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COVID-19: Omicron variants BA5 and BA2.75

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  • COVID-19: Omicron variants BA5 and BA2.75

    Ulrich Elling

    Jul 3 • 13 tweets • 5 min read Bookmark Save as PDF My Authors
    BA.2.75 Maybe the new lineage to worry about? I don’t like the observed mutations.

    Before we are done with the BA.5 wave we might already have to prepare for the next. Let’s take a closer look.
    In India BA.2.75 is growing very fast based on sparse sequencing. This nice thread summarized the current data
    Unroll available on Thread Reader

    Also, another thread by Tom Peacock can be found here
    Unroll available on Thread Reader

    and Cornelius Roemer set up a covSPECTRUM to track it…

    covSPECTRUMcovSPECTRUM is an interactive platform aiming to help scientists investigate and identify variants of SARS-CoV-2.
    Confirmed cases are very few still today, July 3rd. But the international distribution excludes sequencing errors and makes it highly likely that the real numbers are way higher.
    So what Mutations are found in BA.2.75?

    The spike protein carries 8 mutations in addition to BA.2: 147E, 152R, 157L, 210V, 257S, 339H, 446S, 460K;
    Remember it is just 3 in BA.5: del69/70, 452R, 486V;
    Both lineages also share the reversion of 493R.
    The Mutations are covering the surface of both the N-terminal domain and the Receptor binding domain. I am sure @florian_krammer knows most of them by heart already.
    Comparing BA.1 and BA.2 it was obvious, that BA.2 was practically unchanged in the NTD while BA.1 had several deletions here.
    While BA.5 carries the 69/70 deletion again, no other mutations are observed in the NTD.
    In contrast, the NTD is decorated with mutations in BA.2.75 in and around the neutralizing antibody binding “supersite” and could thus enhance immune evasion in that region.
    It is really too early to know if BA.2.75 will take over relative to BA.2 or even relative to BA.5. But it is remarkable to note that BA.2.75 carries alternative “solutions” in the regions mutated in BA.5:
    del69/70 --> 147E, 152R, 157L, 210V, 257S
    452R --> 446S
    In addition, the 493 reversion is shared
    Prominent differences between the lineages are:
    486V in BA.5 vs. 339H, 460K in BA.2.75
    The number of 8 additional mutations in BA.2.75 is remarkable, Delta had 8 in spike in total. 3 mutations can make a huge difference (BA.5). Thus the 11 Mutations distinct between BA.5 and BA.2.75 could allow for yet another wave as BA.5 immunity might not protect.
    I sincerely hope this HIGHLY SPECULTIVE thread will turn out to be false alarm!
    Big shoutout to all colleagues that already shared valuable information.
    ..and those I missed.

  • #2

    ᴛʜᴏꜱᴇ ᴘᴇꜱᴋʏ ᴛ ᴄᴇʟʟꜱ
    BA.2.75 vs BA.5 You'll be pleased to know that relative transmissibility projections dropped slightly over the weekend to a mere [ahem] 894% - 10x fitter than BA.5

    2:45 AM · Jul 4, 2022·Twitter Web App


    • #3
      BA.2.75 — new Covid variant detected in India a mystery, but could ‘have immune-escape property’

      3 July, 2022 11:30 am IST


      New Delhi: Scientists across the world have flagged the emergence of a new coronavirus variant in India, the BA.2.75, which is said to be cropping up increasingly in samples, and may have an increased ability to infect people who have been infected before, as well as those who are vaccinated.

      BA.2.75 is a sub-lineage of the Omicron variant. Sub-lineages of Omicron have become the dominant variants circulating across the globe, with new mutations continuously evolving.

      At least 23 samples of the BA.2.75 variant have been detected in India so far, in Maharashtra, Karnataka and Jammu & Kashmir, according to the data uploaded on Nextstrain, an open-source platform of genomic data.

      Worldwide, just about 37 samples of the variant have been detected, including in Australia, Germany, Canada and New Zealand, according to the Nextstrain data. ...

      Why is this variant expected to infect vaccinated people?

      The BA.2.75 variant includes new mutations in the spike protein, in addition to the mutations that are already present in the Omicron variant, explained the Indian genomic scientist quoted earlier. Spike proteins are the protrusions seen on the outer surface of the novel coronavirus.

      Of particular concern, said the scientist, are the mutations ‘G446S’ and ‘R493Q’, both of which are associated with significant changes in the protein structure of the spike protein, with the potential to give the variant the ability to evade several antibodies.

      As a result, the variant is expected to infect people who have been vaccinated, or have been infected previously.

      However, currently, there is a lack of data on how fast the infection from this particular variant is spreading, owing to insufficient surveillance. There is also not enough data currently to ascertain if the variant has the potential to cause severe infection.