Heavily mutated Covid variant identified

In the past week a heavily mutated Covid variant has been identified, rapidly labelled a “variant of concern” by the World Health Organization and named Omicron. It has been detected in countries including the UK.

It is a rapidly evolving situation. Omicron’s genetic profile has raised concerns, but there’s a shortage of real-world data that means nobody has the complete picture of what it can do.

It is unclear how big a threat it poses.

Yet, it is at this early stage, in an absence of definitive facts and when there is a danger of both underreacting and overreacting, that the UK government has to act.

It’s like you or me deciding whether to marry someone after the first date. Only the stakes are much higher.

It might sound odd, but booster doses could limit any impact. In theory you can compensate for a less efficient immune defence by simply throwing more antibodies and T-cells at the problem, even if they are imperfect.

More than 17 million people have already had a third dose and the government wants to ramp up boosting. Other countries have cut the gap between the second and third dose from six months to five and we should hear from the government’s vaccine advisers soon.

Pharmaceutical companies say they could update vaccines to match the Omicron variant in around 100 days if they were needed.

It is worth noting we do have new weapons in our armoury in the form of anti-viral drugs. Paxlovid and molnupiravir both target the inner workings of the virus and experts have told me there is no suggestion their effectiveness would be knocked by the mutations seen so far.

There is also a desire to understand how sick people are getting with Omicron. It is often incorrectly claimed that a virus must become milder as it mutates. The reality is much more complicated and it will take time to get the answer as the country with the most confirmed cases, South Africa, has a relatively young population. The younger you are the milder Covid tends to be.

According to WHO;

Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern

The Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE) is an independent group of experts that periodically monitors and evaluates the evolution of SARS-CoV-2 and assesses if specific mutations and combinations of mutations alter the behaviour of the virus. The TAG-VE was convened on 26 November 2021 to assess the SARS-CoV-2 variant: B.1.1.529.

The B.1.1.529 variant was first reported to WHO from South Africa on 24 November 2021. The epidemiological situation in South Africa has been characterized by three distinct peaks in reported cases, the latest of which was predominantly the Delta variant. In recent weeks, infections have increased steeply, coinciding with the detection of B.1.1.529 variant. The first known confirmed B.1.1.529 infection was from a specimen collected on 9 November 2021.

This variant has a large number of mutations, some of which are concerning. Preliminary evidence suggests an increased risk of reinfection with this variant, as compared to other VOCs. The number of cases of this variant appears to be increasing in almost all provinces in South Africa. Current SARS-CoV-2 PCR diagnostics continue to detect this variant. Several labs have indicated that for one widely used PCR test, one of the three target genes is not detected (called S gene dropout or S gene target failure) and this test can therefore be used as marker for this variant, pending sequencing confirmation. Using this approach, this variant has been detected at faster rates than previous surges in infection, suggesting that this variant may have a growth advantage.

There are a number of studies underway and the TAG-VE will continue to evaluate this variant. WHO will communicate new findings with Member States and to the public as needed.

Based on the evidence presented indicative of a detrimental change in COVID-19 epidemiology, the TAG-VE has advised WHO that this variant should be designated as a VOC, and the WHO has designated B.1.1.529 as a VOC, named Omicron.

As such, countries are asked to do the following:

  • enhance surveillance and sequencing efforts to better understand circulating SARS-CoV-2 variants.
  • submit complete genome sequences and associated metadata to a publicly available database, such as GISAID.
  • report initial cases/clusters associated with VOC infection to WHO through the IHR mechanism.
  • where capacity exists and in coordination with the international community, perform field investigations and laboratory assessments to improve understanding of the potential impacts of the VOC on COVID-19 epidemiology, severity, effectiveness of public health and social measures, diagnostic methods, immune responses, antibody neutralization, or other relevant characteristics.

Individuals are reminded to take measures to reduce their risk of COVID-19, including proven public health and social measures such as wearing well-fitting masks, hand hygiene, physical distancing, improving ventilation of indoor spaces, avoiding crowded spaces, and getting vaccinated.

For reference, WHO has working definitions for SARS-CoV-2 Variant of Interest (VOI) and Variant of Concern (VOC).

A SARS-CoV-2 VOI is a SARS-CoV-2 variant:

  • with genetic changes that are predicted or known to affect virus characteristics such as transmissibility, disease severity, immune escape, diagnostic or therapeutic escape; AND
  • that has been identified as causing significant community transmission or multiple COVID-19 clusters, in multiple countries with increasing relative prevalence alongside increasing number of cases over time, or other apparent epidemiological impacts to suggest an emerging risk to global public health. 

A SARS-CoV-2 VOC is a SARS-CoV-2 variant that meets the definition of a VOI (see above) and, through a comparative assessment, has been demonstrated to be associated with one or more of the following changes at a degree of global public health significance:

  • increase in transmissibility or detrimental change in COVID-19 epidemiology; OR
  • increase in virulence or change in clinical disease presentation; OR
  • decrease in effectiveness of public health and social measures or available diagnostics, vaccines, therapeutics

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