Thread by @chrischirp

THREAD on concerning variants in England:

Some signs that they are spreading - slowly and from very low numbers - but spreading nonetheless.

Why I think this and what it means - let's dive in: 1/13

The Kent strain (B117) has been over 90% of cases in England since mid-Jan. It is 30-50% more transmissible than the old Covid strain and so came to dominate over about 2 months.

All existing vaccines work brilliantly against B117. 2/13

Vaccines work less well against some other Covid strains.

Particularly concerning are the South Africa (B1351) and Brazil (P1) strains.

Public Health England is tracking these (& similar) variants and doing surge testing to try to contain them.

gov.uk/guidance/surge… 3/13

This plus lockdown has made it hard for these variants to spread in England - a good thing.

*But* some are holding their own (SA, P1) and some spreading (B1525 itv.com/news/2021-02-1…)

See this chart from @Dr_D_Robertson, annotated by me. 4/13

Those nums are from PHE sequencing a sample of cases. Estimates are uncertain & weeks old. gov.uk/government/pub…

ONS infection survey tests 10,000s of random people each week, & gives a less precise, but broader & more current tracking of variants.
ons.gov.uk/peoplepopulati… 5/13

Our Kent strain (B117) causes what's called an "S dropout" in PCR tests (SGTF) while the old variant doesn't. This provided an easy way to track its growth without needing to sequence.

By mid-Jan, Nervtag reported that SGTF cases (ie B117) were over 90% of cases. 6/13

But the *new* variants of concern (SA, Brazil, our home grown SA copycats) do NOT have an "S dropout" - they look like the old variant on PCR tests.

This matters because we can calculate the proportion of cases that do NOT have an "S dropout" from the ONS data. 7/13

This prop'n was <5% since Feb but has now started to grow - i.e. gaining ground against the Kent strain.

It is unlikely that the old variant is gaining ground because we know it's less transmissible.

It's possible that this increase is the new variants gaining ground. 8/13

Numbers are still very low. Likely that new variants like SA are still less than 1-2% of all cases in England.

BUT I will say that's where Europe was with Kent at Xmas and now Kent is dominant there. 9/13

Because Kent is more transmissible than old variant, it's harder for new variants to gain ground against it.

But *if* they can more easily infect people who have had Covid or who've had the vax (esp 1 dose) then they have many more people they can infect & gain ground. 10/13

So even though current vaccines will hopefully prevent severe illness & death (we don't know, but likely), their spread nonetheless presents a much higher risk of a new bad wave in England than if we could stamp them out. 11/13

This is all a bit speculative - but I do think the ONS infection survey data is concerning and we have seen repeatedly this last year how small problems can become very big problems if we ignore them & hope for the best. 12/13

What's needed? No rushing the roadmap, slowing opening if we see cases increase a lot, fixing local contact tracing, supporting isolation, testing all contacts of cases, better ventilation of indoors...

and sequencing as much as we can! 13/13

Ps we also need *rapid* sequencing!