BA2 Omicron Variant is Worth Discussing

BA2 is outcompeting Original Omicron in Denmark

This post offers some news on what will be very important in the coming months. Like many other things, Omicron BA.2 is not on most busy people’s radar, but soon will be the only thing that people talk about. I made a decision to start writing about Omicron very early in the game, and want to write about BA.2 also to keep my readers abreast.

Denmark, which was weeks ahead of the UK and US with its Omicron outbreak. Unlike the US and the UK, however, Denmark’s infections are not decreasing, but conversely are shooting up to the sky.

The slowdown in Denmark that appeared around Jan 5-8, was quickly overtaken by a rapid rise that offers no signs of slowing down. The same thing happened in France 5 days later. A small drop, quickly overridden by another crazy and relentless case growth.

On a cases-per-million-people, Denmark and France are 2.5 times higher than the US and 3 times higher than the UK.

What is going on? A new “variant”, called somewhat incorrectly “Omicron BA.2”, appeared around Christmas and is out-competing, out-infecting, and overall somehow generating even more cases than the original Omicron.

In Denmark, Omicron BA2 is already over 50% of all cases, and rising.

The cases in the UK, which encouragingly were dropping nicely, actually reversed in the recent days and are rising again.

What is it?

BA.2 is considered a sub-lineage of original Omicron (which is now referred to as Omicron BA.1), however these two genetic variants seem to have diverged months BEFORE Omicron actually appeared.

BA.2 has 28 more mutations, than Omicron, with no intermediate variants seen between them.

This is certainly a genetic oddity, just as Omicron is a genetic oddity with the ancestor that disappeared 1.5 years before Omicron appeared. Both of these oddities raise a possibility that both Omicron BA.1 and BA.2 do not have a natural origin. I said that Omicron (now known as BA.1) may be lab-made on December 2.

URGENT -- Omicron "variant" likely to be man-made

As they diverged before either of them was introduced, calling BA.2 a sub-variant of Omicron may be factually and genealogically incorrect and their relationship may be more sibling-like than parent-like.

The genetic distance between BA2 and BA1 is greated than between either of them, and Delta or Alpha.

Interestingly enough, the original Omicron BA.1 has an interesting genetic signature, where spike protein codons 69-70 are missing, thus giving all PCR tests a “Spike Gene Target Failure”, or SGTF. PCR tests three genetic sequences (Spike, Nucleocapsid and Orf1ab), thus the PCR test is positive for Nucleocapsid and Orf1ab but negative for Spike gene. This is a quick and dirty way to tell that the patient has Omicron using a TaqPath PCR platform.

BA.2 does NOT have that 69-70 deletion and thus tests positive on all three PCR subtests, just as all previous variants of Covid did. So on a PCR test, it looks just like Wuhan strain, Delta or Alpha — positive on all three sub-tests.

Is BA.2 Worse than Omicron BA.1?

We do not know this yet. There is literally no data about it. I looked far and wide. The explosion of BA.2 in Denmark and France is literally less than a week old, so not even hospitalization data is yet available, as people are hospitalized a week or two after they get sick.

Denmark’s Serum Institute says that BA.2 may be about as severe as BA.1, but they also admit that it is very preliminary.

Reinfections with BA.2

The most disturbing issue here is that even by the time before BA.2 took off in Denmark a week ago, Denmark was likely running out of Covid-naive, uninfected people. What this means is that possibly, BA2 is especially good at REINFECTING Danes and Frenchmen. Not sure if the vaccinated people are more susceptible to reinfection, but it is possible and always seemed to be the case even before Omicron.

This article from Denmark features Danish researcher Anders Fomsgaard warns that BA.2 may provide a greater risk of reinfection of people who just had Omicron BA.1. It makes sense epidemiologically, because it agrees with the graphs of cases.

What this means, if true, is that people who just had Omicron might have BA2 again. So they have a “mild illness”, then another “mild illness” on top of that, possibly at least doubling their risk of severe outcomes just because of double disease exposure in such a short period of time. (kind of like Russian Roulette done twice in a row)

This could become the reinfected’s “monthly covid” or some such, which is obviously detrimental.

This “Thailand Medical” article features a French scientist Dr Antoine Flahaut, also mentioning seeing cases of people getting reinfected in a short period of time.

Hospitalizations in Denmark are not encouraging

What to read

• Denmark Serum Institute

• Andrew Lover Twitter

• Gabriel Hebert Twitter

• Thailand Medical — this guy has a sensationalist writing style but is informed of latest developments

Thanks to my astute reader Claus L for nudging me to write about BA2, which interested me for a while.

Our astute reader Clarisse also clarified that Covid Alpha caused SGTF as well.