• Omicron genetics and early transmission

    From ScienceDaily@1:317/3 to All on Wed Jan 26 21:30:42 2022
    Omicron genetics and early transmission patterns are characterized in
    new study

    Date:
    January 26, 2022
    Source:
    Penn State
    Summary:
    The Omicron variant of SARS-CoV-2 diverged from previous SARS-CoV-
    2 variants as a result of adaptive evolution, in which beneficial
    mutations are passed on to future generations through natural
    selection, rather than through recombination between previous
    variants, according to researchers.



    FULL STORY ==========================================================================
    The Omicron variant of SARS-CoV-2 diverged from previous SARS-CoV-2
    variants as a result of adaptive evolution, in which beneficial mutations
    are passed on to future generations through natural selection, rather
    than through recombination between previous variants, according to a
    large international team of researchers. The study, which published
    recently in Nature, is the first to describe the genomic profile of
    Omicron and explore the origins of the variant.


    ==========================================================================
    "We have seen SARS-CoV-2 generate three major variants -- Alpha, Delta
    and Omicron -- in about 16 months, which is very surprising because
    other viruses do not make such repeated big evolutionary leaps," said
    Maciej Boni, associate professor of biology, Penn State, who led the recombination analysis for this global collaboration. "The latest variant
    -- Omicron -- is extraordinary because of the even bigger jump it made
    in the evolution of its spike protein." Boni noted that compared to
    previous variants, Omicron's spike protein has more than 30 mutations,
    many of which are known to influence host antibody neutralization.

    "Given that Omicron made such a big leap forward evolutionarily speaking,
    we wanted to investigate why and how this may have happened," he said.

    To do that, the team -- which was led by the Centre for Epidemic Response
    and Innovation in South Africa -- analyzed all 686 Omicron sequences
    that were available by Dec. 7, 2021. They found that Omicron falls within
    the B.1.1 lineage, which also includes the Alpha variant. Interestingly,
    the team found that Omicron is genetically distinct from Alpha, as well
    as any other known variants of interest.

    "What this means is that although Omicron belongs to the same lineage
    as the Alpha variant, it has changed to such a great extent that it is
    largely unrecognizable as a cousin or nephew of the Alpha variant," said
    Boni. "When the Omicron genome was first sequenced, it became clear that
    this virus had the potential to be phenotypically very different from
    previous SARS-CoV-2 variants that we were familiar with." To determine
    when the Omicron variant first emerged, the team used a technique, called time-calibrated Bayesian phylogenetic analysis. They estimated that the
    date when the most recent common ancestor of all Omicrons existed was
    early October 2021.



    ========================================================================== Next, the team applied a selection analysis to the 686 Omicron sequences
    and found evidence of positive natural selection in many genes since
    the variant split from other B.1.1 lineages. "This finding led to our conclusion that adaptive evolution played a significant role in the
    early emergence and establishment of Omicron," said Boni. "This finding suggests that Omicron is likely the result of an evolutionary process
    that created a highly transmissible virus that partially evades our
    antibody responses." Additionally, the finding ruled out recombination
    of previous variants in the origin of Omicron.

    "We found no convincing evidence of Omicron being a recombinant of
    previous SARS-CoV-2 variants," said Boni.

    The team did find that some samples of Omicron displayed weak evidence
    of having inherited genetic material from a Delta virus, but statistical analyses could not rule out random chance or small sequencing errors as
    causes of this curious recombination signal.

    "Given the recent misinformation suggesting that the Omicron and
    Delta variants have recombined to create a 'Deltacron' super variant,
    it is important to note that such recombination is in fact possible,
    but there is currently no evidence that this has occurred," said
    Boni. "Additionally, if it does occur, there's no telling what the
    properties of such a virus would be in terms of its ability to transmit
    and/or cause severe disease, among other factors." Regarding Omicron's transmissibility, the team concluded that partial immune evasion was
    likely a major driver of the rapid spread of omicron in South Africa
    given that the proportion of the South African population that was immune (either from infection, vaccination or both) was above 60%.



    ========================================================================== "This idea that Omicron can partially evade the immune system is
    supported by other recent findings showing an increased risk of SARS-CoV-2 reinfection associated with the emergence of Omicron," said Boni. "We
    also know now that the viral load of Omicron is higher in people who are infected, which also contributes substantially to its high transmission
    rate." Boni noted that the current Omicron wave is a reminder to all
    Americans to keep our COVID-19 vaccinations as current as possible.

    "We can't afford to endure another calendar year with half a million
    deaths," he said.

    Other institutions represented on the paper include Lancet Laboratories,
    the Botswana Harvard HIV Reference Laboratory, the Harvard T.H. Chan
    School of Public Health, the Botswana Presidential COVID-19 Taskforce,
    the National Health Laboratory Service of South Africa, the University
    of KwaZulu-Natal, the University of the Witwatersrand, the University of
    Bern, the University of the Free State, Diagnofirm Medical Laboratories,
    the University of Edinburgh, the University of Pretoria, Emweb bv,
    the University of Cape Town, Stellenbosch University, Fundacao Oswaldo
    Cruz, the Universidade Federal de Minas Gerais, the NHLS Groote Schuur Laboratory, the Wellcome Centre for Infectious Diseases Research in
    Africa, Temple University, the University of Oxford, the Ministry of
    Health and Wellness of Botswana, the NHLS Port Elizabeth Laboratory,
    Walter Sisulu University, the NHLS Tygerberg Laboratory, the Charlotte
    Maxeke Johannesburg Academic Hospital, Botswana-Baylor Children's Clinical Centre of Excellence, Baylor College of Medicine, Centre for the AIDS
    Programme of Research in South Africa, the University of Botswana,
    PathCare Vermaak, and the University of Washington.

    ========================================================================== Story Source: Materials provided by Penn_State. Original written by Sara LaJeunesse. Note: Content may be edited for style and length.


    ========================================================================== Journal Reference:
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    Zarebski, Boitumelo Zuze, Dominique Goedhals, Wolfgang Preiser,
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    in southern Africa. Nature, 2022; DOI: 10.1038/s41586-022-04411-y ==========================================================================

    Link to news story: https://www.sciencedaily.com/releases/2022/01/220126165537.htm

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