1. LONG THREAD (25+ tweets sorry) of my somewhat depairing musings on Covid.

Where we are, how we got here, why I'm sad about it.
2. So I downloaded latest Sanger data on variants for England today after 2 weeks away.

Delta (B.1.617.2) is now at well over 90% of all sequence cases in Englandand Alpha (B.1.1.7, prev "Kent") is dying out.
3. Dominant in every region - some took longer to get there but all are at or over 90% now.
4. And it made me think about the last few months, and the next variant.

Back in April I wrote a long thread about variants and highlighted B.1.617's (as it was then) rapid rise - from 0.2% to 1% of all cases.
5. I argued that while we didn't have definitive proof that it was more transmissible or more vax resistant than Alpha variant there was reason to be worried from situation and early evidence in India.
6. *and* I said that because we sequence much more than India (and most other countries) the first definitive evidence of either would probably come from the UK - but almost certainly after it was too late to contain it.

7. I said it was doubling every week and that - although very early days - it could be dominant by the end of June. In fact, the doubling rate was saying mid May but even I didn't believe it and so pushed it back to June in my tweet.

8. In fact, cross over to Delta becoming dominant in England *was* in mid May.
9. I then laid out three possible scenarios for Delta compared to Alpha:

1) that it was more transmissible than Alpha
2) that it was more transmissible and more vax resistant
3) that it was more transmissible and a LOT more vax resistant
10. I said that the 3rd scenario was the least likely, but had v serious consequences. All the scenarios were worse than keeping Alpha as our dominant variant - the devil we knew.

We are in scenario 2. Our vax programme has sped up which has helped but not enough to stop a wave
11. I urged the UK to add India to the red list (tweet 17), to cancel the PM trip to Delhi and to stamp down on Delta instead of waiting for proof.

India did go on red list 23rd April, Delhi trip was cancelled but few measures were taken domestically to stop its growth.
12 Public Health England first had high confidence in Delta being "at least as transmissible" as Alpha in 13 May risk assessment.

By 3 June PHE had high confidence that it was lot more transmissible than Alpha *and* had more vax escape.

Tho v quick, solid proof took *6 wks*
13. I basically then did at least a thread a week since April all along the lines of "guys, it's still doubling we should be doing something". e.g. here is one from mid-May where latest data (always 1-2 weeks behind) showed it was 30% of cases in England.

14. People were still coming up with possible reasons why it wasn't that bad. The govt tried to blame vax hesitancy.

Me & others were accused of being alarmist, of not understanding the data complexities, of talking down vaccines.

We argued for precautionary principle.
15. Me and others (esp @dgurdasani1 ) also highlighted the need to make schools safer - cases were highest in school age children (unsurprisingly when you have large unvaxxed populations mixing every day!).

16. We were told we were being anti education, alarmist, misunderstanding the data.

Recent REACT study showed large growth in school-age kids.

You keep kids in school best by stopping covid spreading in their communities and by making schools safer.
17. In mid May, overall cases were flat, hospitalisations declining, deaths very low.

SAGE Spi-M's models published 13 May showing how bad a more transmissible or more vax resistant variant could be were ignored.

"everything is fine" people said. Step 3 of roadmap went ahead.
18. But cases were flat because the decline in Alpha was offsetting the increase in Delta. Once Delta became dominant, cases started going up. Then hospitalisations.

By end of May, Govt still saying "no need to delay roadmap" - I thought this was crazy.
19. They did delay it by 4 weeks in the end (right decision). They've accelerated vax roll out (right decision).

We're now told that the NHS won't be "overwhelmed" this summer - that it won't get to Jan '21 or April '20 peak so all good, no need to worry.

I disagree so much.
20. We have been lucky that vaccines work against Delta sufficiently to be effective against severe disease - avoiding worst case scenarios.

But NHS is already overloaded - we should be avoiding extra burden. Even a third Apr 2020 peak is still bad!

21. Many people who have been hospitalised with Covid struggle for months with ongoing problems - even younger adults.

We should be avoiding covid hospitalisation to protect people as well as the NHS!



22. Plus we know that Covid can cause long term symptoms in many who aren't hospitalised - inc 5-10% of children & 10-20% of young adults.

There is increasing evidence that Covid can cause memory / cognitive issues ("brain fog" and fatigue).

23. And every case is a new opportunity for further mutation - both here & abroad (e.g. recent new Lambda variant in S America).

How many chances do we want to give covid to overcome our vaccines? They *are* the way out - we should be protecting them!

24. So no, I think it's wrong and irresponsible of the govt and others to be fine with thousands - potentially soon tens of thousands - of new cases a day here just because we likely won't bring the NHS to near collapse again.
25. We should be trying to get cases *down* by supporting & protecting vax program by adding public health measures like supported isolation, support for ventilation, masks in schools, better communication.

AND tightening border measures to prevent importation of new variants.
26. I can't quite believe that govt is not doing any of this. That many people have given up even asking for these measures.

I know it's frustrating & exhausting to keep asking for the same basic proven measures and being ignored.

But they're still the right thing to do.
27. Israel - a highly vaxxed country with hardly any covid - supported its vax roll out with many public health measures.

