The Imperial report on the new UK B117 strain is out. Very concerning findings, that highlight why we need to act on this *now*. These findings suggest that the situation within the UK is likely to get much worse than it is now. Here's why-

Thread.
First, this study is perhaps one of the most comprehensive evaluations of the impact and spread of the B117 variant- combining epidemiological national evidence with genomic data from large numbers of samples across the UK.
The study examines something called 'spike dropout' as a proxy indicator for the new B117 variant. The B117 variant includes a deletion in the virus genome which has been associated with a different read-out on some PCR tests, - referred to as 'spike dropout'
While 'spike dropout' (S-) does not necessarily signify the B117 variant, as this deletion can occur out with the B117 variant >97% of tests showing S- since mid-Nov have been attributed to the new variant, given it's high prevalence relative to other variants.
We see a very rapid rise in frequency of the B117 variant in London, SE England & E of England - rising to 80% by mid-Dec. Looking at the distribution across England, the estimated frequency varies by region between 15% in Yorkshire to 85% in SE England.
What does this mean?
While the variant is still at low levels across many parts of England, the trajectory in some regions (Oxford & Birmingham) suggest rapid recent increases in frequency - which means it will likely follow the same trajectory as other areas unless we act now.
Studying the Rt associated with the variant strain compared to the previous one suggests an Rt ~1.74x times greater for cases with the variant compared with the previous strain. This is a huge advantage. It would for example mean an R of 0.9 increasing to 1.6.
Worth noting that the multiplicative increase is estimated within the current context, and many not extrapolate the same way to other contexts.
Distribution of the new variant compared to the previous variant by age group suggests that the ratio between S- (variant proxy)/S+ (normal strain) is highest for those in the 0-9 yr and 10-19 yr group - data till mid-Dec. This is concerning on many levels.
It's clear that the variant is more dominant (1.2x) in children aged 0-9 yrs and 0-19 yrs. There could be many reasons for this - including transmission dynamics - due to high levels of unmitigated transmission in schools during lockdown - which has favoured the variant.
It could also mean that children with the variant are more likely to develop symptoms and therefore be tested. Given these are not random samples from healthy people, but results based on pillar 2 testing, we need to interpret these cautiously.
This also does not necessarily mean increased biological susceptibility in children vs adults, & shouldn't be interpreted as such.

Irrespective of the relative prominence of the variant among children the prevalence of the variant is greatest among 10-19 yrs among those tested.
The data also suggests that the standard variant is still predominant among older age groups (at least among those tested) who are most susceptible to severe COVID-19.
Why is this important?
This really highlights the potential impact of waiting to act. We know that virus transmission that begins in younger age groups inevitably spreads to older people, and ultimately results in severe illness & death. We've seen this pattern before.
The geographical & age distribution suggests that although the the UK pandemic is in a critical state now, there's real potential for it to get a *lot* worse. We know increases in R correlate strongly with the variant frequency. We can see the frequency rising in other regions.
We can see it spreading outside South & East England. Given this is only at a frequency of 15% in some regions (and increasing), a rise would increase R much more than it is now, and worsen spread significantly.
Similarly, if infection in children is not curbed, the new variant will likely rapidly become dominant in adults as well, and potentially lead to even more rapid spread of infection in older groups where infection is more likely to be deadly & create further pressure on the NHS
The study shows that the R number associated with the variant *during* lockdown was 1.45 compared with 0.92 for other strains. This means that cases with the variant continued to rapidly grow during the last lockdown. The variant is associated with an increase in R of 0.4-0.7
It's clear that although the situation is dire now, there is potential for it to get much worse & given the rises we're seeing in variant frequency in other regions, if we don't act now, not only with exponential rise continue, but the rate of rise will increase.
This may also mean more cases among older age groups- while the variant is currently dominant among children, the situation is likely to get much worse if this gains dominance among adults, who will be more likely to spread to other adults & older people - which means more deaths
To illustrate this with an example-
Say 15% of a region has the variant now, and has an overall R of 1.1 (fairly realistic given the rises we're seeing in much of England where the variant isn't dominant yet).
Assuming R of 1.7 for the VOC and 1 for the standard strain, the variant would be expected to rise to >70% frequency within a month. This would mean an increase in R to 1.5 in this period from 1.1. In terms of case numbers it would be devastating.
Assuming 2000 daily cases in a region at baseline, in real terms, this would mean - 62,000 daily cases in 2 months time, vs 5,187 had the R remained constant at 1.1.

