Not only do we are we continuing to see rises of the so-called South Africa variant, despite efforts to contain it, we also seem to have imported the double mutant from India - with *77* cases identified so far. When were these identified? And why isn't the govt acting?
Have all these 77 new variants have been identified within the past week? And what is the extent of spread within the community?
Worth keeping in mind that despite knowledge of the double mutant spreading, India has not been on the red list for travel.
What are the features of this new variant?
It has the E484Q mutation (at the same position as the E484K mutation in the SA and Manaus variants), which is of concern with respect to possible escape from vaccines, and natural immunity against previous variants.
It also has the L452R mutation in the part of the spike protein that binds the ACE-2 receptor needed for entry on human cells that's also been detected in the 'California' variant. This has shown to be resistant to monoclonal neutralising antibodies:…
L452R has been studied as part of the 'California variant' (B.1.427/429) with studies suggesting increased escape from antibodies, and cellular immunity, as well as increased infectivity. L452R has also been shown to increase binding affinity with ACE-2…
The California variant, first arose in November and gained dominance across all sequences in the region by March, suggesting that it outcompeted other variants in the background, possibly due to a selection advantage- whether this is due to L452R is not known.
Notable, the California variant did not have the E484Q mutation that's arisen in the so-called Indian variant. This is likely to have similar properties to the E484K mutation found in both the Manaus and South-Africa variant, and in some sub-lineages of B.1.1.7 (Kent variant).
This variant has been identified in several parts of India, and is prevalent in Maharashtra, and has been detected in at least 10 other states. The Ministry of Health has suggested that it may be associated with rapid exponential growth of the pandemic that's being seen.
We need to wait for modelling and surveillance results to assess the rapidity of spread of the variant, and the correlation of growth rate with this to better understand if the variant is associated with increased transmissibility, and/or escape.
So where are we with variants of concern within the UK? We have all major VOCs identified across the world within the UK now, with both B.1.351 (South Africa variant) and P.1 (Manaus) showing increases in number wk on wk. We also have 8 variants under investigation.
The growth in no.s is not simply due to more cases identified during travel. This is due to spread within the community- growth rates shown within the community below from the recent PHE report on this - which is based on Pillar 2 testing from the community.
Looking by mutation rather than variant are also seeing increases in E484K, which is a mutation that has been associated with increases escape from natural and vaccine immune responses. And reduced efficacy at least with mild/moderate disease with several vaccines for B.1.351.
While the absolute numbers of these variants are growing week on week, the B117 variant is still at ~99% frequency in almost all regions, so these are still relatively in small numbers compared with B117, which thankfully our vaccines are highly effective against.
I remember a while ago, JVT claimed during a press briefing that other variants were unlikely to out-compete B117 given the high transmissibility of the variant. Is this something we can say with confidence?
Unfortunately not- we are seeing B.1.351 and P.1 spread in other regions where B.1.1.7 is dominant or gaining dominance. We're seeing growth alongside B117 in the Netherlands which has good genomics surveillance, and in BC.

Is this surprising?
Recent work on P.1 suggests it may be ~2x (1.7-2.4) more transmissible than previous variants & escapes between 20-50% of immunity from previous infection. While there is uncertainty around estimates, it's possible it may be more transmissible than B117.
The only way to directly assess this is to look at dynamics of spread in areas where several strains are prevalent, and see how they spread relative to each other. It's also worth remembering that relative spread doesn't just depend on transmissibility.
The selection landscape for variants may change as vaccination proceeds, given some of these may escape vaccines better than others. Even if vaccines provide good protection against severe disease against infection is likely to be reduced with some VOCs (e.g. B.1.351, P.1)
This may mean that the environment for new variants may shift to favour ones that provide a higher degree of escape against vaccines- there are early signs from relatively small studies that this may already be happening in some regions.
It's very clear that new variants are a risk - to vaccine effectiveness & pandemic control. Let's remember the shape of the pandemic changed when B117 arose within the UK, and spread to much of Europe & the US, which is now seeing another wave of the pandemic as a result.
Was this inevitable?
No- there are countries who have managed to not import these variants. Australia, and NZ have both had cases of B117 entering the country, but have contained these with a combination of strict border restrictions/quarantine & rapid surveillance & response.
Could we have done this?
Yes- but we didn't. Our border policy has made absolutely no sense from an evidence based perspective. Despite the fact that VOCs are now widespread across the world, we only mandate managed quarantine for a small list of countries - only for 10 days
India wasn't on this list despite a new concerning variant having been identified there. People coming from all other countries can test & release at 5 days - this is clearly not based in any evidence, as we know that people can test negative at this point despite being exposed.
We also have >50 exemptions from quarantine, which means many people travelling don't have to quarantine at all.
This is in stark contrast to countries like NZ & Australia that have managed quarantine for 14 days at designated facilities. A system that clearly has worked.
So what do we need to do now?
We're hearing concerning reports of surge testing in parts of London to get on top of the spread of the so-called SA variant- we've been trying to contain this since December, but haven't been able to despite all efforts.
It's clear that prevention is the best strategy here. What we need is a multi-pronged response:
1. Evidence-based comprehensive border policy
2. Urgently contain transmission- especially in areas of community spread of VOCs
3. Fix test, trace & isolate
*alongside* surge testing
To me, new variants provide some of the strongest arguments for elimination.
Our strategy so far has been focusing on vaccines as the primary way out of this, hoping desperately that these will keep up with virus adaptation. If the virus adapts, we will adapt vaccines.
This is a risky strategy. There's absolutely no reason to be taking this risk, when we can *prevent* import of variants. We can *prevent* virus adaptation by containing transmission - something that doesn't appear to be in our long-term plan at all.
This is also the only way to ensure that virus adaptation doesn't outpace vaccine updates. We also need to remember that there are properties of new variants that we don't understand- & won't understand until a while later. e.g. expansion of the host repertoire with some VOCs
The implications of these variants may only become clear much later (e.g. increased fatality with B117 which was only understood a while after it arose)- but just because we don't know, doesn't mean these are risks that are small, or worth taking.
So far, the govt strategy of blind optimism hasn't worked. We didn't think this virus would adapt quickly. It did. When it did, we didn't think it would adapt to become more fatal. It did.
We didn't think it would escape immune responses. It did.
We thought we could contain spread with surveillance and surge testing if we let variants enter (so we never bothered with preventing entry) - we couldn't.
We thought other variants wouldn't grow alongside B117- but they are.
We've consistently looked at uncertainty and assumed the best outcome. We've consistently been wrong.

