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CDC Tracking A New SARS-CoV-2 Variant: BA.2.87.1

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  • CDC Tracking A New SARS-CoV-2 Variant: BA.2.87.1

    CDC Tracking A New SARS-CoV-2 Variant: BA.2.87.1

    CDC Nowcast Feb 3rd 2024


    While we are currently entrenched in a JN.1 dominant COVID season (see CDC Nowcast Chart above), viral evolution continues around the world, and somewhere out there is likely a budding contender for the throne.

    The history with dominant COVID variants is they rarely last more than 6 months at the top. Often they are toppled after only 2 or 3 months.

    While someday we may see a more stable SARS-CoV-2 virus emerge, for now it is an evolutionary free-for-all, with dozens of variants vying for dominance.

    While the next phase for COVID is unknowable, scientists around the world - including at the CDC - are watching a relatively new lineage (BA.2.87.1) with more than 100 mutations (> 30 in the spike protein).

    This variant was first detected in South Africa, two weeks ago the ECDC added it as a VUM (Variant Under Monitoring), writing:

    The newly designated SARS-CoV-2 lineage BA.2.87.1 was classified as a VUM. Currently, a small number of sequences of this lineage (9) were identified in South Africa, with collection dates ranging from 20 September to 12 December 2023. This lineage has been circulating at low levels since September 2023, without any clear signs of an increase in proportions or an impact on epidemiological indicators.
    BA.2.87.1 is genetically distinct from currently circulating variants, carrying around 100 mutations compared with the parental lineage BA.2. It also has a distinct N-terminal domain in the spike protein, including several large deletions, and could therefore potentially be associated with a significant shift in antigenic properties. However, so far there are no virus neutralisation data available for BA.2.87.1 and further studies are needed to elucidate the properties of this variant. BA.2.87.1 is unlikely to have an impact on the epidemiological situation in the EU/EEA in the near future.

    Last August we saw asimilarly heavily mutated lineage (BA.2.86) emerge to some fanfare - only to fail to take off. It did, however, produce an overachieving offshoot (JN.1) - that with the aid of just one RBD mutation (L455S) - quickly soared to global dominance.

    The difference between a hero and a zero in the world of viruses can boil down to one or two fortuitous amino acid changes (see The Lancet Fast evolution of SARS-CoV-2 BA.2.86 to JN.1 under heavy immune pressure).

    Late Friday afternoon the CDC released their own preliminary assessment, and it too finds the risks right now from this variant appear to be low. But they admit that `. . . Experience with BA.2.86 demonstrates that the ability of the virus to transmit can change quickly over time.'

    I'll return with a brief postscript after the break.
    February 9, 2024, 4:20 PM EDT

    CDC is posting updates on respiratory viruses every week; for the latest information, please visit
    CDC Respiratory Virus Updates.

    CDC is tracking and analyzing BA.2.87.1, a new variant of SARS-CoV-2, the virus that causes COVID-19. To date, this variant has been detected nine times in the Republic of South Africa. These viruses came from specimens collected from September-December 2023 and were then posted to a public database on January 31.
    As of February 8, no clinical cases of BA.2.87.1 have been identified in the United States or anywhere outside of South Africa. CDC is monitoring sequences from patient cases and other surveillance systems that include incominginternational travelersand wastewater. The fact that only nine cases have been detected in one country since the first specimen was collected in September suggests it does not appear to be highly transmissible at least so far.

    CDC is closely tracking BA.2.87.1 because it has over 30 changes in the spike protein of the virus when compared to XBB.1.5, the variant that the updated (2023-2024) vaccine is designed to protect against. The spike protein is what our immune system targets when a virus enters our bodies. Our immune systems are primed to protect us through immunity gained from vaccines and previous infections. In theory, variants with multiple changes in the spike protein could increase the possibility of escape from this immunity.

    In the past year, several variants have had significant changes in their spike protein. Yet despite those changes, existing immunity from vaccines and previous infections still provides good protection. We don’t yet know how well existing immunity holds up against BA.2.87.1. However, our immune systems now have several years of experience with this virus and vaccines, generally providing protection against a wide range of variants.

    No indication of increase in infections in South Africa

    Data from the
    Republic of South Africa’s National Institute for Communicable Diseases sentinel surveillance network indicate no detectable increase in COVID-19 cases in recent weeks. Reports of COVID-19 cases to the World Health Organization (WHO) for this region remain low. (Recent data on COVID-19 hospitalizations and deaths are not available for South Africa.)

    Impact on vaccines, treatments, and tests

    It is too early to know how well current vaccines will work against BA.2.87.1. But recent experience with JN.1 suggests that the updated COVID-19 vaccine can
    help increase protection against a diverse range of variants. In addition, we expecttreatments and testing to remain effective based on an analysis conducted by the SARS-CoV-2 Interagency Group, a group of scientific experts representing multiple government agencies.

    CDC’s current assessment of BA.2.87.1
    • CDC will closely monitor this variant given the large number of changes in the spike protein and the potential for escape from existing immunity from vaccines and previous infections.
    • The detection of BA.2.87.1 cases across three South African provinces over three months demonstrates that this variant can spread between people, unlike some other variants with many mutations.
    • However, few cases have been detected since the first specimen was collected in September, suggesting it does not appear to be highly transmissible so far.
    • Experience with BA.2.86 demonstrates that the ability of the virus to transmit can change quickly over time.
    • 2.86 spread relatively slowly, but JN.1, which resulted from a single mutation in BA.2.86, spread very quickly to become the dominant variant across the globe.
    • CDC has not yet detected any cases of BA.2.87.1 in the United States. CDC continues to track the appearance and spread of new variants through national genomic surveillance.
    • At this time, it is not known how well current vaccines will work against BA.2.87.1. CDC expects that the updated COVID-19 vaccine could increase protection, and that treatments and testing will remain effective against this variant.
    Based on current information, the public health risk from BA.2.87.1 appears low. CDC is monitoring this new variant closely and will update as more information becomes available

    Despite continually emerging COVID variants, the world has intentionally dismantled the bulk of their global surveillance, testing, and reporting system in order to `move on' from the pandemic emergency (see No News Is . . . Now Commonplace).

    This CDC release states that South Africa reports `. . . indicate no detectable increase in COVID-19 cases in recent weeks.' but they temper that statement that by adding: `(Recent data on COVID-19 hospitalizations and deaths are not available for South Africa.)'.

    The reality is these reporting gaps have become the norm, not the exception. In their latest (now monthly) epidemiological report, the WHO reported:

    Globally, during the 28-day period from 11 December 2023 to 7 January 2024, 106 countries reported COVID-19 cases and 51 countries reported COVID-19 deaths. Note that this does not reflect the actual number of countries where cases or deaths are occurring, as many countries have stopped or changed frequency of reporting.

    It gets worse. While 23% reported COVID hospitalization data at least once, only 10% of the world's nations reported `consistently' over the past 28 day reporting period (see chart below).

    Data on ICU admissions and deaths are even harder to come by. And much of the data we do get is likely incomplete or potentially misleading. This reluctance to report often goes beyond just COVID, and can also extend to avian flu, MERS-CoV, and other zoonotic threats.

    Ignorance may be bliss, but that happy state only lasts until we get blindsided by the next global health crisis.

    But at least when that happens, the world's leaders can honestly claim they never saw it coming.

    All medical discussions are for educational purposes. I am not a doctor, just a retired paramedic. Nothing I post should be construed as specific medical advice. If you have a medical problem, see your physician.