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31 May, 4 tweets, 2 min read
We've pushed the weekly numbers update (thanks @theosanderson!) at covid19.sanger.ac.uk. As expected, in the most recent 2 week window, B.1.617.2 is the most common lineage in England. Still driven by local concentrations of high case numbers (L cases, R B.1.617.2):
A couple of notes on the site. We have updated the text describing ascertainment: we are no longer excluding surge tests, which make up a large fraction of all tests in key areas in recent weeks. I think this provides least biased frequencies now. Feedback welcome.
I've mentioned this before, but please be cautious interpreting proportions where we have few genomes. For example the "100%" in Dover doesn't mean much because it based on 3 genomes in the most recent 2 weeks of data:
Finally, one thing the proportions map is good for is actually to spot our coverage holes (white areas). Some will be filled soon (e.g. we are now sequencing samples from the Plymouth lab covering some of the Southwest).

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Jeffrey Barrett Profile picture
24 May
It's clear that B.1.617.2 has been growing faster than B.1.1.7 in UK for a few weeks. Key question for policy, not yet fully answered, is how much due to:
1. vaccine efficacy
2. intrinsic transmissibility
3. human epidemiological factors

🧵of my current thoughts on the topic:
Prelim. data show vaccines work somewhat less well against symptomatic infection w/B.1.617.2, so this makes a non-zero contribution to its recent growth. Good threads on vaccine efficacy data from PHE: &
But I think magnitude of observed VE reduction, as well as age distribution of B.1.617.2 infections, makes it unlikely to fully explain growth in UK. B.1.617.2 (blue) is a bit older than recent B.1.1.7 (green), but both more similar to each other than B.1.1.7 from December (red)
Read 16 tweets
Jeffrey Barrett Profile picture
10 May
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.
Read 7 tweets
Jeffrey Barrett Profile picture
22 Apr
Tons of new info about B.1.617 in @PHE_uk's latest technical briefing on covid #variants (which are rather excellent if I do say so). A 🧵on some key points. assets.publishing.service.gov.uk/government/upl…
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.
Read 8 tweets
Jeffrey Barrett Profile picture
18 Apr
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.
Read 12 tweets
Jeffrey Barrett Profile picture
23 Feb
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
Read 11 tweets
Jeffrey Barrett Profile picture
8 Jan
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.
Read 5 tweets

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