And an order of magnitude greater no. of deaths
(assuming similar age distribution which may not be the case)
All the evidence is pointing in the same direction- we need to act urgently to curb spread across *all* of the UK. Letting this variant spread is not an option. And we need to close schools, until we can make them safe, & prevent onward transmission. This is critical now.
Just adding a short note here as many people have asked how the variant increases transmissibility. We don't know the exact mechanism -we know that one of the mutations changes the virus spike protein in a way that it binds to the human receptor needed for infection more strongly
There are also studies that suggest that virus levels in the throat and nose are higher among those infected with the virus, suggesting that this might be one of the ways in which it may make spread easier.

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More from @dgurdasani1

2 Jan
Really disappointed to see scientists furthering false narratives. Zoe is a *symptom* based tracker & doesn't capture *infection* or transmission from children. The ONS data clearly shows that the highest prevalence of infection in secondary schools, young adults & primaries.
The most recent ONS infection survey, which randomly samples people irrespective on symptoms shows prevalence of COVID-19 of 1 in 33 in secondary school children & 1 in 50 in primary school children- higher than in all age groups >25 years.
I'm honestly fed up of scientists quoting deeply flawed data on symptom-based testing/research in children, when we know there's much more asymptomatic infection. There is so much evidence now that doesn't rely on this that clearly supports the role of children in transmission.
Read 4 tweets
1 Jan
I wrote yesterday about the spread of the UK B117 variant based on data up to the 13th Dec warning that it could become dominant across much of the UK & across most age groups. Recent data released up to end of Dec now suggests that this has already happened. Short thread.
Recent data from LSHTM shows that the B117 is either dominant, or very close to dominant in most regions with rapid increases being seen all across England. No region appears to have been spared, and it's very nearly out-competed the usual strain completely in SE England. Image
This means that we will continue to see increases within the next few weeks in other parts of England, where it will likely completely replace the previous strain as it has in much of SE England. This is very bad news- because it makes the spread much harder to contain.
Read 14 tweets
31 Dec 20
I've been seeing a lot of discussion around the dosage gaps recommended by government for the Astra/Oxford & Pfizer/BioNTech vaccines. My thoughts on the potential benefits & risks of such an approach, and the need for much greater transparency around these decisions. Thread.
The UK govt announced recently that both the Oxford & BioNTech vaccines would be now administered with a gap of between 4-12 weeks (so prioritise administration of first dose, given limited resources).

What is the basis of this?
The basis that's been discussed seems to be that
1) the first dose is likely to confer some degree of protection against disease, so better to roll this out as fast as possible, and
2) that for Oxford/Astra efficacy may be higher when the gap between doses is greater.
Read 27 tweets
30 Dec 20
I'm honestly at a loss as to understanding what our government is thinking & what evidence they're considering in enacting gravely negligent policies that will almost certainly lead to tens of thousands of deaths in the coming weeks. Thread.
To recap - NHS capacity is critical in many places. Hospitals have reported oxygen shortages, and doctors are talking about having to choose who to put on ventilatory support. We have rapidly rising case numbers, >50,000 daily reported cases & 981 deaths reported yesterday.
Let's remember that the impact of socialising over christmas hasn't even begun to show in our numbers yet. And that hospitalisations are indicative of infections that happened ~2-3 wks ago (since then we have been seeing exponential rises in cases).
Read 16 tweets
29 Dec 20
@mgshanks @IndependentSage has done a lot of work on this- and made specific recommendations. But overall - mask wearing, ventilation with monitoring, small class sizes (with recruitment of additional staff), use of empty spaces, provision of support for blended/rota or remote learning
@mgshanks @IndependentSage This includes provision of practical and financial support to students, & their families, including laptops/tablets, broadband, and carer support for children who may need to study remotely.
@mgshanks @IndependentSage Mass testing in schools - but of everyone regularly (not just contacts). Contacts should be quarantined anyway regardless of negative tests (as recommended by the CDC).
Read 4 tweets
29 Dec 20
A brief summary of the very precarious situation we are in now, and why we have a very narrow window to act in the UK. If we don't act now, it's likely the window for containing COVID-19 will pass- not just for the UK but globally. Here's why. Thread.
The UK is home to a new variant strain of virus- one that's thought to be ~56% more transmissible than the previous strain of virus. This viral strain continued to spread through the previous lockdown, where cases were rising in London & the SE England even under lockdown 2/N
This means even with national lockdown, surges of cases will be very difficult to control. It also means we will need much higher vaccine uptake ~90% or even more to achieve an R below 1 - if this is possible at all (given we don't know the vaccine efficacy on transmission) 3/N
Read 22 tweets

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