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.… 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…)

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.…

ONS infection survey tests 10,000s of random people each week, & gives a less precise, but broader & more current tracking of variants.… 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!

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More from @chrischirp

24 Mar
I've been looking at latest English data by age.

Cases in school age children are definitely going up while other age groups are flat or falling (slowly).

Some of this increase is undoubtedly because of mass lateral flow device testing rolled out to schools. But NOT all. 1/7
*Primary* school age kids are *not* getting routinely tested - tests are still symptom based. We see little change in cases week of 8th March but we start seeing quite rapid increase 14th March onwards.

This is consistent with increased spread since schools opened. 2/7
*Secondary* school age cases started going up around 8 March - when mass testing started.

But if it was *only* mass testing, then you'd expect cases to flatten the next week (15th March onwards), as similar number of LFDs done both weeks.

But cases keep going up. 3/7
Read 7 tweets
22 Mar
THREAD: Boris Johnson is basically talking bollocks about the 3rd wave in Europe inevitably coming here and he must know it.

It's cynical opportunism to blame any resurgence in England on the European wave. It is frankly absurd. Here's why: 1/6…
The Europe wave is not coming here *because we've already have it*.

Instead, it's taken two months for our "Kent" strain (B117) to spread across the EU and start a new wave there. OLD restrictions work on the OLD strain but NOT Kent. So cases go up as soon it is dominant. 2/6
If cases start steadily going up here it will be for one of two reasons (or both!):

1) As we found out in Dec, OLD mitigations don't work on B117. But opening up with OLD mitigations relying on vaccination to help keep cases down & chaotic mass testing (esp schools). 3/6
Read 7 tweets
20 Mar
Many headlines today about Europe's third wave, what it means for us and, in particular, international travel.…

Some thoughts about what it means... 1/11
Firstly, the current increases in Europe are because B117 (the Kent strain) has become dominant there - move than 70% in Denmark, NL, 50-70% in France, Belgium, Itlay, Germany & Austria. 2/11
As with us in Dec, they didn't act decisively to stop its spread - instead they've been in semi-restrictions (similar to our tier 3) - enough to bring *down* cases of old variant but not enough to stop B117.

B117 was only 5-10% in EU early Feb 3/11
Read 12 tweets
20 Mar

It's now 4 weeks since Scotland & Wales started a phased return to primary schools (secondary schools went back last week) & 2 weeks since all schools in England went back.

What is happening? 1/15
First let's look at Wales. They started sending young kids back to nursery and primary schools 22nd Feb. Older primary school kids & secondary school went back last week.

Wales publish new Covid incidents in schools - and (unsurprisingly) incidents are increasing. 2/15
Secondly, Scotland. There we have case data by age.

Primary school kids only get a test if they get symptoms. School staff can get tested without symptoms if they want. All positive cases from lateral flow device tests (LFDs) are PCR confirmed.

Testing has stayed flat. 3/15
Read 18 tweets
20 Mar
THREAD on vaccine effectiveness:

Public Health England released its updated report on real world effectiveness of Pfizer & AZ in England this week.…

I thought would be helpful to explain what they found...

TLDR: pretty good! 1/9
Firstly, both vaccines work almost equally well, so going to treat them as one in below.

Secondly, will focus on effect of ONE dose in OVER 80 year olds (most data!).

Effectiveness is higher in younger people and after second dose. 2/9
Right, so let's consider two lots of over 80s - 100,000 people in each group.

One group is unvaccinated and the other is more than two weeks out from their first dose.

(There seems very little real world protection for first two weeks after vaccination!!) 3/9
Read 10 tweets
17 Mar
THREAD on vaccination slowdown story:

TLDR: Don't panic!

Tonight a reduction is vaccine supply is being widely reported leading to a pause in rolling out vaccination to the under 50's...… 1/5
Basically, we gave about 11 million people their first dose mid Jan - mid Feb. They need their 2nd dose by end April.

We've been vaxxing about 2.5m/wk last few weeks, but let's say vax supply drops to about 2m/wk for April. Then we need ALL those doses to honour 2nd doses. 2/5
Once most of those are done, we can start rolling out vaccination to new people again (adults under 50) in May.

Assuming we can ramp up to 3.5m/wk from May, we can still offer everyone a 1st dose by mid July. 3/5
Read 6 tweets

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