Billy Quilty

How have UK social contact patterns changed post-pandemic? How assortative are they by age, ethnicity, and socioeconomic status? Pleased to share our new @plosmedicine.org paper, jointly led by @lucygoodfellow.bsky.social and myself, with @kevinvzandvoort.bsky.social and John Edmunds. #IDSky

www.theguardian.com/commentisfre...

theguardian.comPalantir is worming its way into the British state – it’s time to curb this controversial US company’s influence | George MonbiotTom Watson has said ‘mob rule’ must not decide public contracts. Perhaps he should take a look at his new employer, says Guardian columnist George Monbiot

Billy Quilty reposted

STAT

@statnews.com

We are going to miss you very much, Helen. https://www.statnews.com/2026/10/13/helen-branswell-stat-reporter-obituary/

statnews.comHelen Branswell, whose reporting on infectious diseases and public health drew acclaim, dies at 69Helen Branswell, STAT's infectious disease reporter who earned the respect of experts and public health officials with her accessible, prescient dispatches, has died at age 69.

antibot4navalny | bot blocker | блокировщик ботов

"We show that a distributed botnet of IoT devices... could also provide enough compute to run a capable model." "We run Gemma4-26B-A4B, distributed over 15 inexpensive off-brand Android TV boxes (~$55 each)... at 0.39 tokens per second." www.anthropic.com/research/sel...

Billy Quilty@bquilty.bsky.social

There are already many rogue agents on the web - we've just previously called them computer viruses, or bots. A capable agent on OpenAI may not escape containment itself could rent server space, infect people's computers, etc., and create many more agents, then direct them to do nefarious things.

Billy Quilty reposted

@antibot4navalny.bsky.social

Replying to @antibot4navalny.bsky.social

3️⃣ as you can see in Russia-totals chart, volume of bot traffic this week (as measured by CloudFare) is largely the same as any other week. radar.cloudflare.com/bots/ru?date...

Will be interesting to see what "sticks" from this vibe-coded software revolution. It's clear that you can get to impressive ends really easily (just don't think about the means too much), but maintaining that is much more difficult (see all those "games in a browser" that worked - for about a day).

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Science is going the same way, with journals swamped by AI-accelerated research. Maybe we'll have fewer giants to stand on the shoulders of, and millions of ants instead?

journals.plos.orgBest practices for estimating and reporting epidemiological delay distributions of infectious diseasesEpidemiological delays are key quantities that inform public health policy and clinical practice. They are used as inputs for mathematical and statistical models, which in turn can guide control strat...

But ants typically don't appreciate being stood on. However, they can do remarkable things when coordinated - who knows. ...probably pushed that metaphor to its limits.

And now as its so easy to spin up your own version, there's little incentive to contribute to larger open-source projects - but most maintainers of legacy projects are so vehemently anti-AI they won't accept any AI-assisted pull requests. But I guess what can you do given the likely deluge of PRs?

Billy Quilty reposted

Sam Abbott

@seabbs.bsky.social

A few years ago we (Kelly Charniga @sangwoopark.bsky.social et al.) did some thinking on how we should estimate and report epidemiological delay distributions (i.e incubation periods etc. etc.). journals.plos.org/ploscompbiol...

I would have thought the development of something which is able to make the working class obsolete would be something the left would take more seriously, but nope its all BS apparently. Real head in the sand behaviour which will come back to bite us, big time.

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arxiv.orgPaper2Agent: Reimagining Research Papers As Interactive and Reliable AI AgentsWe introduce Paper2Agent, an automated framework that converts research papers into AI agents. Paper2Agent transforms research output from passive artifacts into active systems that can accelerate dow...

A nice concept but seems a bit... obvious...? to be in Nature? Ah, it was first up on arxiv a year ago. Perhaps says a lot about how quickly things are progressing in the field that this seems less than revolutionary - like in COVID, journals will struggle to keep up arxiv.org/abs/2509.06917

Nature@nature.com

The AI agent can respond immediately to questions about the paper, providing a convenient way for scientists to grasp advances in unfamiliar fields go.nature.com/4xrHsLG

go.nature.comAI tool turns any paper into an ‘agent’ that can collaborate and answer complex queriesThe Paper2Agent system makes it easier for researchers to reproduce papers and understand work in unfamiliar fields, authors say.

