matters arising regarding your nature paper
12 messages over 10 days, 2021-11-19 – 2021-11-29.
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Dear Zhengli, I hope you're well. I'm afraid we've been contacted by a scientist who has submitted a Matters Arising to the journal, regarding your 2020 Nature paper. I've attached the MA here. One of the points raised is something we already discussed, which is why there is a difference in sequence identity between SARS-CoV and RaTG13 and SARS-CoV and the virus labelled Ra4991-Yunnan in the thesis which appeared online. You already responded to a journalist's query about this, and told us that the difference was due to different bioinformatics approaches. The other concerns seem to be points that have not been raised with us before. The author notes that the original Nature paper did not contain any information about how the RaTG13 genome was assembled and has some concerns regarding the timeline of the sequencing and assembly as well as missing methods (e.g. primer sequences). The addendum touched on the timing of the sequencing, but not the methods, and the author has some concerns regarding the timeline and asks for further details to clarify how the full RaTG13 sequence was obtained. Would you please be able to send us a response to these new concerns so that we can discuss how to proceed? If you could return a response within one week that would be greatly appreciated. With best wishes, Clare Clare Thomas Senior Editor Nature
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Dear Zhengli, I hope you're well. I'm afraid we've been contacted by a scientist who has submitted a Matters Arising to the journal, regarding your 2020 Nature paper. I've attached the MA here. One of the points raised is something we already discussed, which is why there is a difference in sequence identity between SARS-CoV and RaTG13 and SARS-CoV and the virus labelled Ra4991-Yunnan in the thesis which appeared online. You already responded to a journalist's query about this, and told us that the difference was due to different bioinformatics approaches. The other concerns seem to be points that have not been raised with us before. The author notes that the original Nature paper did not contain any information about how the RaTG13 genome was assembled and has some concerns regarding the timeline of the sequencing and assembly as well as missing methods (e.g. primer sequences). The addendum touched on the timing of the sequencing, but not the methods, and the author has some concerns regarding the timeline and asks for further details to clarify how the full RaTG13 sequence was obtained. Would you please be able to send us a response to these new concerns so that we can discuss how to proceed? If you could return a response within one week that would be greatly appreciated. With best wishes, Clare Clare Thomas Senior Editor Nature
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[External - Use Caution] Dear Clare, I'm sorry that you continue to recieve such emails. It's a pity that there are someone who is contining to doute and scruetine our work. This person has beeninterrupting me and my colleagues and want to find evidence to show that the SARS-CoV-2 is a lab leak. I don't think I should answer his unreasonable questions and crazy ideas. But for your refrence, I would like to send you more details although I think they are not whinth the duty of you and neither the scope of my publication in your journal. Best regards, Zhengli, Bown. iov.cn
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Dear Clare, I'm sorry that you continue to recieve such emails. It's a pity that there are someone who is contining to doute and scruetine our work. This person has been interrupting me and my colleagues and want to find evidence to show that the SARS-CoV-2 is a lab leak. I don't think I should answer his unreasonable questions and crazy ideas. But for your refrence, I would like to send you more details although I think they are not whinth the duty of you and neither the scope of my publication in your journal. Best regards, Zhengli, Bown iov.cn
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[External - Use Caution] Dear Clare, I'm sorry that you continue to recieve such emails. It's a pity that there are someone who is contining to doute and scruetine our work. This person has beeninterrupting me and my colleagues and want to find evidence to show that the SARS-CoV-2 is a lab leak. I don't think I should answer his unreasonable questions and crazy ideas. But for your refrence, I would like to send you more details although I think they are not whinth the duty of you and neither the scope of my publication in your journal. Best regards, Zhengli, Bown. iov.cn
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Dear Clare, I'm sorry that you continue to recieve such emails. It's a pity that there are someone who is contining to doute and scruetine our work. This person has been interrupting me and my colleagues and want to find evidence to show that the SARS-CoV-2 is a lab leak. I don't think I should answer his unreasonable questions and crazy ideas. But for your refrence, I would like to send you more details although I think they are not whinth the duty of you and neither the scope of my publication in your journal. Best regards, Zhengli, Bown iov.cn
