Trevor Bedford

@trvrb

Scientist , studying viruses, evolution and immunity.

Seattle, WA
Vrijeme pridruživanja: prosinac 2010.

Medijski sadržaj

  1. 3. velj

    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

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  2. 3. velj

    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

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  3. 3. velj

    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). 3/9

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  4. 2. velj
    Odgovor korisnicima i sljedećem broju korisnika:

    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.

  5. 2. velj
    Odgovor korisniku/ci

    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. 1/2

  6. 1. velj

    "Insert 4" (QTNSPRRA) shares GTNS with the bat virus RaTG13, while PRRA represents unique material in . 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

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  7. 1. velj

    "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 spike protein. 7/9

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  8. 1. velj

    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 . 6/9

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  9. 1. velj

    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 genome. 5/9

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  10. 1. velj

    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

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  11. 31. sij

    Combined modeling of Wuhan incidence with travel cases by 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

  12. 31. sij

    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. 2/2

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  13. 31. sij

    I've written a blog post on genomic epidemiology and the global scientific response to the outbreak:

  14. 31. sij

    These short inserts do indeed exist in relative to its closest sequenced relative (BetaCoV/bat/Yunnan/RaTG13/2013, seen here ). However, a simple BLAST of such short sequences shows match to a huge variety of organisms. No reason to conclude HIV.

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  15. 31. sij

    With increasing numbers of transmission steps we get the following distribution of the number of mutations: 5/9

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  16. 31. sij

    First, I use the epidemiological parameters from this NEJM paper 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: 2/9

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  17. 31. sij
    Odgovor korisnicima

    Improved with better y axis labeling to make this more clear:

  18. 30. sij

    Just updated from Jan 30. We still see an exponential increase in international travel cases of confirmed . This may stop being a direct proxy for cases within China as air travel slows. Will need to adjust for airplane seats denominator.

  19. 30. sij

    We had previously hypothesized that US 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.

  20. 30. sij

    Some very interesting contact tracing from the first 425 patients: , . 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 ~2.2

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