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NSR - On the origin and continuing evolution of SARS-CoV-2 

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  • NSR - On the origin and continuing evolution of SARS-CoV-2 

    h/t Shiloh


    On the origin and continuing evolution of SARS-CoV-2

    Xiaolu Tang, Changcheng Wu, Xiang Li, Yuhe Song, Xinmin Yao, Xinkai Wu, Yuange Duan, Hong Zhang, Yirong Wang, Zhaohui Qian ... Show more
    Author Notes
    National Science Review, nwaa036, https://doi.org/10.1093/nsr/nwaa036
    Published:

    03 March 2020


    ABSTRACT


    The SARS-CoV-2 epidemic started in late December 2019 in Wuhan, China, and has since impacted a large portion of China and raised major global concern. Herein, we investigated the extent of molecular divergence between SARS-CoV-2 and other related coronaviruses. Although we found only 4% variability in genomic nucleotides between SARS-CoV-2 and a bat SARS-related coronavirus (SARSr-CoV; RaTG13), the difference at neutral sites was 17%, suggesting the divergence between the two viruses is much larger than previously estimated. Our results suggest that the development of new variations in functional sites in the receptor-binding domain (RBD) of the spike seen in SARS-CoV-2 and viruses from pangolin SARSr-CoVs are likely caused by mutations and natural selection besides recombination.

    Population genetic analyses of 103 SARS-CoV-2 genomes indicated that these viruses evolved into two major types (designated L and S), that are well defined by two different SNPs that show nearly complete linkage across the viral strains sequenced to date. Although the L type (∼70%) is more prevalent than the S type (∼30%), the S type was found to be the ancestral version.

    Whereas the L type was more prevalent in the early stages of the outbreak in Wuhan, the frequency of the L type decreased after early January 2020. Human intervention may have placed more severe selective pressure on the L type, which might be more aggressive and spread more quickly.

    On the other hand, the S type, which is evolutionarily older and less aggressive, might have increased in relative frequency due to relatively weaker selective pressure.

    These findings strongly support an urgent need for further immediate, comprehensive studies that combine genomic data, epidemiological data, and chart records of the clinical symptoms of patients with coronavirus disease 2019 (COVID-19).

    https://academic.oup.com/nsr/advance...searchresult=1

  • #2
    Response to “On the origin and continuing evolution of SARS-CoV-2”

    Oscar A. MacLean*, Richard Orton, Joshua B. Singer, David L. Robertson.
    MRC-University of Glasgow Centre for Virus Research (CVR).

    Summary
    Given these flaws, we believe that Tang et al. should retract their paper, as the claims made in it are clearly unfounded and risk spreading dangerous misinformation at a crucial time in the outbreak.
    http://virological.org/t/response-to...sars-cov-2/418

    Comment


    • #3
      I have been keeping eye on the new sequences and mutation and ignored this paper as I do not believe it is possible to make the calculation. The reason for this is where and when the two strains emerged and spread. The first graphic show the cases over time with ORF8 L84S divided by colour. The second shows where they came from with the time scale showing when. Click image for larger version

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      Click image for larger version

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      Comment


      • #4
        Fascinating. Thank you all for providing a critique of that paper. So, do you think the serine/leucine divergence is significant after all?

        Comment

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