Reading Room Production — page 69

Thank you! Alice On Sun, Apr 5, 2020 at 5:01 PM Alice Latinne Bo ccohealthalliance.org> wrote: Hi Ben, 1) RaTG13 is not included in the Figure 3. The closest sequence is a sequence from GenBank (KP876546) and published in 2016 in a paper from your lab: Ge X-Y, Wang N, Zhang W, Hu B, Li B, Zhang Y-Z, Zhou J-H, Luo C-M, Yang X-L, Wu L-J, et al. (Ge2016 coauthors). 2016. Coexistence of multiple coronaviruses in several bat colonies in an abandoned mineshaft. Virologica Sinica 31:31-40. This sequence is 100% identical to RaTG13, is it the same sample? I'll delete the word "we" in the sentence. 2) I'll check and correct this as needed. Cheers, Alice On Sun, Apr 5, 2020 at 4:24 PM dhe own iov.cn> wrote: Hi Alice, Thanks for the supplementary material. Now I have two more concerns regarding the manuscript: 1) In lines 48-49 in the PDF, you mentioned that "this emerging human virus is closely related to SARS-CoV, and also appears to have originated in horseshoe bats -- with its full genome 96% similar to a virus we discovered in Rhinolophus affinis". Here this virus refers to RaTG13. Could you please delete the word "we" in this sentence? Otherwise, some readers may think that RaTG13 was detected in our joint study (e.x.PREDICT) and we shared the sequence with EHA earlier. This may be used by some conspiracy theorists to make rumors. Actually, the sequence of RaTG13 was not included in the dataset I provided to you. It was not deposited into Genbank until this January. So I think it was not included in your dataset, and you used this sequence during the revision phase after COVID-19 outbreak. Though not labeled clearly, RaTG13 is also shown in the phylogenetic tree in Figure 3 (the one most closely related to 2019-nCoV from Rhinolophus affinis in Yunnan). So could you please revise the figure legend of figure 3 AS: Maximum clade credibility tree including 201 RdRp sequences from theSarbecovirus lineage isolated in bats, including RaTG13_ (Genbank accession numbers: MN996532) and two sequences of 2019-nCoV isolated in humans (GenBank accession numbers:MN908947 and MN975262). This will mean that in your analysis you downloaded the sequence from public database, but it was not included in the original dataset of bat CoVs that I provided to you. 2) In lines 89-91 in the PDF. It says 'Our geographic datasets included 694 a-CoV sequences from six zoogeographic regions (22 provinces) and 519 BCoV sequences from five zoogeographic regions (21 provinces) . The dataset contains some sequences detected from bats in Laos. Are the lao bat CoV sequences also counted in the 694 and 519 sequences? They are not from any Chinese province. If so,the numbers here needs to be corrected. Besides, CAS now requires authors from CAS institutes to deposit coronavirus sequences not only in Genbank but also in the public database of China National Center for Bioinformation when we publish our researches. So I will submit the sequences which I submited to Genbank last year to the Chinese database next week. If you have any questions please let me know.