Regardless, it's good to see this stuff, perhaps indicative of a move towards papers being a dynamic interactive process rather than a static PDF. But also heralds the coming reproducibility crisis as hoards of agents attempt to run creaking GitHub code, finding plenty of bugs along the way...

10 Sept

Seeing a lot of pedantic hang-up on the phrasing of "AI could kill all humans". Yes full-on extinction is unlikely for a number of reasons, but there's a wide range of possibilities between 0 and 7 billion deaths that would still be very bad indeed

10 Sept

Basically this again but swap pandemic for AI bsky.app/profile/bqui...

Billy Quilty@bquilty.bsky.social

The current online dichotomy between "it's the next pandemic, panic" and "it's not, nothing to worry about" hides a wide spectrum of possible intermediate trajectories that would still present a real challenge if they played out.

@drmichaelmarks.bsky.social

10 Sept

💯

Billy Quilty reposted

Michael Marks

18 Aug

Come & join our group. Modelling post @lshtm.bsky.social working on STI transmission & new interventions in the UK. Working closely with @ukhsa.bsky.social Applications close 17th September. @adamjkucharski.bsky.social @rozeggo.bsky.social @bquilty.bsky.social @grahammedley.bsky.social

jobs.lshtm.ac.ukJob Opportunity at LSHTM: Research FellowThe London School of Hygiene & Tropical Medicine (LSHTM) is one of the world’s leading public health universities. Our mission is to improve health and health equity in the UK and worldwide; working i...

@lshtm-vaccines.bsky.social

11 Aug

Both the state and the free market have comprehensively failed on the availability of eclipse glasses. Where are they? It's not like we haven't known this was going to happen for hundreds - if not thousands - of years.

Why haven't we seen a sci-fi movie on AI called "Alignment" yet? Nolan, you can have that one for free.

Billy Quilty reposted

LSHTM Vaccine Centre

3 July

💉 Vaccines against Pneumococcal disease are expensive to provide long-term where they're needed most. 🆕 long-term @lshtm.bsky.social research confirms that two-doses of PCVs are as effective as three, helping countries address the vaccine "funding gap" & continue to save lives. 👉 bit.ly/4v6CwLj

Billy Quilty reposted

Ian M. Mackay, PhD (he/him) 🦠🤧🧬📑🦟🧀

@mackayim.bsky.social

18 May

Some past published examples of incubation periods (IP) of hantavirus pulmonary syndrome (HPS) cases. Note that the extremes of 6+ weeks (42+ days) are the exception, not the rule.

Billy Quilty reposted

Epiverse TRACE

@epiverse-trace.bsky.social

1/5 🌍 Real-world outbreak analytics training, now open for July 2026 · 55 participants last cohort · 31 countries 🗓️ Tue & Wed AM/PM sessions 💰 50% off for LMIC applicants (deadline 6 Jun) ❓ Got questions? We're hosting a drop-in Q&A next Tuesday — details below 👇

theguardian.comCanada confirms first hantavirus case in isolation in British ColumbiaThe person was on board the MV Hondius, the center of the outbreak that has claimed three lives Canadian officials said on Saturday that one of the four Canadians currently quarantining in British Columbia after being exposed to the hantavirus while on board the cruise ship where the outbreak occurred has presumptively tested positive. Speaking at news conference, Dr Bonnie Henry, British Columbia’s provincial health officer, said the individual developed mild symptoms, including fever and headache, two days ago, and that the individual and their partner, who had also been on board the cruise ship where they had been isolating together, were transferred to a hospital in Victoria for assessment and testing. Continue reading...

17 May

A key question now is whether this is part of the initial cluster likely spawned by the index case, or potentially a third generation case. Based on what's known about the incubation period/serial interval, I estimate that there is a 74% chance that this a third gen case: github.com/bquilty25/ho...

The Guardian@theguardian.com

Canada confirms first hantavirus case in isolation in British Columbia

17 May

So not definitive (but 95% CrI is 53-91%, so more than pure chance). Cases we see from now on are more likely to be due to transmission beyond that from index case. Given serial interval It'll be a while before we can say anything about transmission happening off the ship (tho depending on context)

Billy Quilty reposted

Thomas House

@tah-sci.com

17 May

When there's a new outbreak, yes there's always the possibility of a major pandemic and that puts some weight on the need for a fast, cooperative and effective public health response but really the immediate, foreseeable consequences of the outbreak should be the focus and are reason enough to act.

