Prof François Balloux

I'm slowly warming up to BlueSky. Not having Elon Musk's nonsense constantly shoved in my face arguably plays a role.

It remains unclear to me where BA.2.86* is headed next. I'm not convinced it will ever become the dominant SC2 lineage in circulation.

Figure 1. Lineage dynamics and genetic diversity through time. (a) Proportion of swabs taken as part of the ONS-CIS that were positive with Ct ≤ 30 (electronic supplementary material, figure S1), with bars coloured by the proportion of sequenced samples belonging to each major lineage. (b) Number of variant of concern (VOC) sequenced samples from rarer lineages (i.e. not classified as a major lineage). (c) Per day growth rate advantage of each of the major lineages compared to all other contemporary samples. BA.4 and BA.5 were considered together due to their concordant trajectories, and uncertainty is represented by 200 data bootstraps. The horizontal lines represent how long it would take the VOC prevalence to double (14 days, dashed; 7 days dotted; 2 days dot-dash). (d) Proportion of sequenced samples with both the given lineage and S-gene target failure (SGTF) pattern. The bold markers represent the proportion of sequenced samples that were of both the indicated lineage and had S-g

New paper!

"Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey"

Presents analysis of the genomic data provided by a large representative community survey of SARS-CoV-2 infections.

royalsocietypublishing.org/doi/full/10....

Thanks. I had completely forgotten about this. It made me chuckle and feel a bit nostalgic ...

There is very little unbiased surveillance for flu. The studies that report actual surveillance at a regional level probably never reach a 1000x ratio of cases between summer and winter. Influenza A has often a secondary spring peak, and summer peaklets are not uncommon (for both A and B).

True, but flu (influenza A and B) doesn't fully disappear in summer either, and outbreaks outside winter are not uncommon. See eg. surveillance data from China 2014-2018 below.
www.nature.com/articles/s41...

A fairly high confidence prediction is that SC2 will be just another endemic HCoV (throughout their lifetime) for those who are kids now and for future generations. Conversely, I'm not too sure what to anticipate for the rest of the population.
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I'm aware of no existing data suggesting that SARS-CoV-2 is intrinsically more severe than the other four human coronaviruses, which are not harmless BTW. That said, it may take a while for SC2 to turn in just another endemic HCoV.
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Conversely, I have little doubt Covid will settle into a predictable seasonal pattern, as (essentially) all other 200 respiratory bugs in circulation.
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"Covid turning into another flu" was the 'bad' scenario we considered in a review we wrote in 2022. My low confidence prediction is that the 'good' (fifth endemic HCoVs) scenario or something in between 'good' and 'bad' is more likely.
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academic.oup.com/ooim/article...

Until coming across that exchange, I had some hopes Bluesky may be a reasonably sane social media platform. Those hopes have been dashed now ... 😔

Ironically, universities may be among the least well placed institutions to provide live commentary on the ongoing world's horrors, but likely best placed to provide thoughtful, retrospective commentary and reflection on past events, even fairly recent ones.
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That doesn’t mean that students/university staff shouldn't be allowed to express their views. They should feel free to do so, as any other member of the public, but when they do, they should do so as individuals, and avoid dragging their institutions into toxic public debate.
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Politicisation of universities is corrosive and counterproductive. This disease can take ‘mild’ forms (e.g. when most in society fail to understand the political / ideological posturing taking place at universities), or more acute ones, as with the recent atrocities in Israel.
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Universities should be places where respectful debate is tolerated and encouraged, which precludes any form of ‘cancel culture’. I really like the views of Michael Spence, the provost of UCL on this.
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www.ucl.ac.uk/news/2021/ap...

Universities are an essential component of democratic societies and generate considerable income, investment, and financial return to the community, both through higher education and R&D.
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What universities should do when a major crisis arises, like any other responsible employer, is to ensure that all their staff / students feel valued, protected and listened to.
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The role of universities is not to generate media / social media hot takes; however horrible the world may feel. Universities should be places devoted to teaching and research, and not social media outrage / praise farming.
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I see ... 😆

There's stiff competition in that field ...

I've been wondering for a while if some of the protection we've assigned systematically to T-cells may not be in part provided by non-neutralising antibodies. Though, I can't figure out at this stage how we could attempt to computationally disentangle between the two mechanisms ...

A question for you @trattenrabbit.bsky.social.

This preprint is extraordinarily idiotic. It is beyond me how anyone could fail to recognise the importance of a proper denominator after 3.5 years. And it wouldn't even have been hard to analyse this properly ...

I'm sorry to break it to you, but wombats were not eligible as Australian bird of the year ...

Hi all! We are recruiting again. If you can ID European birds, bats, frogs or plants and fancy some flexible, paid, work - please fill out our form: 🧪 🪶 🌍 forms.office.com/pages/respon...

I'm recruiting PhD students for Oct 24 start at University of Bath. Fully funded for UK students only. If interested in developing data structures/algorithms for bacterial genomics, or exploring plasmid epidemiology, or ML/AI on bacterial/phage geno/pheno data, give me a call!

I think I know that place. I haven't been there in ages.

A welcome gift for your arrival on the sky site @trattenrabbit.bsky.social.

Have some 🥕🥕🥕!

That could work. But it could also have disastrous consequences ...