Reading Room Production — page 303

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: Bown 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