Thread by @dgurdasani1

UKHSA tech report out - TL;DR:
-BA.2 now represents >80% of omicron in England
-Growth rate 80% greater relative to BA.1 per wk
- regional growth seems to correlate with BA.2 frequency
-?lab reports indicating that BA.1 infection may lead to lower neutralisation against BA.2
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BA.2 does not produce the spike gene failure (SGTF) on TaqPath PCR tests that BA.1 did, so it can be detected on some routine PCR tests. Looking at this 'SGTP' signature, it looks like 83% of cases are BA.2. This won't be fully representative of England but in the ballpark.

There are regional differences - which may at least partly explain the differences in prevalence and rises of cases in different regions. Highest in London, and the SE and EoE south, and lowest in the North.

The frequency of BA.2 in regions seem to correlate with case rates as per the UKHSA surveillance report (likely to be underestimates) and the ONS report that came out today. The timing and geographical correlation suggests to me that case rises are linked to BA.2 rise.

So what is the BA.2 growth advantage?
It appears to be growing 80% faster than BA.1 per week. That's not trivial at all.

This growth rate would translate to 30-40% higher R, depending on serial interval (time it takes from one person to infect the next).
Looking at household contact data, it appears to have a 30% higher secondary attack rate (proportion of contacts infected) compared to BA.1

Increased growth rate could result from increased transmissibility or escape, or both? What is it for BA.2?
Hard to know. The report refers to 2 studies suggesting possibly neutralisation of BA.2 among those infected with BA.1. But one showing infection & boosters may protect.

Looking at viral loads- these seem similar between BA.1 and BA.2 for the most part, except possibly small differences in the first 2 days of symptoms when viral loads for BA.2 may be slightly higher (Ct levels very slightly lower).

Severity (likelihood of hospitalisation once infected) appears to be similar for BA.2 compared with BA.1, but worth remembering that higher growth and more cases itself can lead to more hospitalisations, even if each infection isn't more severe.

While we talk about variants as if they are static entities, BA.2 is continuing to evolve & likely adapt, as will happen as transmission continues and provides more opportunities for favourable mutations to emerge. This is happening all the time with all variants as they spread.

I'd love to be wrong but I seriously doubt that BA.2 will be the last variant we encounter. It's worth remembering BA.2 is vastly divergent from BA.1 even if they do come under the omicron umbrella. I'm not sure why it hasn't yet been designated a VOC.

Overall, this builds a concerning picture. Given the huge growth advantage omicron had over delta, another 80% advantage on top of this or 30-40% increase in R is quite substantial. We're seeing very high transmission in Northern Ireland as well where BA.2 became dominant first.

To me it looks like BA.2 rises are partly driving the current surge - likely made worse by ending self-isolation mandates and contact tracing. I'd really like to see data on re-infections to understand the level of escape with BA.2 especially for those infected with BA.1

While the narrative may be the pandemic is over and manageable now, we're seeing fairly rapid adaptation and emergence of variants very quickly with growth advantages over previous ones. This does not bode well.

With each variant, suppression of the virus becomes harder. Even former elimination zones have hugely struggled to contain omicron (see S. Korea, China, HK, Japan, NZ). Suppression now isn't the same as two years ago. I wish we'd taken it more seriously then.

In two years we've seen this virus go from an R0 of ~2.5-3 to ~6 for delta to whatever it is now with BA.2. Hard to know given part of its advantage came from escape & it's smaller serial interval. It's evaded vaccines reducing protection further and further with each variant.

With every iteration, this virus becomes fitter - more able to transmit, more able to evade. There is a huge space for adaptation, and who know where it'll go next? What worries me is that even as SARS-CoV-2 has shown us what it can do, we've just denied what it can do even more.

Yes, vaccines have been a huge game changer, but so has every single new variant that's come along. And we're not even trying to reduce adaptation - rather we're giving it lots of space and opportunity to mutate. It's clear vaccines can't keep up with rate of adaptation.

And long COVID is still very much present, and numbers have increased even as the impact of omicron just begins to be felt. And a large proportion of our population isn't even boosted, and millions aren't even vaccinated with one dose (children!).

One can hope that new variants won't be more severe, and vaccines will be able to keep up if given frequently enough. But what is the long term plan? Surely it can't be to pretend that it's all gone away?

Full report here:
assets.publishing.service.gov.uk/government/upl…