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Dear Zhengli, I hope you're well. We have been contacted by someone who claims that a thesis from the Wuhan Institute of Virology contains information that seemingly questions the relationship of RaTG13 to the sample originally named 4991. You can see the correspondence that we've received below. We have not clicked on these links, so have not looked at the thesis itself, but would you please be able to provide some clarification about these claims? I believe the concern is that if Ra4991 and RaTG13 are the same virus, as claimed in the addendum, then their identity to SARS-CoV should be the same and the table pasted below indicates that they differ to some extent in the spike gene. Thanks in advance and best wishes, Clare Clare Thomas Senior Editor Nature A Dissertation submitted to The University of Chinese Academy of Sciences in 2019 by Yu Ping at the Wuhan institute of Virology has recently surfaced online. Original: https://drive.google.com/drive/folders/1cJBYAkjkZX9KbNfHCaeaaMhNDoffielg English translation: https://docs.google.com/document/d/15U2uE7Eru0QxRbf8QVRPRMpssCoYhGvT/edit The document has been uploaded by an anonymous user on Twitter, and contains potentially new information the RATG13 virus sequence and its relationship to bat sample 4991. The RATG13 sequence was first mentioned in the article 'A pneumonia outbreak associated with a new coronavirus of probable bat origin» published by Nature. In the addendum to this article, that was published November last year, the authors clarify that RATG13 sequence is the full virus sequence collected from bat sample 4991. However, the newly uncovered thesis by Ping, raises new questions on the raw data in regards to the RATG13 sequence and its relationship to the 4991 sample. In the thesis the full sequence of bat sample 4991 is shown to be 75,4% identical in the spike gene compared to SARs-CoV Tor2. Table 3.2 Comparison of ORF amino acid identities between bat SARSr-CoVs and human SARS-CoV Tor?. CoV ORFla S ORF3' E M ORF6 ORF7 ORF8 N LYRal1/Yunnan 95.8 90.8 97.7 WIV16/Yunnan 98.0 %.8 97.0 100.0 98.1 95.0 16.1 99.5 WIV1/Yunnan 97.9 92.1 96.7 100.0 98.1 93.6 99.7 Rs4084/Y unnan 97.9 97.0 85.9 99.5 Anlong-103/Guizhou 98.1 89.7 100.0 95.0 98.3 Rp3/Guangxi 96.5 $83.5 97.8 HKU3-7/Guangdong 94.0 82.8 98.1 HKU3-I/Hong Kong 94.1 719° «81.7 100.0 14.7 Rfl/Hubei 94.0 16.6 86.1 96.0 97.7 91.8 23.9 95.4 Jiyuan-84/Henan 94.0 76.8 96.0 97.7 92.0 94.2 25.3 96.2 Rp/Shaanxi 95.4 799.0 82.4 97.3 92.0 97.8 HeB2013/Hebei 94.1 87.2 96.0 97.7 25.3 96.2 JL2012/Jilin 93.2 86.1 97.3 97.2 NA 95.7 Ra4991_ Yunnan 80.0
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Dear Zhengli, I hope you're well. We have been contacted by someone who claims that a thesis from the Wuhan Institute of Virology contains information that seemingly questions the relationship of RaTG13 to the sample originally named 4991. You can see the correspondence that we've received below. We have not clicked on these links, so have not looked at the thesis itself, but would you please be able to provide some clarification about these claims? I believe the concern is that if Ra4991 and RaTG13 are the same virus, as claimed in the addendum, then their identity to SARS-CoV should be the same and the table pasted below indicates that they differ to some extent in the spike gene. Thanks in advance and best wishes, Clare Clare Thomas Senior Editor Nature A Dissertation submitted to The University of Chinese Academy of Sciences in 2019 by Yu Ping at the Wuhan institute of Virology has recently surfaced online. Original: https://drive.google.com/drive/folders/1cJBY AkjkZX9KbNfHCaeaaMhNDefflelg English translation: https://docs.google.com/document/d/15U2uE7Erm0QxRbf8Q VRPRMpssCoYhGvT/edit The document has been uploaded by an anonymous user on Twitter, and contains potentially new information the RATG13 virus sequence and its relationship to bat sample 4991. The RATG13 sequence was first mentioned in the article "A pneumonia outbreak associated with a new coronavirus of probable bat origin» published by Nature. In the addendum to this article, that was published November last year, the authors clarify that RATG13 sequence is the full virus sequence collected from bat sample 4991. However, the newly uncovered thesis by Ping, raises new questions on the raw data in regards to the RATG13 sequence and its relationship to the 4991 sample. In the thesis the full sequence of bat sample 4991 is shown to be 75,4% identical in the spike gene compared to SARs-CoV Tor2. Table 3.2 Comparison of ORF amino acid identities between bat SARSr-CoVs and human SARS-CoV Tor2. CoV ORFla S ORF3' E M ORF6 ORF7 ORF8 WN LYRal 1/Yunnan 95.8 90.8 97.7 97.8 WIV16/Yunnan 98.0 %.8 97.0 100.0 98.1 95.0 16.1 99.5 WIV1/Yunnan 97.9 92.1 96.7 100.0 98.1 93.6 99.7 Rs4084/Y unnan 97.9 97.0 95.9 85.9 99.5 Anlong-103/Guizhou 98.1 89.7 100.0 95.0 31.8 98.3 Rp3/Guangxi 96.5 83.5 97.8 HKU3-7/Guangdong 94.0 82.8 98.1 HKU3-I/Hong Kong 94.1 81.7 100.0 14.7 96.4 Rfl/Hubei 94.0 16.6 86.1 96.0 97.7 93.6 91.8 23.9 95.4 Jiyuan-84/Henan 94.0 76.8 86.8 96.0 97.7 92.0 25.3 96.2 Rp/Shaanxi 95.4 799.0 82.4 97.3 92.0 97.8 HeB2013/Hebei 94.1 87.2 96.0 97.7 93.6 25.3 96,2 JL2012/Jilin 93.2 86.1 97.2 90.1 NA 95.7
