The new variant: how much of a concern?

Worldwide, media ran the story this morning of a new variant of the Covid-19 virus from South Africa which is causing anxiety and leading to travel restrictions.  We may remember  previous headlines about the India-Delta variant as well as other variants that hit the news: Brazil – Gamma, South Africa – Beta, that also led to travel bans from those counties.

What is this variant:

  • This new variant was identified this week by South African scientists
  • It is currently referred to as B.1.1.529 but I think will be given the Greek letter ‘Nu’*
  • It has  32 mutations in the all-important spike protein, as compared with the original Covid-19 strain (Wuhan) strain

*Since posting this blog WHO decided this evening to call the variant after the Greek letter Omicron rather than Nu (which was the next letter in the Greek alphabet)

Useful also to remember

  • This new variant was only picked up because of the very sophisticated DNA testing by South African virologists when they were investigating a sharp rise in cases in a province in South Africa 
  • We don’t know whether in other parts of the world, without such sophisticated laboratory systems, there are other variants, or indeed this one, which might also be becoming rampant 

Will this variant spread to Europe?

  • The first handful of cases were confined to countries in Africa but over the past 24 hours there have been cases in Hong Kong, Israel and now Belgium
  • Unless countries that are islands stop all inward movement , we have to expect cases in Europe 
  • Indeed this has just come up on my screen as I am typing this post:

What mutations does the Delta Strain have?

  • The Delta strain has  between 15 and 17 mutations  on its spike protein which make it different from the Wuhan strain
  • These differences make it easier for the virus to enter the cells and reproduce
  • This leads to a shorter incubation period 
  • And also increases the transmissibility of the virus
  • The Delta mutations did not mean this strain caused more severe disease
  • Though the fact that it resulted in a higher total number of cases – then there was be a proportionate increase in the total number within a population requiring hospitalisation
  • More importantly the vaccines worked against Delta, reducing substantially the risk of severe infection

Are the mutations on the Omicron strain more significant?

  • Firstly, because there are more mutations, the spike protein will have a different shape which the body’s immunity defences will have to respond to
  • The picture below on the left shows the whole virus with its spikes in red
  • The picture on the right is a detailed view of one spike and shows how the spike protein can be a very complicated shape and the greater the number of mutations the greater the change in shape
  • Scientists say these mutations make the spike protein quite different to the shape of the Wuhan spike protein in 4 distinct ways
  • These mutations are predicted to make it easier for the virus to enter cells, in the same way that the original South African (Beta variant) did
  • The Beta strain was also predicted to cause more severe disease
  • Of greater concern though were concerns that the Beta strain could ‘escape’ the protection from the current vaccines
  • In fact the Beta strain never took a hold and whilst vaccines may not have been so successful against Beta, the lack of increased transmission ensured that Beta strain did not become a public health problem

What is the concern with this variant Omicron?.

  • The theoretical concern is that this variant could be both more transmissible and (relatively) more resistant to the vaccines, ie equivalent to the combined effects of the Beta and Delta strains
  • Vaccine resistance has been seen in South African patients with Omicron who have had vaccines, including Pfizer and AstraZeneca, but we don’t know if any of these people had severe disease
  • We should also remember that the level of immunity from the current vaccines, especially after a booster, is very high, with some spare capacity which experts believe could cope even with some quite different spike proteins.
  • For the moment we just don’t know if this new variant poses in practice an increased risk of 
    • Greater transmissibility
    • Greater severity
    • Vaccine resistance
  • These consequences are related to some extent


  • Is the media hype justified or have we been here before?
  • The changes in the spike protein are substantial but the theoretical risks above may not prove to be real
  • Whilst not being complacent, and we need to keep a watching brief, the anxiety may be misplaced
  • The key thing is to look out for any data on vaccine resistance, and development of severe disease in fully vaccinated (plus booster) individuals.  My guess and hope is that when these data emerge, they should be reassuring 

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2 replies on “The new variant: how much of a concern?”

What’s not clear is what is the likelihood of a more transmissible variant also having more severe health impacts. The virologists/health experts have been saying up until now that it would highly unlikely for this to be the case. Have assumptions changed or are we ‘just’ seeing governments understandably adopting the precautionary principle.


There is no obvious reason why even a heavily mutated variant should make the disease more severe. The theoretical concern is that the way a new variant would lock onto out cells could make it harder for out naturally produced antibodies to find their way in to block the virus. Just be because this omicron variant is likely to be more transmissible does not make it more less likely to mount an effective immune response


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