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.
You'll see the UK sequences (blue dots) are all over the tree above, and also all over the map below, strongly suggesting multiple introductions, rather than substantial community spread.
And indeed, 97% of cases with completed investigations have either recently traveled to the UK, or are contacts of someone who has:
What if the question is flipped around: what variants of the virus are found in people who have recently arrived from India? Unsurprisingly there is re-import of B.1.1.7 (though that was covered less breathlessly by the media), and as expected we do see an increase in B.1.617
So, in the space of a week we've learned that B.1.617 isn't what people assumed it was, and that the surveillance system in the UK has detected it at the border and (so far) kept it from community transmission. Big congrats to all the PHE team who did this work so fast.
Finally, while I hope these analyses help understand the virus, which variants are infecting people doesn't change hte tragedy in India. What matters now is supplying oxygen, sharing vaccines, and preventing transmission. Best wishes to those in the front lines of this fight.
• • •
Missing some Tweet in this thread? You can try to
force a refresh
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.
Big update posted last night by @PHE_uk on the new UK variant of #SARS-CoV-2 (aka B.1.1.7 or VOC 202012/01), including first solid evidence that it does not cause more severe clinical disease. Highlights in the 🧵...
We can now see that the S-gene target failure (SGTF) in the Thermofisher TaqPath assay I've discussed before is a very good proxy for the new variant almost everywhere in England.
So we can use SGTF as a near-real-time proxy for spread of the new variant. It is present at some level everywhere in England, and has almost replaced all other variants in London and the Southeast.