Thread by @chrischirp

THREAD on VARIANTS, VACCINES & POTENTIAL FUTURES:

I’ve been looking at data on sequenced variants. I’ve also been thinking about our vax programme & India.

TLDR: the Indian variant needs to trigger surge testing in England. And India needs to be on red list. 1/23

Some dates: while over 60% of adults have had 1 dose of vax, we've got another ~15 weeks before *all* adults could have immunity from at least 1 dose.

And another 20+ weeks before all adults could be fully vaxxed. And we don't yet know what uptake will be in younger adults. 2/23

So what can variants do while we are vaxxing people?

We already know that B117 can infect some partially vaccinated people and (far far) fewer but still some fully vaccinated. edition.cnn.com/2021/04/14/hea… 3/23

I’m concentrating on 5 variants in England: our dominant B117 (“Kent”) variant, B1351 (“S Africa”), B1525, P1 (“Brazil”) & B1617 (“India”).

The Sun has a good graphic explaining different variants – I’ve highlighted the 5 I'm looking at in pink.
thesun.co.uk/news/14666288/… 4/23

The UK Covid genetics consortium (COG) have sequenced about 10%+ of cases a week chosen to be representative. Now they sequence up to 20,000 +ve cases a week.

With current numbers, this means they are sequencing *most* cases (much more than 10%).
cogconsortium.uk 5/13

This chart shows the cumulative number of sequenced cases for the 5 variants.

Our B117 (Kent) variant grew fast between Sept & Xmas before being controlled by Jan lockdown.

The fastest growing new variant - esp as it started during lockdown - is the Indian one (B1617). 6/23

I've now looked at just the 4 new variants as a % of overall cases.

SA (B1351) has been kept to small numbers by combo of lockdown & surge testing. It started increasing after schools opened. Most recent spike might be the big S London cluster & associated surge testing. 7/23

SA is thought to be bit less infectious than B117 (good for us) but can infect some vaccinated people although no indication that it makes them very sick. But it is worrying & warrants the surge testing and close tracking. 8/23

B1525 and P1 have struggled to get a foothold thankfully - especially P1 (Brazil) which is causing havoc in S. America and in British Columbia in Canada.

theguardian.com/world/2021/apr…

9/23

However (showing same plot again), B1617 (India) has gone from under 0.2% to over 1% of cases in *two* weeks.

It's doubling in number every week - similar to B117 back when it started growing. But B1617 is doing it under much tigher restrictions & more vaxxed people. 10/23

Because B1617 ("India") is a "variant under investigation" it does NOT trigger surge testing or forensic contact tracing.

This is cos there is no definitive proof that it is either more infectious or better at immune escape than B117 (Kent). BUT here's the problem 11/23

We know that it is dominant in some (but not all) of India, going from ~20% to ~60% of cases in Maharashtra state in a few wks.

This article digs a bit more into what is worrying about B1617 science.thewire.in/health/sars-co…

We def know that India is going through a massive surge. 12/23

India sequences fewer than 1% of cases & many who have had covid never got (or get) a test.

Only 8% of its population have had 1 dose of vaccine.

So definitive evidence of either more infectiousness OR infecting people who've had covid or a vax is likely to take a while 13/23

In fact, because *we* are very good at sequencing, we might be the first country to provide such definitive evidence.

But by the time we do, B1617 is likely to be quite widespread and it might be too late to contain it. 14/23

Note that what follows is based on v low overall numbers and so the estimates of growth rate are v v uncertain.

That said, it is doubling every week or so right now - similar to B117 when it first took off. 15/23

At current rate of growth, we could be seeing 1000 B1617 cases a week in 4-5 weeks. Still not massive - but v hard to contain without more restrictions.

It could be dominant by end June - 10-12 weeks away.

It depends on what is driving its growth. 16/23

If many of our cases are *imported* (implied by Sue Hopkins today - bbc.co.uk/news/uk-567927…), then its growth in India could be causing the growth here.

BUT then India should *def* be on the red list! As highlighted in this flight to Singapore:

https://twitter.com/KarenGrepin/status/1383785013548777475?s=20

17/23

If it is more infectious than our B117 but susceptible to vaccines then B1617 will likely cause us (maybe big) problems (basically a worse case of the SAGE Spi-M models)
assets.publishing.service.gov.uk/government/upl…

but it is self limiting - by Autumn almost all adults could be fully vaxxed. 18/23

Note: If B1617 is suscpetible to vaccines, then as we vaccinate more & more people this will limit its growth - but this might be offset by the extent and speed to which we open up and more people mix - at least over the next 8-10 weeks. 19/23

So finally - worst case scenario - if B1617 can infect vaccinated people, it could be much worse.

If vaxxed people can pass it on more but not get too sick, it will mean more unvaxxed people getting sick this summer (cos it can spread through more people). 20/23

If B1617 can escape immunity more completely (better than S African variant), then it cld cause severe illness even in those who have been partially or fully vaxxed.

That means our whole vax programme is damaged until booster vax available. It means new lockdowns likely. 21/23

Now this last scenario is definitely the *least* likely - but it's not impossible.

And letting B1617 spread (potentially alongside the SA or other variants) also risks new, potentially more dangerous, variants emerging. 22/23

We are (rightly) treating P1 (Brazil) and B1351 (SA) variants as real threats to our vaccination programme.

We must treat B1617 as a threat too & start surge testing it here and *stop* new importations from abroad.

Waiting for proof might be waiting too long. 23/23

and PS: Boris Johnson should NOT be going to Delhi in a few weeks!

finance.yahoo.com/news/1-india-u…

PPS last week it was reported there were 77 cases of B1617 in the UK. The latest COG figures now show *135* cases. 115 of them in the last 4 weeks.

And this

https://twitter.com/fascinatorfun/status/1383910462878744578?s=19