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Trevor Bedford
+ Your AuthorsArchive @trvrb Scientist @fredhutch, studying viruses, evolution and immunity. Collection of #COVID19 threads here: Feb. 01, 2020 1 min read

Based on the content of my mentions, I feel like I need to further debunk crazy #nCoV2019 / HIV conspiracy preprint. This is a thread doing so. 1/9

This paper proposes that there are 4 short "insertions" in the spike protein in #nCoV2019 copied from HIV. Yesterday, I showed that the proposed inserts are tiny strings that randomly match a whole bunch of things. 2/9

#nCoV2019 is a member of the SARS-like virus family. These circulate naturally in bats and undergo all sorts of evolution during this natural circulation. Two of these viruses (SARS in 2002-03 and nCoV in 2019-20) have spilled over into the human population causing outbreaks. 3/9

Here, I include additional SARS-like viruses in an alignment of spike protein to show that these "inserts" are nothing of the sort proposed by the paper and instead arose naturally in the ancestral bat virus 4/9

Looking at each "insert" in turn. We see that "insert 1" (GTNGTKR) is present in the closely related virus bat/Yunnan/RaTG13/2013. It is impossible that this sequence was "inserted" into the #nCoV2019 genome. 5/9

We see that "insert 2" (YYHKNNKS) doesn't appear to be an insertion at all, but an alignment artifact of the authors. Also, it is present in the closest bat virus RaTG13 with related sequences in closely related viruses. No way this is an insertion into #nCoV2019. 6/9

"Insert 3" (GDSSSG) also appears to be a possible alignment artifact, though this is equivocal. However, this "insert" is most definitely in RaTG13. There was no insertion of RNA into the #nCoV2019 spike protein. 7/9

"Insert 4" (QTNSPRRA) shares GTNS with the bat virus RaTG13, while PRRA represents unique material in #nCoV2019. This is a tiny tiny sequence and in no way suggests engineering. This sorts of small indels occur all the time in natural evolution of SARS-like coronaviruses. 8/9

Again, there is absolutely no evidence for either (1) sequence insertions or (2) their relationship to HIV. If you'd like to look at the alignment yourself, I've posted it here:  9/9

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