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Additionally, I thought to look at the distribution of amino acid changes across genes in the virus genome. In this case, we see highly similar distributions between the nCoV lineage and its closest bat virus relative. 8/9pic.twitter.com/oLyZPHSNgy
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And in fact we see that the RaTG13 lineage has 79 amino acid changes and 563 nucleotide changes for a ratio of 14.2%. Thus we see that the outbreak virus has a similar distribution of nucleotide vs amino acid changes as its closest bat virus relative. 7/9pic.twitter.com/Uw2Evu9qTo
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The nCoV lineage is shown as a dashed line under the "nCoV" label (lower right). The RaTG13 lineage is shown as a dashed line above the "RaTG13" label (also lower right). 3/9pic.twitter.com/SGYigEXAFy
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Small envelope is 100% conserved out to ZC45 and ZXCC21 and 94% conserved all the way out to SARS. This completely looks like natural evolution.pic.twitter.com/IcsJdwLgCz
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I used the sequence provided (1378 bases beginning with "ctcag") to align with full genomes for nCoV outbreak, SARS-like bat viruses and SARS. You must have made an alignment error as this "insert" does not exist. The segment aligns nicely with existing diversity. 1/2pic.twitter.com/bGIEGpWd0e
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"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. 8/9pic.twitter.com/w7K9Ca8xHQ
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"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. 7/9pic.twitter.com/3bW16ZG2UC
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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. 6/9pic.twitter.com/jUkVSY9nD3
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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. 5/9pic.twitter.com/ziizAGv7d5
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#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. 3/9pic.twitter.com/YjeZPoRuug
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Combined modeling of Wuhan
#nCoV2019 incidence with travel cases by@AdamJKucharski et al. A couple things I particularly like here: 1. Data that the model is being fit to is clearly shown 2. R0 and mobility are not treated as constants https://cmmid.github.io/ncov/wuhan_early_dynamics …pic.twitter.com/qbIH6KIV7T
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This alignment shows SARS at top, related SARS-like viruses from bats in the middle and nCoV at the bottom. Note the repeated gain and loss of RNA during natural evolution. 2/2pic.twitter.com/ghqWqGyt5k
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I've written a blog post on
#nCoV2019 genomic epidemiology and the global scientific response to the outbreak: https://bedford.io/blog/genomic-epi-for-ncov-response/ …pic.twitter.com/N2yuhx1jWV
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These short inserts do indeed exist in
#nCoV2019 relative to its closest sequenced relative (BetaCoV/bat/Yunnan/RaTG13/2013, seen here https://nextstrain.org/groups/blab/sars-like-cov …). However, a simple BLAST of such short sequences shows match to a huge variety of organisms. No reason to conclude HIV. https://twitter.com/biorxivpreprint/status/1223245639296978951 …pic.twitter.com/mUfxwB6GsP
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With increasing numbers of transmission steps we get the following distribution of the number of mutations: 5/9pic.twitter.com/dL0cN7SQnH
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First, I use the epidemiological parameters from this NEJM paper https://twitter.com/trvrb/status/1222685857372459008 … to sketch out two infections that are directly connected, finding an expectation of 9 days of viral replication from sample from index infection to sample from secondary infection: 2/9pic.twitter.com/8BbDs2s4e0
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Improved with better y axis labeling to make this more clear:pic.twitter.com/bbH5oRGUT3
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Just updated from Jan 30. We still see an exponential increase in international travel cases of confirmed
#nCoV2019. This may stop being a direct proxy for cases within China as air travel slows. Will need to adjust for airplane seats denominator. https://twitter.com/trvrb/status/1222046080608555008 …pic.twitter.com/KD5dMZzPGJ
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We had previously hypothesized that US
#nCoV2019 cases in IL, WA, AZ and CA with mutations at sites 8782 and 28144 represented direct exports of a variant circulating in Wuhan. The new sample Wuhan/WH04/2020 supports this as a parsimonious explanation. https://twitter.com/trvrb/status/1221218730383798272 …pic.twitter.com/HH0dTkDDgC
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Some very interesting
#nCoV2019 contact tracing from the first 425 patients: https://www.nejm.org/doi/full/10.1056/NEJMoa2001316 …, . Brief observations: * No reported exposure to market or person with ARI in 70% of Jan cases * ~5.2 day incubation period * ~7.5 day serial interval * R0 of ~2.2pic.twitter.com/9Fj2iE7ulX
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