--- type: Conversation title: matters arising regarding your nature paper description: "email conversation, 12 messages, 2021-11-19." tags: - conversation - email medium: email message_count: 12 started_at: "2021-11-19T02:09:00" ended_at: "2021-11-29T09:37:00" duration_seconds: 890880 sources: - { id: reading_room, resource: /sources/reading-room.md, title: Reading Room Production, author: "process:senate-hsgac-release" } generated: { by: randpaul-corpus-pipeline/1.0, at: "2026-08-01T12:42:27Z" } status: stable --- A email conversation of 12 messages spanning 247h 28m. # Metadata - **Started:** 2021-11-19T02:09:00 - **Ended:** 2021-11-29T09:37:00 - **Duration:** 247h 28m - **Participants:** 9 - **Source:** [reading_room](/sources/reading-room.md) - **Pages:** 79-314 # Participants * [Clare Thomas](/people/clare-thomas.md) # Transcript **[2021-11-19T02:09:00] Clare Thomas:** 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… **[2021-11-19T02:09:00] Clare Thomas:** 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… **[2021-11-24T09:10:00] unknown:** [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 **[2021-11-24T09:10:00] unknown:** 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 **[2021-11-24T09:10:00] unknown:** [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 **[2021-11-24T09:10:00] unknown:** 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 **[2021-11-24T19:51:00] Clare Thomas:** 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… **[2021-11-24T19:51:00] Clare Thomas:** 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… **[2021-11-29T09:07:00] unknown:** [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… **[2021-11-29T09:07:00] unknown:** [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… **[2021-11-29T09:37:00] Clare Thomas:** Dear Zhengli, Thank you very much. All the best, Clare **[2021-11-29T09:37:00] Clare Thomas:** Dear Zhengli, Thank you very much. All the best, Clare