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Dear Zhengli, Thanks again for providing very helpful responses to the Matters Arising. We do have an obligation to look into any comments about papers that we publish, particularly if they relate to concerns about insufficient methodological detail etc. I just wanted to ask you about a two more things, about the sample source, for the sake of completeness. The Matters Arising author points to a preprint that claims the raw data contain lower levels of bacterial reads than would be expected from a fecal swab. I cannot see from the methods anywhere that the nature of the sample was described. Was it a fecal swab? If so, is there an explanation for the low bacterial reads, if indeed that claim is true? And along the same lines, what was the sample used for the sequencing of the 5'end done in September 2020? Thanks in advance for clarifying these details, which do seem pertinent to the methods described in our paper and therefore we do have to ask. Once again I'm very sorry for having to trouble you on so many occasions with these queries. With best wishes, Clare
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Dear Zhengli, Thanks again for providing very helpful responses to the Matters Arising. We do have an obligation to look into any comments about papers that we publish, particularly if they relate to concerns about insufficient methodological detail etc. I just wanted to ask you about a two more things, about the sample source, for the sake of completeness. The Matters Arising author points to a preprint that claims the raw data contain lower levels of bacterial reads than would be expected from a fecal swab. I cannot see from the methods anywhere that the nature of the sample was described. Was it a fecal swab? If so, is there an explanation for the low bacterial reads, if indeed that claim is true? And along the same lines, what was the sample used for the sequencing of the 5'end done in September 2020? Thanks in advance for clarifying these details, which do seem pertinent to the methods described in our paper and therefore we do have to ask. Once again I'm very sorry for having to trouble you on so many occasions with these queries. With best wishes, Clare
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[External - Use Caution] Dear Clare, Please see our answers as follows: The reasons for the low bacterial reads in the raw sequencing data of RaTG13 could be: 1) The sample is anal swab, not a fecal pellet. 2) We used the High Pure Viral RNA Kit for the RNA extraction. 3) The sequencing depth was not high. For the 5'race done in September 2020, we used the viral RNA previously extracted from that anal swab sample. Best regards, Zhengli, Bown. iov.cn From: Clare Thomas Date; 2021-11-24 19:51 To: wh.iov.cn Subject: RE: Matters Arising regarding your Nature paper Dear Zhengli, Thanks again for providing very helpful responses to the Matters Arising. We do have an obligation to look into any comments about papers that we publish, particularly if they relate to concerns about insufficient methodological detail etc. I just wanted to ask you about a two more things, about the sample source, for the sake of completeness. The Matters Arising author points to a preprint that claims the raw data contain lower levels of bacterial reads than would be expected from a fecal swab. I cannot see from the methods anywhere that the nature of the sample was described. Was it a fecal swab? If so, is there an explanation for the low bacterial reads, if indeed that claim is true? And along the same lines, what was the sample used for the sequencing of the 5'end done in September 2020? Thanks in advance for clarifying these details, which do seem pertinent to the methods described in our paper and therefore we do have to ask. Once again I'm very sorry for having to trouble you on so many occasions with these queries. With best wishes, Clare
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[External - Use Caution] Dear Clare, Please see our answers as follows: The reasons for the low bacterial reads in the raw sequencing data of RaTG13 could be: 1) The sample is anal swab, not a fecal pellet. 2) We used the High Pure Viral RNA Kit for the RNA extraction. 3) The sequencing depth was not high. For the 5'race done in September 2020, we used the viral RNA previously extracted from that anal swab sample. Best regards, Zhengli, Bown. iov.cn From: Clare Thomas Date; 2021-11-24 19:51 To: wh.iov.cn Subject: RE: Matters Arising regarding your Nature paper Dear Zhengli, Thanks again for providing very helpful responses to the Matters Arising. We do have an obligation to look into any comments about papers that we publish, particularly if they relate to concerns about insufficient methodological detail etc. I just wanted to ask you about a two more things, about the sample source, for the sake of completeness. The Matters Arising author points to a preprint that claims the raw data contain lower levels of bacterial reads than would be expected from a fecal swab. I cannot see from the methods anywhere that the nature of the sample was described. Was it a fecal swab? If so, is there an explanation for the low bacterial reads, if indeed that claim is true? And along the same lines, what was the sample used for the sequencing of the 5'end done in September 2020? Thanks in advance for clarifying these details, which do seem pertinent to the methods described in our paper and therefore we do have to ask. Once again I'm very sorry for having to trouble you on so many occasions with these queries. With best wishes, Clare
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Dear Zhengli, Thank you very much. All the best, Clare
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Dear Zhengli, Thank you very much. All the best, Clare