The Battle of the (Sub-)Variants

It seems like a lifetime ago that were talking about Alpha and Beta, and even Delta, variants of COVID-19. Then, the Omicron variant arrived at the end of 2021, and everything changed. Since then, we have become used to talking knowledgeably about Omicron sub-variants: BA.1, BA.2, BA.2.12.1, and now BA.4 and BA.5.

So, where are we right now with the variants, and does it really matter any more?

Unfortunately, I have not seen a good visualization of the waves of variants and subvariants, along the likes of this one in Nature, which is now hopelessly out of date.

The current state of affairs seems to be that the BA.2.12.1 sub-variant is officially dominant in North America, taking over from BA.2, which in turn took over from BA.1.

However, even BA.2.12.1 is in the process of being pushed out by the double threat of BA.4 and BA.5 (which both seem to be part of the B.1.1.529 designation, which is the general descriptor for the Omicron variant, but who knows how all THAT works?). The BA.2.12.1 variant accounted for 59% of all variants identified this week in the USA, up from 52% last week, so it is still increasing in prevalence. The BA.4 and BA.5 strains, though, increased from 3.4% to 6.1% over that same week, so relatively speaking they are growing faster, and it seems only a matter of time before they overtake BA.2.12.1. Some states and provinces seem to be more affected by the new variants than others.  

In South Africa, where all these new Omicron variants seem to originate for some reason, the BA.4 and BA.5 sub-variants have already out-competed BA.2.12.1, and together account for over 90% of new cases as early as the end of April. This is also the case in some European countries like Portugal. 

(Incidentally, South Africa feels that it is being unfairly stigmatized for its early reporting of new variants, which it says is merely a reflection of its highly-developed genomic sequencing facilities, and not anything to do with its own poor management of the disease. But the fact remains that the new variants do seem to take hold there before other countries, so I am not sure their argument holds water)

But does all this matter? Well, in a way, yes. BA.2.12.1 is almost twice as resistant to vaccinations compared to previous Omicron variants, which is why it has become so dominant. BA.4 and BA.5, though, are over 4 times as resistant, and so can be expected to lead to substantially more breakthrough infections in vaccinated (and even boosted) individuals, and re-infections of people who were previously infected with Omicron. These new variants are so different from previous ones that neither vaccinations nor previous infections in either vaccinated or unvaccinated people will help much.

So, yes, there will be a new spike in cases, possibly the worst ever (although we will probably never know just how bad it is because testing is almost non-existent these days).

And we're all fixating on Monekypox!