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Indian variant, vaccines and immune escape: what do we know?

Hitting the headlines this week is news about yet another mutant strain, particularly newsworthy because of the accelerating tragedy of the pandemic in India.  This variant is now present in 40 countries. What do we know about this strain, its impact and in particular any possibility that the success of the vaccines could be imperilled?

Is this strain different from other ‘Variants of Concern’?

  • As before, the bit of the virus we are interested in is the spike protein
  • That’s the bit that allows the virus to enter cells and that’s the bit that the vaccines are designed to attack
  • Previous research had shown there were a couple of genetic differences between the ‘natural’ virus (referred to as the Wuhan strain for obvious reasons) and the  other worrying variants such as ‘South Africa’ and ‘Brazil’
  • The ‘Indian’ variant has lots of differences, as shown in the picture below by the code numbers shown in red (Amazing that such a tiny part of such a tiny organism can be so complicated!)
  • Obviously just because there are so many differences, doesn’t mean that any or all of them matter

Any reason that this multi-mutant has arisen?

  • Viruses do mutate all the time 
  • The more the virus reproduces, the more likely it is each time that a mutant can arise
  • In areas with high infection rates such as India, especially with people being quite sick, there are even more reproductions
  • Interestingly some biologists have suggested that often viruses have the ability to weed out mutants that stray from their origins, but Covid-19 is not that careful
  • What we don’t know is how much these new variants would have arisen naturally in any population and how many are brought in
  • The Indian variant may have started life as an import of the UK variant

Is the Indian variant more transmissible?

  • It is quite remarkable how quickly this variant has taken over and seems to be the predominant one across that country 
  • Shown by the arrows:  Kerala in the south, Maharashta in the west, Delhi in the north and West Bengal in the east
  • There has certainly been a phenomenal rise in the number of cases, which can only realistically be explained by the newer variants having a much greater ability to transmit
  • Data emerging from the UK, would also suggest that this variant, like the UK (‘Kent’) variant before, is more transmissible than previous variants

Are cases of the new variant more severe?

  • The brief answer is we don’t know 
  • Laboratory studies on human tissues  suggest that this particular strain is more likely to enter cells lining the lungs
  • Studies on hamsters deliberately infected with different strains showed that the Indian strain produced more severe infection – but not substantially so
  • BUT:
    • Laboratory studies on tissues do not necessarily replicate what happens in whole animals
    • Studies on hamsters may have no relevance for humans (though to be fair it is not unreasonable to do these studies, as it is not ethical to deliberately infect volunteers for the same purposes) 
    • It is not obvious anyway why infection with these strains should be more serious, as opposed to being more transmissible

Will immunity from previous infection protect from the new variant?

  • You may have read the term ‘escape mutant’, which would imply that a previous Covid-19 infection would not protect someone from getting an infection with the new strain
  • There was evidence that prior infection did not protect against the Brazilian variant
  • A study from Germany this week studied the serum from people with a previous infection
    • The study was done entirely based on testing samples in the lab
    • They ‘infected’ these sera with small amounts of either the Indian or the old variant
    • They wanted to see if there was any difference how the existing antibodies in these serum samples would neutralise the infection between these 2 variants
    • They found that these existing antibodies were only 50% as effective against the new variant compared to the old one
    • BUT: 50% might still be enough
    • AND (as above) laboratory studies are not real life

Will the vaccines still protect against the Indian variant?

  • Not surprisingly, we don’t have too much data as yet!
  • There have been some studies on both the Pfizer and the AstraZeneca vaccines
  • For the Pfizer vaccine, I am aware of 2 studies but with quite different results :
    • A study from Cambridge:
      • They tested  serum after one dose of vaccine
      • The sera studied had 80% of the ability to neutralise the spike protein derived from the Indian variant compared to the standard variant
    • A study from Germany:
      • They tested serum after two doses of vaccine
      • The sera studied had only 33% ability to neutralise the spike protein derived from the Indian variant compared to the standard variant
  • For the AstraZeneca vaccine I am also aware of just two reports (which don’t really count as formal research!)
    • The first was anecdotal reports that some health care professionals in Delhi, despite being vaccinated, developed Covid-19 
    • The second was only in the form of a Tweet- reassuring but hardly peer -reviewed – what has the research world come to in only releasing research in Tweets!!!

  • The fact that some of the lab studies suggest that vaccines are less effective against the Indian variant doesn’t mean that they not sufficiently effective – the vaccines have spare capacity in the level of antibodies they produce
  • As regular readers of the blog will know, we also have another part of our immune system – T cells – and even if the antibody response to the new variant is not as strong, our T cells may do the trick (the research to show this is trickier)
  • There is also the reassurance that the vaccines from other laboratory studies are likely to be sufficiently effective against other highly transmissible variants, such as the ‘South African’ one.
  • Finally, given what I have said above, the Indian variant I am sure will be followed by others as the virus continues to mutate and transmit especially in those who are unvaccinated

For further reading and the studies mentioned see: https://www.nature.com/articles/d41586-021-01274-7?utm_source=Nature+Briefing&utm_campaign=9a8cc368a5-briefing-dy-20210511&utm_medium=email&utm_term=0_c9dfd39373-9a8cc368a5-45876838

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2 replies on “Indian variant, vaccines and immune escape: what do we know?”

Once again an informative blog. Thank you. There is much disagreement in the UK about whether restrictions should be being released while so much is unknown about this variant. Many of the arguments I have seen against are there may be increased hospitalisations, but as we don’t know whether the new strain will result in such an increase, I think this line of debate is not hitting home. I am no epidemiologist, but is it the case that increased cases result in a higher risk of mutations? And if that is true why is this not being shouted from the rooftops by the people advocating caution in releasing restrictions?

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Thanks for this really interesting comment. In brief you are correct the more cases that arise and,or the longer the pandemic goes on for, the higher the number of mutations – in theory! Covid-19 did not obey ‘that rule’ early in the pandemic and was remarkably stable genetically. Your second point is mathematically correct – even if the hospitalization rate was constant between variants (which it probably is) then the more the number of cases, the more the number of admissions BUT in the UK it seems that any growth in the number of cases would be in younger people – who have lower severity – hence not necessarily would more cases lead to proportionately more hospitalizations. This is I assume the government’s thinking based on the (thus far) higher than expected success from vaccination

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