Director @UGI_at_UCL. Interest in Infectious disease epidemiology, pathogen genomics and global health
Mastodon account: @FBalloux@genomic.social
79 added to My Authors
Nov 27 • 8 tweets • 3 min read
The Covid situation in China is not looking good right now. The authorities have trapped themselves into a situation from which there's no obvious escape strategy. Whatever they choose - or will be forced - to do next will be very costly.
China has managed to suppress SARS-CoV-2 with brutal restrictions. Those are becoming increasingly untenable as the population is suffering. A major surge seems largely inevitable in the short term unless the authorities chose to enforce even more ruthless measures.
Nov 26 • 6 tweets • 2 min read
New paper on non-lethal sampling of Ranavirus in amphibians.
Ranaviruses are DNA viruses with an exceptionally broad host range among cold-blooded vertebrates (amphibians, reptile and fish). 1/ mdpi.com/1999-4915/14/1…
Ranavirus are a major threat for several species of amphibians. They reduce the viability of infected amphibian populations, which often already struggle with pollution and habitat loss, but can also cause devastating outbreaks in pristine habitat. 2/ sciencedirect.com/science/articl…
Nov 18 • 4 tweets • 1 min read
I find the fall from grace of Professor Didier Raoult fascinating to watch. Though, what few seem to fully appreciate is that he's merely a symptom of many things that are deeply dysfunctional in academia, rather than a cause, or even an outlier.
He represents the epitome of absolute power in academia, putting his name on endless papers he may not even have read, with many of those being completely irrelevant, and using his huge power to heap abuse on anyone who dares to challenge him.
Nov 14 • 5 tweets • 1 min read
I generally try to avoid 'Tik-Tok takes' on Covid, because I appreciate things are complicated, and there are alway exceptions to any pattern. That said, for the sake of everyone's sanity, let me be clear.
There is no evidence at all that mild Covid does 'destroy immunity' and make people more susceptible to other infectious diseases. The naive T-cell depletion, super-antigen trope or whatnot doomsday immunity hypotheses are nonsense supported by no robust scientific evidence.
Nov 9 • 5 tweets • 1 min read
New preprint suggesting that rapid expansion of naive T cells can provide a fast and effective immune response to SARS-CoV-2, and likely other viral infections. 1/ biorxiv.org/content/10.110…
We all have a large repertoire of naive T-cell precursor clones that recognise different bits of pathogens (epitopes). The relative frequency of those populations of clones is highly variable, with some being far more common than others.
Nov 6 • 12 tweets • 3 min read
As all the cool kids are migrating to Mastodon, I've also set up an account there. The way things are going, I may well relocate all my social media activity to Mastodon. If so, I hope to meet many of you there in the future.
Twitter's ability to deliver information in real time is amazing. I also value the opportunity to debate with people from all ways of life. Conversely, Twitter's noxious. I anticipate quality content to go down and abuse to go up under its new unsustainable business model.
Nov 3 • 4 tweets • 2 min read
Intriguing new study from Qatar. In short, the reported risk of Omicron re-infection was found to be lower in people who had 2 vaccine doses vs. those unvaccinated, but higher in people with 3 vaccine doses vs. those who had only 2 doses. 1/ medrxiv.org/content/10.110…
This study looks well done to me and the same team of scientists has consistently produced robust studies during the pandemic. Though, it remains a retrospective observational study, and the results may thus be affected by all sorts of biases.
Oct 31 • 8 tweets • 2 min read
I spent more time on the distribution of type IIS restriction sites in SARS-CoV-2, and revised my views. The distribution of the sites can be explained by extensive genetic recombination between viral lineage and does not provide evidence for a lab-origin for SARS-CoV-2.
In my initial assessment, I gave too much weight to some 'atypical' patterns such as the excess of 'silent mutations' within restriction sites, and not enough to the underlying recombination process. I apologise for the confusion this has caused.
Oct 14 • 6 tweets • 2 min read
This 'OMG the Pfizer CEO admits that Covid vaccines don't reduce transmission' furore is tiresome and unhelpful. Covid vaccines were not trialled for their effectiveness in reducing infection / transmission and neither the Pfizer or Moderna CEO promised they would at the time.
What happened is that soon after the start of the vaccination campaign - before vaccine antibodies started waning (as they were predicted to do), and before Omicron emerged - Covid vaccination significantly reduced the risk of infection and transmission.
Oct 7 • 6 tweets • 2 min read
I feel very sorry for the immunocompromised people who feel extremely threatened by Covid. Though, I believe there has been a problem in the way this risk has often been conveyed.
The primary risk factor for Covid morbidity / mortality is age. The risk of dying from Covid in the early stages of the pandemic doubled for every 6 years of age. This remains largely true at this stage, even if everyone's risk has decreased. 2/
There is a lot of discussion on twitter whether monkeypox (MPX) - outside endemic areas in Western/Central Africa - is a sexually transmitted disease (STD), or not. Let's have a look.
The global outbreak of MPX is essentially exclusively circulating in men who have sex with men (MSM). There have been a few cases outside MSM but with no onward transmission so far, This is not due to lack of testing outside MSM. 2/ cdn.who.int/media/docs/def…
Jul 4 • 13 tweets • 4 min read
There is a SARS-CoV-2 wave underway in many countries. Current cases are made up of a mix of Omicron BA.2.x, BA.4 and BA.5 strains. All those lineages are fairly closely related and all derive from BA.2 (pink below), which caused the previous wave. academic.oup.com/ooim/article/3… 1/
The BA.5 and its sister lineage BA.5.1, which differ from each other by a single pretty obscure mutation (ORF10:L37F) now account for >50% of cases in the UK. BA.2.1.12 is probably still dominant in the US at this stage.