Variant of Concern Omicron. Here we go again...
What we know about the variant, what we need to know, and why we should've seen this coming. Also, what you should be doing right now.
By now, you have probably heard the news about a new Variant of Concern (B.1.1.529), which the World Health Organization (WHO) has dubbed Omicron.
You would not be alone if your first reaction was to groan and to say, “here we go again!”
But once you compose yourself, you will guess that there’s really an awful lot that we don’t yet know about this Variant of Concern. To the credit of scientists in South Africa, the variant was identified very quickly, though where it first arose is not yet known.
But is Omicron worse than Delta or is it more like Lambda and Kappa, two variants that did not spread as rapidly as Delta did?
So what do we know about Omicron?
Omicron was first identified in Botswana and reported to WHO from South Africa.
It is spreading at an alarming rate in Gauteng province in South Africa, and has been detected in a few other countries and regions such as Hong Kong and Israel.
The spread of Omicron seems to be faster than the spread of Delta, but there are huge caveats here also. The numbers are low overall so far and mostly confined to South Africa. Small numbers can inflate actual effects especially if there is a founder effect.
Omicron has a very large number of mutations, especially in the gene coding for the Spike protein that gives the virus access to human cells. Some of these have been mapped to earlier variants so we know what properties they confer. But others are new.
Very preliminary evidence suggests an increased risk of reinfection with this variant, though the exact extent compared to other variants is unknown.
We do not know the extent of protection of those who have been vaccinated with two doses or three doses of a vaccine and/or infected earlier. Antibody titres post vaccination as well as T-cell immune responses will be determined soon. Notably, the rate of vaccination in southern Africa is high compared to other parts of Africa but low overall (20-25% fully vaccinated). We do not know how well the variant spreads in a vaccinated population compared to an unvaccinated one.
Current SARS-CoV-2 PCR diagnostics are able to detect the variant despite its numerous mutations. However, one of the target genes is not detected because of something called an S gene drop-out in this variant. Actually, that dropout can be used as a diagnostic feature of the variant.
So there we have it. Not much is known yet about Omicron especially with respect to people who are already vaccinated or have been infected.
A head to head comparison with Delta will come soon with respect to transmissibility, reinfections, vaccine breakthroughs, and disease severity. To the credit of the public health infrastructure in South Africa, Omicron was identified fairly rapidly.
But we saw this coming
We have been saying for months that as long as one part of the world remains unprotected, new variants can emerge. And Africa has received very few vaccines.
About two months ago, I wrote a column on the trajectory of the pandemic for Hindustan Times. In it, I wrote the following—
A year ago, most virologists did not predict the rapid emergence of variants of SARS-CoV-2. Right now, of the variants we know, the Delta variant (which was first detected in India) spreads most rapidly. Although other variants are emerging, Delta is still the most problematic because it replicates much better than the ancestral Wuhan lineage…
…That said, new variants will emerge, and they may supplant Delta in the future. Where and when these variants will emerge is much harder to predict. We know that immunosuppressed individuals who received antibody therapy had persistent infections that lasted for months. In these people, viral lineages acquired many mutations and became variants. But variants can also emerge over time as a result of rapid spread through many people instead of in one person.
Vaccine inequity has been a problem in 2021. Parts of the world will still be unvaccinated at the end of 2022. Variants can emerge in any part of the world where the virus is spreading. As more people are vaccinated, there will be selection pressure on variants to escape from vaccine-induced immunity.
Which brings me to the second set of factors that will determine how quickly the pandemic ends — immunity against emerging variants. As a substantial portion of the population is vaccinated or become immune post-infection, peaks of successive waves of infection may subside…
…The robustness of immunity after vaccination also matters. Populations that received both vaccine doses earlier this year are losing the ability to prevent transmissions caused by variants. With waning immunity and variants that are mismatched to existing vaccines, vulnerable populations will need booster shots to prevent severe outcomes. Here, a comparison of Covid-19 vaccines can be made to flu vaccines; annual flu shots protect well against severe disease, but not against infection from all circulating strains.
All of these points are still relevant today. Delta (which was identified in India) is still the variant that caused the most damage globally because it was highly transmissible compared to all other variants, even if it did not evade immune responses to the same extent as the Beta variant (which was also identified in South Africa).
Epidemiological studies will trace this especially in places where Delta is already established. If Omicron can outcompete Delta and get established then that would be a cause for concern.
In my view, the biggest cause for concern so far is the number of mutations that have been identified in the Spike region- more than 30 in all. And the crucial experiment will be to create pseudotyped Omicron viruses and see how well they replicate in cells compared to other variants like Delta. I think we can expect these experiments to be published as preprints in the next few days.
What should you do right now then?
Hopefully, you will continue to do all the responsible things you’ve been doing throughout this pandemic such as wearing a proper, well-fitting mask, physical distancing, improving ventilation of indoor spaces, avoiding crowded spaces, and getting vaccinated (if you haven’t already). If you are in a high-risk group and a booster is available, consider getting it.
I’m relatively healthy, under 50, and not in a high-exposure situation, so I’m in no rush to get the booster (my third dose of the COVID-19 vaccine). Others need vaccines more than I do. That said I will likely get it before the end of the year.
That is it for now. This was a hastily drafted newsletter on a fast-moving story, but normal programming will resume again with the next newsletter. And as new research on Omicron becomes available, I’ll be sure to share with you.
Stay well.
Anirban
Variant of Concern Omicron. Here we go again...
Thank you so much Anirban. Amongst the barrage of 1-200 worded flash news, I was looking for your studied views and inputs on this.
Thank you Sir, this insight is useful.