It's not alarmist to be cautious. In the face of uncertainty, when the losses can be large, the best strategy is to reduce risk as far as possible.

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More from @dgurdasani1

10 Apr
@jburnmurdoch Absolutely, and I'm not saying the declines are down to Easter- I've linked you to the thread by @ChrisGiles_ that shows that recent estimates from the ONS always show plateaus and declines. It's the trends before recent times that are reliable- and quite clear in direction.
@jburnmurdoch @ChrisGiles_ What I'm saying here is that one cannot conclude at all that school openings did not result in a surge in cases, as the data support that they did- both in Scotland (where schools have been open longer) & in England. The REACT-1 data also support this.

@jburnmurdoch @ChrisGiles_ It's very hard to explain the rises in cases in England & Scotland in recent times after school openings, given the trend was consistently downward prior to this, with very low infection rates in children (you can see this in the previous ONS data).
Read 4 tweets
10 Apr
If anyone at this point things that school openings haven't resulted in a surge in cases among school-age children, I'd urge them to look at the latest ONS data. There's been an *8-fold* increase in positivity in Scotland among children since schools opened on the 22nd Feb.
Recent trends less reliable, so need to be interpreted with caution, as outlined. We should expect to see positivity declines in line with Easter break - but should prepare for surges again once schools-re-open. Urgent need for mitigations in both primary & 2ndary schools.
Thanks to @BibblerBrizzy for pointing out that Easter break in Scotland started on the 2nd April and *not* on 26th March, as indicated in the graph for Scotland (sorry about the error - the 26th was the start for much of England).
Read 4 tweets
10 Apr
Just worth clarifying that this isn't correct. Both the ONS & REACT-1 data show clear rises in infection rates among school age children- both in England & Scotland since schools opened- with highest prevalence among these age groups. Expect to see plateauing over Easter break.
We need to look at the raw ONS data- which I've plotted here. Even in the extremely short period schools were open in England after 8th March (later for some secondaries), we see rather rapid rises among school age groups. Schools recently closed for Easter.
Looking at Scotland data, where schools have been open for longer (P1-3 opened on 22nd Feb) - positivity among children has increased from 0.10% to 0.80% - 8 fold increase. It's impossible to look at this and conclude that school openings have not resulted in a rise in cases.
Read 4 tweets
7 Apr
Important study out from @TheLancetPsych on neurological & psychiatric manifestations across 236,379 people with 6 months follow up after COVID-19 in the US- examined using electronic health records.

What did it find?…
Important to note first that the study only included survivors- so people who had survived for at least 6 months following infection were included.

Several neurological and psychiatric outcomes were examined in electronic health record data from health-care facilities.
Healthcare facilities data were collected from including primary care facilities, hospitals, specialist units, ICUs. It's unclear from the study how representative these are of infection across the general population (i.e. who would have ended up in the study if infected)
Read 12 tweets
7 Apr
It's been rather disconcerting to have had false claims made about my conduct by someone I've never engaged with directly. I wrote about this earlier & bizarrely, since, even more false claims have been made.

While the claims are false, the targeting has been very real. 🧵
In the thread above I addressed a false claim made about me by another scientist @sailorooscout - the claim being I had engaged in 'name-calling' and 'degrading' conduct against them - when I hadn't engaged with them at all. I reasonably asked that this be corrected by them.
It became very clear that I didn't engage in the behaviour claimed by @sailorooscout
Rather than acknowledging the claim was incorrect, they suggested I 'forget quickly', linking to a tweet that hadn't been written/liked by me. It seems to have been by one of their followers.
Read 8 tweets
6 Apr
I'm seeing very concerning attacks against scientists seeking to provide accurate information around vaccine efficacy- especially in the context of new variants, or legitimately discussing the recent reports of thrombotic events associated with Astrazeneca. Short thread.
I'm sure many saw an exchange a few weeks ago, that was also platformed in the Spectator, which is quite odd given the context. In this exchange, a scientist urging pandemic control due to concerns about low efficacy of vaccines against the B.1.351 variant was met with attacks. Image
The account suggesting @devisridhar tweet was misleading complained they were blocked by her after the interaction. This was picked up by the Spectator & presented in negative light. This seems odd as this account has pre-emptively blocked me & others.…
Read 14 tweets

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