A recent outbreak of Delta variant in two schools has triggered public health action and consideration of reinstating mask wearing.
28. And what I really really want is that the *next* time we see a variant doubling every week - outcompeting the dominant strain (now Delta) - that we take it seriously.

That we learn from other countries (if it's emerged their first).
29. These 2 months has felt like an exemplary cateloguing of Delta's victory by PHE, COG, Sanger etc.
When early doubling times are only a week, we can't wait for solid proof.
For the *next* variant, we need to *do* something when it's less than 5% of all cases. /END
this should say a "third of" April 2020 peak (about 1000 admissions a day)

• • •

Missing some Tweet in this thread? You can try to force a refresh

Keep Current with Prof. Christina Pagel

Prof. Christina Pagel Profile picture

Stay in touch and get notified when new unrolls are available from this author!

Read all threads

This Thread may be Removed Anytime!


Twitter may remove this content at anytime! Save it as PDF for later use!

Try unrolling a thread yourself!

how to unroll video
  1. Follow @ThreadReaderApp to mention us!

  2. From a Twitter thread mention us with a keyword "unroll"
@threadreaderapp unroll

Practice here first or read more on our help page!

More from @chrischirp

15 Jun
THREAD on England short term Covid outlook:

Thread on some of the implications of latest SAGE SPI-M models about English roadmap, step 4 & Delta.

TLDR: medium term v uncertain but in short term expect hospital admissions to keep rising.
2. They point out that current increase in cases will only stop if at least one of below happens:
1) people change their behaviour
2) govt changes policy (more restrictions and/or more public health interventions)
3) enough immunity is built up (through vax or infection)
3. Govt is basically doing 3 -> trying to get as many people fully vaxxed as fast as possible & tolerating high infections in younger people in the meantime.

It also delayed step 4 deciding (wisely!) that throwing petrol onto the fire wasn't a good idea.
Read 23 tweets
15 Jun
SHORT THREAD on the US & Covid:

The US has made rapid progress in vaccinating its population, and supply is not an issue.

But demand has steadily fallen since April. The UK meanwhile has kept up a more constant rate of vaccination - we've not exhausted our demand yet! 1/5
And this is translating into population coverage.

The UK is ahead of the US now in both first doses *and* people fully vaccinated (even with our longer interval between doses) - and our coverage is increasing faster than the US. 2/5
The US has more vaccine hesistancy than the UK and this is now making itself felt - with particularly Republican states having lower rates of vaccine uptake.

States are trying to incentivise vaccination through prizes, food, beer...

newsweek.com/states-sending… 3/5
Read 5 tweets
4 Jun
Here are cases in 4 regions - all showing highest rates in secondary school children - and increasing and moving up to adults over time too.
Here is data from PHE yesterday showing the the *top activity* by far for new confirmed cases was a child in school.
Data from a couple of weeks ago showing the incredibly high rates of infection in secondary school age children in variant hotspots - higher than their equally unvaccinated older counterparts.
Read 5 tweets
31 May
THREAD Some back of the envelope examples about how things could get difficult even with vaccination.

This is *no* replacement for the proper SAGE Spi-M models but gives you the idea. (11 tweets)
Between Oct & early Jan there were about 2.3 million confirmed cases of Covid, 135K hospital admissions & 28K deaths. Hardly anyone was vaccinated.

If we had a similar situation now but WITH vaccination then cases would be lower & admissions (~25K) & deaths (~3K) MUCH lower.
I think this is what most people have in their minds when they don't believe it could get bad this summer.

And if cases on same or lower scale then that is true - vaccination (particularly of vulnerable) protects us & the NHS.
Read 12 tweets
31 May
THREAD latest on B.1.617.2 variant in England:

B.1.617.2 (1st discovered in India) is now dominant in England. Here is a thread summarising latest PHE report and Sanger local data.

TLDR: it is NOT good news. 1/7
Firstly, B.1.617.2 is now dominant in England.

This data excludes traveller data and surge testing as much as possible.

In absolute numbers, B.1.617.2 ("India") overtook B.1.1.7 ("Kent") about 15 May.
PHE report estimates a few days earlier. 2/7
B.1.617.2 is now dominant in almost every region of England.

Even NE and Yorks are catching up very fast. 3/7
Read 9 tweets
30 May
THREAD on variants & borders:

SAGE warned in Jan that a red list border policy "geographically targeted travel band" was unlikely to keep variants out.

This is because we don't know in advance where the *next* concerning variant is coming from.

UK spent Jan & Feb making red list policy about variants discovered in Brazil & S Africa. But wasn't paying any attention to the situation, in say, S Asia.

SAGE also said that red list policy works best if implemented very quickly & if in countries with low UK traffic. 2/11
India has strong travel links with the UK and started its awful surge in March. By 24th March, the Indian govt was warning about a new fast spreading variant.

UK waited until 23rd April before India was added to red list - and it did work to reduce travel. But too late. 3/11
Read 11 tweets

Did Thread Reader help you today?

Support us! We are indie developers!

This site is made by just two indie developers on a laptop doing marketing, support and development! Read more about the story.

Become a Premium Member ($3/month or $30/year) and get exclusive features!

Become Premium

Too expensive? Make a small donation by buying us coffee ($5) or help with server cost ($10)

Donate via Paypal Become our Patreon

Thank you for your support!

Follow Us on Twitter!