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Dear Zhengli, I wonder whether you have had a chance to consider my email below? I am sorry to bug you about it, but we do have an obligation to look into any queries that we receive about any Nature paper that we publish. I can imagine that you must be quite frustrated with these sorts of queries, but if there is an explanation for the apparent discrepancy highlighted to us then it would be great if you could please let us know. Many thanks in advance and all the best, Clare
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Dear Zhengli, I wonder whether you have had a chance to consider my email below? I am sorry to bug you about it, but we do have an obligation to look into any queries that we receive about any Nature paper that we publish. I can imagine that you must be quite frustrated with these sorts of queries, but if there is an explanation for the apparent discrepancy highlighted to us then it would be great if you could please let us know. Many thanks in advance and all the best, Clare
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2021-06-29 00:13
unattributed
Dear Clare, Thank you for your information. I'm fine with the passing to the journalist on the information I told you. Best regards, Zhengli, nooo JAAD E--- AEA: "Clare Thomas" im puecom> BIKA [A] :202 1-06-29 04:39:21 ital wh.iov.cn" a iov.cn> S RE: RE: A question about the addendum to your Nature paper Dear Zhengli, Thanks again for replying to my question about the discrepancy highlighted to us. We've received some queries about it from journalists. Conversations between editors and authors are confidential but I wanted to ask you if you would have any objection to our passing on the information that you have told us? Would you be willing for us to tell the journalists that you have told us that the bioinformatics approaches used to analyse the genome sequences in the Nature paper and the thesis were different? We are considering how to respond and wonder whether this might help dampen the speculation. Please could you let me know? All the best, Clare
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Dear Clare, Thank you for your information. I'm fine with the passing to the journalist on the information I told you. Best regards, Zhengli, nooo JAAD E--- AEA: "Clare Thomas" im puecom> BIKA [A] :202 1-06-29 04:39:21 ital wh.iov.cn" a iov.cn> S RE: RE: A question about the addendum to your Nature paper Dear Zhengli, Thanks again for replying to my question about the discrepancy highlighted to us. We've received some queries about it from journalists. Conversations between editors and authors are confidential but I wanted to ask you if you would have any objection to our passing on the information that you have told us? Would you be willing for us to tell the journalists that you have told us that the bioinformatics approaches used to analyse the genome sequences in the Nature paper and the thesis were different? We are considering how to respond and wonder whether this might help dampen the speculation. Please could you let me know? All the best, Clare
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Dear Zhengli, I wonder whether you have had a chance to consider my email below? I am sorry to bug you about it, but we do have an obligation to look into any queries that we receive about any Nature paper that we publish. I can imagine that you must be quite frustrated with these sorts of queries, but if there is an explanation for the apparent discrepancy highlighted to us then it would be great if you could please let us know. Many thanks in advance and all the best, Clare
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Dear Zhengli, I wonder whether you have had a chance to consider my email below? I am sorry to bug you about it, but we do have an obligation to look into any queries that we receive about any Nature paper that we publish. I can imagine that you must be quite frustrated with these sorts of queries, but if there is an explanation for the apparent discrepancy highlighted to us then it would be great if you could please let us know. Many thanks in advance and all the best, Clare