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Trevor Bedford
@
trvrb
Seattle, WA
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Scientist @fredhutch, studying viruses, evolution and immunity.
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2.021
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Pratim
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8.984
Osobe koje vas prate
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Trevor Bedford
@trvrb
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8 h |
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All cases descend from a single virus that existed sometime in Nov or Dec 2019. There have been a few small mutations since then.
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Trevor Bedford
@trvrb
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10 h |
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Cool. Thanks for pointing this out. I hadn’t seen this for SARS. Would you mind sharing the reference?
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| Trevor Bedford proslijedio/la je tweet | ||
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Nextstrain
@nextstrain
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20 h |
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Thanks to open data sharing by @KoreaCDC, we've updated nextstrain.org/ncov with #nCoV2019 genome from Korea sampled on Jan 25. It is part of an emerging genetic cluster that contains viruses from Wuhan, Guangdong, England, the US, but has two additional nucleotide changes. pic.twitter.com/PPmcOfSjLl
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Trevor Bedford
@trvrb
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3. velj |
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Ah! My mistake. Yes, fantastic work by NCID.
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Trevor Bedford
@trvrb
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3. velj |
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Nice work Monica and team!
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Trevor Bedford
@trvrb
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3. velj |
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Nice work with this Marcus!
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| Trevor Bedford proslijedio/la je tweet | ||
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Nextstrain
@nextstrain
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3. velj |
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Thanks to rapid data sharing by @PHE_uk, nextstrain.org/ncov has been updated with two #nCoV2019 genomes from England. These appear to be a transmission cluster with just one mutation difference between them. 1/2 pic.twitter.com/kpGodxQqPg
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| Trevor Bedford proslijedio/la je tweet | ||
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Nextstrain
@nextstrain
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3. velj |
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Thanks to open data sharing by Singapore's National Centre for Infectious Diseases, we've updated nextstrain.org/ncov with #nCoV2019 genome sampled from Singapore on Jan 24. It has one unique nucleotide mutation at site 25060 and is consistent with direct export from Wuhan. pic.twitter.com/ytnd27pjer
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Trevor Bedford
@trvrb
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3. velj |
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Not a concern, just an observation. #nCoV2019 is still for people with genuine interest as opposed to the memes, etc… in #coronavirus. But people with genuine interest have expanded from initially being mainly scientists to a broader cohort.
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Trevor Bedford
@trvrb
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3. velj |
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I’m glad #nCoV2019 exists as a separate hashtag, but things have seemed to have flipped from mostly scientists talking to each other to scientists doing public outreach.
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Trevor Bedford
@trvrb
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3. velj |
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Yes. I tried my best to reproduce this gap. It appears to be a simple alignment error. The “insert” provided nicely aligns with existing SARS-like diversity. It is not real.
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Trevor Bedford
@trvrb
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3. velj |
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It’s a good question. The genetic data support both RaTG13 and nCoV spending equal amounts of time “in the wild”. This is because they each have ~550 nucleotide mutations from common ancestor. This doesn’t make freezer impossible, but there is no evidence for such.
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Trevor Bedford
@trvrb
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3. velj |
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My guess is that these were Sanger sequenced (like the one from Japan). This helpful for confirming identify (yes it is part of nCoV outbreak clade), but not very helpful for genomic epidemiology (need full genome to have enough temporal resolution due to rate of mutation).
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Trevor Bedford
@trvrb
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3. velj |
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There’s 18 vs 14 changes in spike. It’s conceivable that the additional 4 arose in response to pressure from intermediate host, but basically impossible to say at this point.
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Trevor Bedford
@trvrb
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3. velj |
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Correct. Observed mutations are consistent with natural evolution.
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Trevor Bedford
@trvrb
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3. velj |
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If you'd like to investigate yourself, you can either run the entire openly available bioinformatics pipeline here github.com/blab/sars-like… or just work from the resulting JSON file that contains all of these mutation calls here raw.githubusercontent.com/blab/sars-like…
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Trevor Bedford
@trvrb
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3. velj |
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Looking at mutation distributions, it appears that the genetic differences in #nCoV2019 are consistent with differences expected to arise during natural evolution, as I would expect engineering to have a distorted AA to nuc ratio and to focus on changing a subset of genes 9/9
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Trevor Bedford
@trvrb
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3. velj |
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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. 8/9 pic.twitter.com/oLyZPHSNgy
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Trevor Bedford
@trvrb
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3. velj |
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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. 7/9 pic.twitter.com/Uw2Evu9qTo
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Trevor Bedford
@trvrb
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3. velj |
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Evolutionary biologists commonly use the ratio of amino acid changes to nucleotide changes to look for natural selection (en.wikipedia.org/wiki/Ka/Ks_rat…). Observing 14% of changes as amino acid changes fits with common expectations for sequences evolving under purifying selection. 6/9
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