Last week @PHE_uk designated B.1.617.2 a VOC (excellent summary from @kallmemeg below). Today we released another week's worth of surveillance genomes at covid19.sanger.ac.uk, and I'd like to walk through some of the features & findings. 🧵
First, headline result, as reported by others, is that B.1.617.2 has hit 6% in England in our 2-week rolling average (>10% in the most recent week). Other VOCs & VUIs steady.
It is hard to know exactly what this means for transmissibility. There were hundreds of imported cases in a short span, and while those are not counted here, they arrived in both a quantity and at a moment of loosening restriction that we have not seen before for other variants.
That mix makes it inevitable that there will be hotspots of community transmission (e.g. Bolton). Low case numbers more broadly can make it look alarming, and it certainly is something that should be monitored, and against which public health measures should be deployed.
For those using our data, please take care around local authorities with low numbers. For instance, South Northamptonshire looks scary with 80% B.1.617.2, but that's based on a handful of sequences, so might be noise.
The fundamental question is how well vaccines work against this variant, and I know that lots of excellent scientists are working around the clock on that question. There's evidence on other variants that the effect is likely modest, so I'm cautiously optimistic.
Finally, while more evidence is accumulated, the plan remains the same: vaccinate as widely and quickly as possible; behave responsibly, even as restrictions are loosened.
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First off: what is the "India variant", well, it turns out that there are actually three clades of B.1.617, which have now been termed B.1.617.1, B.1.617.2 and B.1.617.3. All three clades appeared in India, likely descended from a common ancestor there some time ago.
The "full" VUI that has garnered attention is B.1.617.1, but interestingly B.1.617.2, which does *not* have the E484Q mutation (apparent reversion) is enriched in the most recent sequences in the UK & elsewhere. So the already dumb "double mutant" label makes even less sense now.
A few thoughts on the B.1.617 variant, first seen in India in late 2020, recently seen in >100 cases in the UK, and very much in the news here. TLDR: we should watch carefully, but I don't think any of our best lines of evidence on variants are yet cause for concern. 🧵
In the "variant era", there are 4 kinds of evidence we can use to evaluate a new variant: (1) how fast it is spreading in different places, (2) pre-existing info about specific mutations it carries, (3) lab experiments (ACE2 binding, Ab evasion, etc), (4) real world vaccine data.
3 & 4 are very important (at the end of the day, arguably all that matters is vaccine efficacy), but take time, even when labs around the world are focusing on these questions. I haven't seen anything yet on B.1.617, so won't comment further.
There was a scary story published today in the LA Times about the "California variant" of coronavirus, but the data behind the claims are not yet published. So here's a 🧵about this variant that does have some data in it. 1/N
What's claimed in the newspaper? Well, it sounds pretty bad: "it not only spreads more readily than its predecessors, but also evades antibodies generated by COVID-19 vaccines or prior infection and is associated with severe illness and death" 2/N
That's in the first of six paragraphs of terrifying conclusions, but we then learn the study is, "currently under review by the public health departments of San Francisco County and the state...It is expected to post late this week to MedRxiv" 3/N
In the latest @PHE_uk Technical Briefing we see the #b117 variant of concern continues to spread throughout England, get bigger numbers on the secondary attack rate analysis, and see a glimpse of planned virology experiments to come. 🧵assets.publishing.service.gov.uk/government/upl…
Using the S-gene target failure (SGTF) as a proxy (details in previous reports, updated in this report) we can see that as of January, #b117 is more than half of new infections almost everywhere in England. Of all TaqPath tests in the UK in the past few days >75% are #b117.
The SGTF data allows analysis of 2ndary attack rate in about half a million contacts of infected people. It is consistently 40% higher for #b117. This isn't a fully matched cohort, but is pretty compelling that the new variant transmits more readily in typical contact situations.
Out today: two academic publications (not yet peer reviewed) that formally test whether the new B.1.1.7 variant is more transmissible. Both conclude yes, about 50% more. 🧵
First, a pre-print led by @erikmvolz and @neil_ferguson at Imperial, which applied a variety of different models using both genome sequence data and the S-gene dropout data I've mentioned before. imperial.ac.uk/mrc-global-inf…
Comparing genomes (sparse and lagged) and S-gene dropout (dense and up-to-date) shows the same rapid expansion we all know about in London, the East and the Southeast.
MHRA approval document has some information on the basis for approving Oxford/AZ vaccine. Efficacy numbers are the same (pooled) as from the Lancet paper. assets.publishing.service.gov.uk/government/upl…
There's no mention of 1/2 doses, but what's interesting is this table on antibody titres after doses 1 & 2. First of all, some effect after 1 dose, secondly way higher antibodies if second dose is >12 weeks after 1st.
Of course will be key to see if that translates into better clinical efficacy (presumably trials ongoing or starting), but I can now see rationale behind UK gov't's apparent plan: get first jab into tons of people, and space out second jab.