-genomics-options-for-governance/Baric-Synthetic-Viral-Genomics.pdf
You are about where I was early last year, I can't understand how Baric is talking to the press in 2020-21 and carefree about his obvious creation (BsaXI, UGGUCGC, ENaC, etc). But I take their <2020 interviews as gospel and Baric was on record that my hACE2 mice are safe. They don't sneeze, don't transmit, and "the process of adapting these viruses to mice actually makes the germs less able to infect human cells." He's adamant in this interview he doesn't do transmission studies, and I've never found one, it's all infection studies.
https://www.npr.org/sections/health-shots/2014/11/07/361219361/how-a-tilt-toward-safety-stopped-a-scientists-virus-research
And then in 2022, the 'virus' spilled into deer and I quickly became suspicious of RML taking Baric's creation and turning it into a contagious bat vaccine. They also have deer mice, mink, EFB bats, and Syrian hamsters, the only 5 transmission models for a Wuhan wet market strain (WA1) that I've found. Let me know if you find others?
And we may disagree but SARS2 doesn't infect lab mice, but it does transmit in Munster's hamsters, which aren't found in WIV
https://x.com/jhas5/status/1729711704857088107?s=20
And Munster used Syrian hamsters in DARPA Preempt
https://x.com/jhas5/status/1736525922797248597?s=20
I've reread that creepy 2006 "dual use" Baric paper, and now interpret: I, Ralph Baric can create any genome on the planet, used for any purpose, but I will use it for 'benevolent' purposes like animal vaccines.
Baric's only done 1 interview since Defuse leaked, and it was basically to throw Munster under the bus for his "edgy" transmission work. Munster and Linfa and Dani were close bat colleagues (I don't think Baric had ever held a live bat).
https://time.com/6290193/covid-lab-leak-ralph-baric/
Still, was it possible for Ralph to
Engineer Sars-Cov-2 and not know he created the Munster Virus he was trying to create a Vaccine for, before sending it to Shi Zheng Li , knowing she did most of her work in a BSL-2
Any hypothesis as to how that happened is welcome
Baric in Feb 2020 ‘forecasting’ an animal reservoir (like NA wt deer, deer mice, mink) that US has but China doesn’t
https://x.com/jhas5/status/1495254438264684544?s=20