New Omicron variants coming our way soon: how protected are we?

As the original Omicron variant continues to mutate, its greater ability to transmit has been offset in terms of the public health risk by (i) the milder illness it causes and (ii) the protection against severe disease from both natural infection and the current vaccine regimes.  However, should we now be worried about the new variants now spreading from South Africa to Europe and North America?

A bit about the original Omicron 

  • The original Omicron variant when originally identified was not thought to have significant subvariants 
  • Then in South Africa, in late 2021, 3 sub-variants of Omicron were identified, and are now referred to as BA.1, BA.2 and BA.3
    • These 3 had many different genetic mutations from the original Omicron, but also differed from each other
    • All these subvariants were associated with mild infection, although some of the protection against serious infection will be a consequence of immunity from either, or both of, vaccines and natural infection
  • One or more of these variants rapidly predominated in Europe
  • Indeed in the UK, during the 2021/22 winter peak of Omicron, around 95% of new cases reported were from BA.2
  • There have been many reports now of people having a repeat attack from one of these original Omicron variants, but these have also been mild
  • As a consequence, and despite the greater transmissibility of Omicrons BA.1-3, the milder disease consequent on our natural and vaccine immunity led to the lifting of behaviour rules and also a reduction in self testing which has had a knock-on effect on our not knowing the exact numbers of cases

What are Omicron BA.4 and BA.5?

  • These are two quite different subvariants of the original Omicron BA.1-3
  • Both were first identified in South Africa this year in two provinces: BA.4 in Limpopo in the far north and BA.5 in KwaZulu-Natal in the south east. 
  • These two subvariants have some of the same mutations as the original Delta variant
  • They also have different mutations on the spike protein to other Omicron subvariants,  which makes them more sticky onto human cells and hence more likely to lead to infection
  • Thus, not surprisingly, there has been a massive increase in the proportion of cases in South Africa due to these subvariants over a very short time
  • As shown in the picture below, almost all cases in South Africa now are either BA.4 or 5

Have these variants spread to other countries?

  • Indeed yes and they are already contributing to a growing proportion of cases in the few countries that have been able to test for these
Proportion of current cases due to BA.4 or BA.5: selected European countries
  • Thus they probably amount to 15% of all cases in the UK (both variants combined)

Do we need to worry about these subvariants?

  • Obviously, the big question!
  • Compared to the original Omicron subvariants, BA.4 and 5 are probably more transmissible so the absolute number of new cases is likely to increase (compared to what the numbers would have been if BA.1-3 were predominant)
  • Indeed, the number of notified cases in South Africa has risen from around 1000/day in mid-April to over 10,000/day by the end of last week, a tenfold rise in less than 4 weeks
  • As a consequence of the numbers alone, this has had a knock-on effect on the numbers being admitted to hospital; and indeed the challenge of increasing sickness amongst South African health workers with the new sub variants
  • As with the original Omicron subvariants, the disease though is predominantly mild

What about protection from vaccines and previous infections with the older Omicron subvariants?

  • That at the moment is the big unknown
  • Experts are asking if this surge in cases in South Africa means that these new subvariants can evade our acquired immunity?
  • Alternatively is any protection from the vaccines/previous infections waning? Hence the increase in cases from these subvariants just represents that phenomenon and would have happened with any circulating variant.
  • This is where a research paper published this week might provide some insights to address this issue:
  • This is what the research did

Their conclusions as summarised below was interesting and perhaps sobering!

  • In brief the ability of this virus to mutate means that herd immunity is not an achievable outcome 
  • Just giving boosters of the existing vaccines derived from the original Wuhan variant may not be of much benefit

But to some extent this is the situation with seasonal flu – except that Covid-19 mutations seem to be occurring in a 6-month cycle (see this picture from this week’s Nature)

And finally are there new more effective vaccines coming on stream?

  • Before the BA.4/5 issue, both Moderna and Pfizer were already  modifying their mRNA vaccines to be effective against Omicron BA.1-3
  • They have promised results by June 30th
  • I wonder if the BA.4/5 story means that the virus is mutating so quickly that major beneficial changes cannot be achieved with these new Omicron-derived vaccines
  • The virus can mutate more quickly than vaccines can be developed to stop transmission


  • Covid-19 is clearly here to stay and will continue to mutate
  • The good news is that whilst repeat infections are likely, and may be impossible to prevent, the dire consequences of 2020 should not recur

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6 replies on “New Omicron variants coming our way soon: how protected are we?”

At the risk of sounding pedantic, I query the statement: “Both also arose in South Africa this year in two provinces: BA.4 in Limpopo in the far north and BA.5 in KwaZulu-Natal in the south east.” More correctly, these variants were first identified in South Africa from patients in the two provinces. Given the specific provinces, these two have a high level of illegal immigration from Zimbabwe and Mozambique – often to receive free medical attention in South Africa, and it is quite possible that the variants did not originate in South Africa.

Unfortunately, South Africa’s far superior technologies with regard to viruses, PCR etc often make the country appear to be THE hotbed of Covid-19 and the variants. In fact, the medical professional who identified the first variant even jokingly said that if he found another one, he would keep it quiet. – such was the negative impact on the world’s perception of the situation in South Africa. Certainly a case of being victims of our own success.

It might also interest readers to know that only Egypt, South Africa, Tunisia, Algeria, Cape Verde, São Tomé and Príncipe, Seychelles and Mauritius have what are called functioning, compulsory and universal civil registration systems which record deaths in Africa. Therefore, even attempting to understand the death rate of the 44 other countries is impossible.


This is a very fair comment and indeed South Africa has a very well developed genetic sequencing service so you could well be correct. I have changed the wording from ‘arose’ to ‘first identified’. Thanks!


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