NEW: latest update on B.1.617.2 in UK



First, today’s Sanger data on variants at local level. On the surface, this doesn’t look good. Cases of non-B.1.617.2 are in decline, but those red peaks are the variant sending overall rates climbing
To state the obvious: that pattern is not what we want to see, and if things keep going in that direction, we could see national cases rapidly climb again.

But there are a couple of reasons to pause before assuming we’re going to see those peaks steepen and proliferate.
First, the Sanger data is sequences with specimen date before May 8.

We’ve got more days of data since then. It’s not broken down by variant, but it can show us what’s happened to total cases in those areas since May 8.

Answer: growth rates have slowed, in some cases reversed
That’s also apparent in a plot of B.1.617.2 prevalence vs overall weekly growth.

The diagonal upward trend here is becoming less clear. Some areas where B.1.617.2 is though to be dominant are seeing cases fall. Many areas where little B.1.617.2 has been detected are seeing rises
It’s certainly very much possible that there *is* still a link between the two (which would suggest greater transmissibility of B.1.617.2).

A lot of local authorities have had very few cases sequenced, meaning we don’t really know how prevalent the variant is in many areas.
But between the slowdowns and reversals in B.1.617.2 hotspots, and the increasingly fuzzy relationship between its prevalence and overall growth, that link feels less clear today than it has done to date.
This would be in line with what some, including @arambaut @andrew_croxford @mugecevik have theorised, which is that the higher early growth rates seen from B.1.617.2 may be caused by other factors than an innate transmissibility advantage:
One possibility is that the contrast between very very low rates of the virus in early April, vs the sheer volume of cases imported from India, caused travel-linked clusters to have an outsized impact on overall rates.
Essentially, you have a scattering of clusters sparked by the introduction of B.1.617.2 from abroad. These are concentrated in highly vulnerable communities: low vaccination rates, dense living conditions etc, so they initially spread relatively efficiently within these areas.
After a couple of generations of transmission, they lose momentum. In some areas (perhaps Sefton) they burn out entirely and cases recede back towards their baseline level. In others, conditions are ripe for a longer initial burst, but then that gradually loses momentum.
This would initially look like a transmissibility advantage, but when you consider how low rates were in Bolton in early April (20 confirmed cases per day in a town of ~200,000 people), it’s arguable B.1.617.2 was never really "in competition" with B.1.1.7 in any meaningful sense
And as pointed out by @mugecevik, this pattern — imported variant causes spikes in prevalence that then peter out — is not new. Some of you may remember 20A:EU1 (originated in Spain) that arrived last summer to much fanfare but never took hold here
To be clear, the above is just one theory. It remains entirely possible B.1.617.2 is more transmissible and could fuel a UK resurgence.

But so far, that’s not happening. A brief rise in cases last week now appears as a small bump, possibly caused by bank holiday testing patterns
And here’s an update of case rates by age in some of the areas of concern, again showing that the rise has been concentrated among younger, less-vaccinated groups while cases among older groups remain at low levels.
So I’d continue to suggest that we all keep a very close eye on this, but I don’t feel more worried today than I was before.

And regardless, any prolonged rise in cases anywhere in the UK is worthy of investigation, regardless of the role B.1.617.2 may be playing.
Finally, I’d strongly encourage people to listen to what @kallmemeg and co at @PHE_uk have to say in their next variant update later this week, where we can also expect updated S-gene figures. Those technical reports are rapidly becoming indispensable…
And one addendum:

I think that in some cases, the focus on B.1617.2 is providing more heat than light.

What really matters is whether more people are getting sick or hospitalised, not the number or % of B.1.617.2 sequences.
If a new variant is what tips a country into a new, lethal wave, it’s important to spot it & to use that understanding to turn things around.

But at the moment it feels like there’s a lot of "B.1.617.2 numbers are up!" without reference to whether it’s causing things to worsen.

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More from @jburnmurdoch

16 May
Good, measured thread from @JamesWard73 as ever.

If B.1.617.2 does prove to be more transmissible, we may need to keep things like indoor masking and tests for entry to large events for a while beyond June 21.
My thoughts:
• No, that wouldn't mean "lockdown never ends". No, it wouldn't be curtailing freedom. It would be a very small compromise for a very large benefit
• As vaccination rates continue to climb further into the year, those few remaining measures could then be eased
• It's still entirely possible any transmissibility advantage will prove to be much smaller than some have estimated. In that event, June 21 plans can proceed as planned
Read 4 tweets
14 May
Here's the latest from @AnnaSophieGross and I on the Indian variant, digging into how serious a threat it is currently believed to pose…
One thing I think it's important to be clear about is that public health officials and epidemiologists are looking extremely closely at this stuff.
To the extent that policy has not followed one particular path or another, it's because the people looking at the evidence have yet to determine where it points. This is the scientific method, not complacency.
Read 7 tweets
14 May
NEW: this chart is important

It’s early days, but there are signs that the vaccines may be working against the Indian variant B.1.617.2

Resurgences in Bolton & Blackburn are so far confined to younger people. Cases remain low & flat among the mostly-vaccinated older population.
(We must also note that in the past, the higher levels of social mixing you typically see among younger people have led cases to rise among them first before climbing in the older groups, so vaccines are not the only thing that can cause this. We need this pattern to hold)
What about in India, where the variant originated and is believed to be dominant?

Age-stratified data on cases & deaths here is very patchy. But what little there is also hints at a vaccine effect: share of cases/deaths taken up by the elderly (the most vaccinated) is falling 📉
Read 14 tweets
12 May
NEW: is the Indian variant B.1.617.2 escaping the vaccines? @AnnaSophieGross, @AmyKazmin, @jyots43 and I investigate

Story here:…

And now time for a thread where I complain about persistent misreporting of breakthrough infections and vaccine escape:
First, the fact that a small portion of fully vaccinated people can still get infected is not news. That a tiny portion of fully vaccinated people *die* of Covid is not news.

Vaccines greatly reduce your risk of infection, transmission, illness & death. They do not eliminate it.
This is why it’s been so frustrating seeing tweets go viral for screenshotting vaccine trial results with "deaths: 0" in them.

In a trial of hundreds or a couple of thousand people, you may get zero deaths. In the real world (315m people now fully vaccinated) you don’t.
Read 18 tweets
7 May
NEW: time for a proper thread on B.1.617.2, the subtype of the Indian variant that has been moved to "variant of concern" today by Public Health England.

First, it’s clear case numbers from this lineage are growing faster than other imported variants have done in the UK.
Here’s the same thing on a logit scale (HT @trvrb), which makes it easier to compare growth rates.

As we can see, B.1.617.2 is on a fairly steady upward trajectory, which other variants failed to achieve.
So we know its trajectory looks different to the other imported variants, but that doesn’t tell us enough. We need a better benchmark: how does its growth compare to B.1.1.7 at the same stage of its emergence?

Remarkably similar, it turns out:
Read 19 tweets
5 May
Quick mini-thread on the Seychelles:

There has been a surge in cases in the last few days, but as we’ve often seen lately, when you dig beneath the surface this is consistent with the vaccines working as advertised.
• More than half of people in the Seychelles are fully vaccinated. The rest are mostly unvaccinated (very few with just one dose)
• But only one-third of active cases there have been vaccinated
• So that means the unvaccinated are roughly twice as likely as the vaccinated to have been infected, which is completely in-line with the 50% efficacy reported for Sinovac (the main vaccine in use in the Seychelles)
Read 6 tweets

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