iiinova — where your digital self keeps evolving

Prof François Balloux @proffballoux.bsky.social · 21/11/2024

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

Prof François Balloux @proffballoux.bsky.social · 24/10/2023

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.

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Reposted by Prof François Balloux

Thomas House @tah-sci.com · 18/10/2023

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....

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

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Prof François Balloux @proffballoux.bsky.social · 18/10/2023

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

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Prof François Balloux @proffballoux.bsky.social · 18/10/2023

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).

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Prof François Balloux @proffballoux.bsky.social · 18/10/2023

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...

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Prof François Balloux @proffballoux.bsky.social · 17/10/2023

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. 2/

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Prof François Balloux @proffballoux.bsky.social · 17/10/2023

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. 1/

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Prof François Balloux @proffballoux.bsky.social · 17/10/2023

Conversely, I have little doubt Covid will settle into a predictable seasonal pattern, as (essentially) all other 200 respiratory bugs in circulation. 2/

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Prof François Balloux @proffballoux.bsky.social · 17/10/2023

"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. 1/ academic.oup.com/ooim/article...

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Prof François Balloux @proffballoux.bsky.social · 12/10/2023

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

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Prof François Balloux @proffballoux.bsky.social · 12/10/2023

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. 7/

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Prof François Balloux @proffballoux.bsky.social · 12/10/2023

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. 6/

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Prof François Balloux @proffballoux.bsky.social · 12/10/2023

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. 5/

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Prof François Balloux @proffballoux.bsky.social · 12/10/2023

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. 4/ www.ucl.ac.uk/news/2021/ap...

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Prof François Balloux @proffballoux.bsky.social · 12/10/2023

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. 3/

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Prof François Balloux @proffballoux.bsky.social · 12/10/2023

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. 2/

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Prof François Balloux @proffballoux.bsky.social · 12/10/2023

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. 1/

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Prof François Balloux @proffballoux.bsky.social · 07/10/2023

There's stiff competition in that field ...

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Prof François Balloux @proffballoux.bsky.social · 07/10/2023

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 ...

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Prof François Balloux @proffballoux.bsky.social · 07/10/2023

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 ...

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Prof François Balloux @proffballoux.bsky.social · 06/10/2023

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

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Reposted by Prof François Balloux

Dani cRabaiotti 🦀 @danirabaiotti.bsky.social · 05/10/2023

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...

forms.office.com

Microsoft Forms

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Reposted by Prof François Balloux

Zamin Iqbal @zaminiqbal.bsky.social · 04/10/2023

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!

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Prof François Balloux @proffballoux.bsky.social · 02/10/2023

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

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Prof François Balloux @proffballoux.bsky.social · 02/10/2023

A welcome gift for your arrival on the sky site @trattenrabbit.bsky.social. Have some 🥕🥕🥕!

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Prof François Balloux @proffballoux.bsky.social · 02/10/2023

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

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Prof François Balloux @proffballoux.bsky.social · 01/10/2023

Note Silver's latest Substack article is a great read, approachable and super-clear. It makes a robust case for Covid-19 vaccines having saved many lives in the US, without belittling and insulting those who believe otherwise. Science communication at its best! www.natesilver.net/p/fine-ill-r...

natesilver.net

Fine, I'll run a regression analysis. But it won't make you happy.

State partisanship and COVID vaccination rates are strongly predictive of COVID death rates even once you account for age.

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Prof François Balloux @proffballoux.bsky.social · 29/09/2023

As an aside, it feels really relaxing to be able to discuss science on social media without worrying that some crazies may crash the discussion with some accusations that we're eugenicists or whatnot ...

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Prof François Balloux @proffballoux.bsky.social · 29/09/2023

You may be right, but computationally at least, evidence for extensive cross-reactivity/immunity between SARS-CoV-2 and the HCoV endemics (in terms of linear epitopes) remains weak. www.sciencedirect.com/science/arti...

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Prof François Balloux @proffballoux.bsky.social · 29/09/2023

I've been surprised how little cross-immunity there seems to be between SARS-CoV-2 and the two betacoronavirus endemics (HCoV-OC43 and -HKU1). In the early stages of the pandemic I was hopeful this would help. This is one thing I apparently got wrong.

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Prof François Balloux @proffballoux.bsky.social · 29/09/2023

Thanks. Makes sense. I also guess that lab hamsters - which as far as I know are all derived from a single family of golden hamsters - have essentially no diversity at their MHC genes by now, which, well, makes me wonder how generalisable such experimental results may be, even to hamsters ...

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Prof François Balloux @proffballoux.bsky.social · 29/09/2023

I tend to agree, but given the number of unique mutations and deletions it carries, I'm surprised it didn't come with at least a minor serotype shift of sorts.

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Prof François Balloux @proffballoux.bsky.social · 29/09/2023

How portable do you feel those results are to humans?

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Prof François Balloux @proffballoux.bsky.social · 29/09/2023

I'm really not too sure what to make of the BA.2.86 variant. It's still going up in frequency globally, but soooo slowly. At the current rate it will still take a few weeks for it to reach a 1% relative prevalence. Note: UK outbreak downsampled to one observation in the plot below

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Prof François Balloux @proffballoux.bsky.social · 26/09/2023

I appreciate I may be in a minority here, but I don't find this paper illuminating, at all. To me, if anything, it just adds further confusion to the debate, by over-interpreting and overselling results, which, well, are not that clear.

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Prof François Balloux @proffballoux.bsky.social · 26/09/2023

Thank you for flagging this article. This looks like an interesting piece of work.

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Prof François Balloux @proffballoux.bsky.social · 21/09/2023

I've just come across that interesting fungus, basket stinkhorn (Clathrus ruber), I presume. It's the first time I saw one in Switzerland. It's weird and smelly, but still cool.

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Prof François Balloux @proffballoux.bsky.social · 21/09/2023

Every person accused of any crime is considered innocent until proven guilty ... 😉

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