Information about Omicron (aka B.1.1.529) continues to pour in, after the avalanche of information yesterday. This is an open diary for folks here to add to the discussion based on information they have gleaned from reliable sources and to ask/answer questions about Omicron.

Here are some updates on the Omicron situation —

Lots of discussion on whether travel bans are a good idea or are they counter-productive …


… or whether they are short-term solutions that buy us time?

  • In which case how best do we make use of the bought time?
  • One common theme is to ramp up vaccination globally

Is the scientific community over-reacting to a situation we do not fully understand?

  • It is damned if we do, and damned if we don’t.

Is the variant present only in the countries identified so far?

  • That is unlikely given the level of airline travel in the modern world.
  • Also, genomic surveillance is strong in S. Africa, other countries not so much.

Did Omicron originate in South Africa?

  • It is possible it originated elsewhere but was detected in South Africa due to its stellar genomic surveillance system.

How much has the new variant spread so far?

  • See table from… below
  • The 2 cases in England has authorities there rattled
  • We can expect this list to get longer today. Viruses travel faster in this jet age than we can detect them.
Location Confirmed Probable Links
South Africa 88 990 Source
Botswana 6 9 Source
England 2 Source
Hong Kong 2 Source
Italy 1 Source
Israel 1 7 Source
Belgium 1 Source
Czech Republic 1 Source
Netherlands 61 Source
Germany 3 Source
Denmark 2 Source
Austria 1 Source

Think about how many flights originated from Africa and other countries in the past week.

Also, aren’t international travelers required to be tested 72 hours before departure? Why is the positivity rate so high in this case?


    Will existing COVID tests detect this virus?

    • Yes
    • They will also be able to identify this variant.

    How well will existing vaccines provide protection against the variant?

    • That is a burning question that scientists are feverishly working on
    • The expectation is that they will protect against severe disease and hospitalization

    How soon can vaccines be adapted to the new variant, if necessary?

    • Wanna bet that they are have already tweaked the vaccine in the lab, esp. for mRNA and protein based vaccines?
    • It is the testing and manufacturing that will take time.

    How did so many mutations appear together so abruptly?

    • A possible explanation provided by virologists is that the virus evolved in a single immunocompromised patient with a long duration infection.

    That’s a sobering thought, that harmful mutations can develop in a single person.


    Here is a hypothesis about the link between mutations, immunocompromised individuals and the prevalence of HIV in Southern Africa –


    More from the thread –

    Often ignored by the rest of the world, Southern Africa has a large HIV epidemic, with around 20% of the population infected. Despite large national government efforts, only 71% of infected people in South Africa have access to antiretroviral therapies.

    The regional emergence of several SARS-CoV-2 variants with long branches and concerning mutations in Southern Africa suggests that its HIV epidemic is a driving factor. This is a factor that the global pandemic response may have to acknowledge.

    The international pandemic response may therefore have to look not only at providing equitable access to SARS-CoV-2 vaccines and financial support for public health systems — but also into HIV and SARS-CoV-2 antiviral therapies.

    Nobody is safe until everyone is safe.

    On vaccine equity, hesitancy and politics –


    But vaccine supply has been lacking as well and rich countries need to step up. None of us are safe until all of us are safe.



    The COVID pandemic is hardly over, as we are reminded every day; nor is the ability to virus to evolve. Even without this variant, a new wave seems to be forming in Europe and the USA as winter approaches. Anti-vaxx sentiments, pushed by the right in many countries, is making things worse, so is waning immunity from vaccines. The probability of new variants arising remains high so far as the virus circulates in a large section of the population.

    The B.1.1.529 variant may create new challenges or it may fizzle out, we do not know yet. It may have vaccine escape properties, but vaccines could still provide protection against severe disease.

    This is  a global problem and requires a global response. Otherwise, we will be chasing variants forever. The whol e world needs to get vaccinated. Nobody is safe until everyone is safe


    As we all understand, we need to stay vigilant, get the booster shot if we have not already done so, keep practicing masking and social distancing protocols, encourage others to do so and keep an eye on the news from reliable sources.

    Let’s keep our discussion rooted in science and reliable sources and avoid tidbits of info. based on hearsay.

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    This is a Creative Commons article. The original version of this article appeared here.


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