15 May

It would be beneficial if prominent public health voices could avoid solely framing outbreak risks through the lens of whether they should be something for people in high-income countries to "worry about" or not.

journals.plos.orgOn the evolution of the company we keep: Implications for infectious disease modelingIn this Perspective, Joël Mossong discusses the importance of understanding social contacts and how they have evolved for infectious disease modeling, and the need to factor in additional consideratio...

A great Perspective piece from @joelmossong.bsky.social on the evolution of social contact surveys, from the POLYMOD study he led in 2008 (which became the template for all others), to CoMix during the pandemic, and now on to Reconnect: journals.plos.org/plosmedicine...

Billy Quilty@bquilty.bsky.social

zenodo.orgSearch Social contact data

NB: many more contact surveys in many other countries than those exist, with datasets collated here: zenodo.org/communities/...

Billy Quilty reposted

PLOS Medicine

@plosmedicine.org

plos.ioSocial contact patterns in the United Kingdom following the COVID-19 pandemic: The Reconnect cross-sectional surveyIn a cross-sectional survey, Lucy Goodfellow and colleagues collect information from over 13,000 people on demographics and their social contacts after the COVID-19 pandemic in the UK.

How have social contact patterns changed since the #COVID-19 pandemic? In this cross-sectional survey, Lucy Goodfellow & colleagues collect information on social contacts of over 13,000 people in the UK post-pandemic, including social mixing by ethnic & socioeconomic groups🧪 #MedSky plos.io/4nmJyck

Billy Quilty reposted

PLOS Medicine

@plosmedicine.org

plos.ioOn the evolution of the company we keep: Implications for infectious disease modelingIn this Perspective, Joël Mossong discusses the importance of understanding social contacts and how they have evolved for infectious disease modeling, and the need to factor in additional consideratio...

This Perspective by Joël Mossong discusses findings from the Reconnect study, highlighting the importance of understanding social contacts & how they have evolved for infectious disease modeling, & the need to consider ethnic & socioeconomic backgrounds🧪 #MedSky #COVID-19 plos.io/42CQPLI

PLOS Medicine@plosmedicine.org

Finding 3: This social structure may drive observed infection inequalities. Using a next-generation matrix approach, we found that per-capita infection risk for a novel respiratory pathogen would be disproportionately higher for minority ethnic groups.

journals.plos.orgSocial contact patterns in the United Kingdom following the COVID-19 pandemic: The Reconnect cross-sectional surveyIn a cross-sectional survey, Lucy Goodfellow and colleagues collect information from over 13,000 people on demographics and their social contacts after the COVID-19 pandemic in the UK.

To help improve post-pandemic mathematical models, we have made the socially stratified contact matrices available. Researchers can now incorporate ethnicity and socioeconomic status into future outbreak projections. Paper: journals.plos.org/plosmedicine... Data: zenodo.org/records/1733...

Finding 1: People reported 9.1 daily contacts on average. This is around 20% lower than pre-pandemic levels seen in POLYMOD (2005-06), but about 40% higher than last reported by CoMix in late 2022.

Finding 2: Mixing is highly assortative. Beyond the expected age mixing, we found strong assortativity by ethnic group and socioeconomic status, particularly in home and workplace settings.

We ran the Reconnect social contact survey across the UK between November 2024 and March 2025. In total, 13,238 participants recorded their social contacts over a 24-hour period.

As @tah-sci.com says, a "reasonable worst case scenario" could look something like some of the Ebola outbreaks we've seen in the past 15 years - slow-burning, spluttering chains of transmission in hard-to-manage low-resource settings: bsky.app/profile/tah-...

Thomas House@tah-sci.com

> Given this, a reasonable best case is no further infections and deaths. For a reasonable worst case, we could look to the larger Ebola outbreaks - not a major pandemic like COVID, but we do sometimes see extended epidemics of pathogens that are ultimately controlled. >

@drmichaelmarks.bsky.social

12 May

That's not to say that's what will happen, but it is in the range of possible outcomes. Of course we can make those futures less likely with effective control measures now.

Billy Quilty reposted

Michael Marks

11 May

Replying to @bquilty.bsky.social

It is