New study out reporting antibody neutralisation of the BioNTech (Pfizer) vaccine. Two doses provided a strong response against 'pseudoviruses' carrying the spike mutations of five different 'concerning' SARSCoV2 lineages (including B.1.617.2 / delta).
Intriguingly, the lowest - but still highly satisfying -antibody titers were measured for B.1.617.1, a fairly unsuccessful sister lineage of B.1.167.2, which has also been around for a while.
This is highly speculative, but the lower success of B.1.167.1 relative to B.1.617.2 (delta) might point to a tradeoff between transmissibility and 'immune escapiness', here possibly in part due to the spike E484Q mutation. B.1.617.1 carries E484Q, B.1.617.2/3 don't.
E484Q is rare outside of B.1.617.1 (<0.001%), but E418K is common and independently emerged hundreds of times. Though, despite the mutation contributing to immune escape, most lineages carrying it weren't particularly successful, so far.…

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More from @BallouxFrancois

4 Jun
I'm extremely impressed by the quality of the UK #COVID19 data. Their near-real time analyses or the PHE reports are unparalleled in their quality. I'm also in awe of the efforts to present those findings in an approachable way on social media for instance by @kallmemeg.
The scientific capacity and rapid release of data and analyses makes the UK the country which may be most transparent and open about the epidemiological situation and its evolution.
There have many complaints aired about data about circulation in schools being withheld. This may well be true, though it does not necessarily imply anything nefarious going on. Real-time epidemiological data is not always ideal.
Read 8 tweets
27 May
I'm getting very annoyed with the unfair criticisms of @sailorrooscout. Science communication comes in different guises and needs to be adapted to its target audience. Her ability to convey difficult concepts to a wide audience whilst remaining factual is remarkable.
@sailorrooscout has an idiosyncratic, approachable style of public outreach and she indeed tends to put a positive spin on scientific evidence. By doing so, she's done more to educate the public and fight vaccine hesitancy than any of her detractors.
To those who don't like her style of communication, I recommend they stop following her and get their updates on the latest vaccine news from other sources. There are plenty to choose from on twitter.
Read 5 tweets
21 May
I anticipate the emergence of many #SARSCoV2 'variants' in the near future with features comparable to the current four Variants of Concern (VoCs), and numerous Variants of Interest (VoI). The latest candidate is AV.1, which emerged in Yorkshire (B.1.1.482.1, I presume).
We tend to consider 'variants' as discrete entities. Our view may be largely coloured by the unexpected emergence of B.1.1.7, which seemed to come out of nowhere and spread globally. B.1.1.7 in the tree below forms the clade between 3-8 o'clock.
Though 'variants' continuously evolve as do all other #SARCoV2 lineages, by acquiring on average ~2 mutations/month as thy replicate. There is some convergent evolution between VoCs/VoIs with the presence of some shared mutations/deletions between VoCs.
Read 12 tweets
20 May
There may be sound epidemiological arguments for tighter travel restrictions in parts of the world. Though, I personally don't support border closures as I don't believe they are effective to achieve #COVID19 endemicity through vaccination, which is my objective, personally.
That said, I feel uncomfortable with the widespread unpleasant language used to call for tighter borders.

'Leaky borders' not protecting 'our shores' from 'a flood' of 'foreign variants' brought by 'human bodies' and whatnot ...

This all sounds ideologically dark to me.
There is no such thing as compassionate chauvinism, kind jingoism, or gentle xenophobia, even during a pandemic.

Language matters, and normalisation of dehumanising arguments will have long-term consequences, well beyond the pandemic.
Read 5 tweets
14 May
It looks increasingly plausible that the #SARSCoV2 B.1.617.2 lineage might be more transmissible than B.1.1.7, at least in parts of India and the UK. This would be in line with a trend for #SARSCoV2 having become more contagious over time as it adapts to its human host.
Since #SARSCoV2 jumped into humans in ~Oct/Nov 2019, the viral population has acquired thousands of different mutations and deletions, some of which have arisen independently hundreds of times in different lineages.
Some combinations of mutations/deletions have been particularly successful, leading to those linages being referred to as Variants of Concern (VoCs) or Variants of Interest (VoIs). The 4 current VoCs display some evidence for convergent evolution.
Figure credit: @LucyvanDorp
Read 9 tweets
8 May
New preprint. We estimate the transmissibility of #SARSCoV2 lineages based on their genomic makeup. Overall, transmissibility of #SARSCoV2 went up over time, but fitness of individual clades tends to decay due to accumulation of deleterious mutations.
We focus on mutations / deletions that arose repeatedly as those are likely to increased viral transmission. Some arose independently hundreds of times. Below (panel A), four muts/dels associated with 'Variants of Concern' (VoCs). B.1.1.7 clade shown 3-8 o'clock in the trees.
Each time a recurrent mutation appears in the #SARSCoV2 tree, we count the descendants from that node with and without the mutation and calculate the ratio of offspring of either type. We then normalise those ratios over viral generation times and average over replicates.
Read 12 tweets

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