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James Hay

@jameshay.bsky.social
1.5K followers 599 following 63 posts

Research Fellow at the Pandemic Sciences Institute, University of Oxford. Using maths and stats to understand infectious disease dynamics, mostly viral kinetics and serology. hay-idd.github.io

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Reposted by James Hay
Mariana Lenharo @marilenharo.bsky.social · 06/10/2026
The flu season seems to be off to an early start in the Northern Hemisphere and scientists are worried about one particular mutation. That means it's a good idea to go get vaccinated as soon as possible! I wrote about what the early data tell us: www.nature.com/articles/d41...
nature.com
Flu season could kick off ‘incredibly’ early — what scientists are watching
Cases in the Northern Hemisphere are cropping up weeks early, and they are dominated by a virus with a concerning mutation.
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James Hay @jameshay.bsky.social · 02/10/2026
Now published in PLOS Global Health! @mhairijan.bsky.social journals.plos.org/globalpublic...
journals.plos.org
SARS-CoV-2 neutralising antibody profiles reveal variant specific antibody dynamics and regional differences in infection histories in Malawi
Serological data provide important insights into SARS-CoV-2 transmission and immunity, particularly in regions with limited routine surveillance such as sub-Saharan Africa. However, antibody waning an...
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James Hay @jameshay.bsky.social · 18/09/2026
I hope that by making serosolver and other tools increasingly accessible and flexible, we can move the field towards a more mature state on par with Rt estimation and phylodynamics! Please do check it out, and get in touch if this is something you’re interested in.
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James Hay @jameshay.bsky.social · 18/09/2026
Methods to get the most information from serological data are still fairly specialist, though there have been some great developments in the past few years (e.g., serocalculator ucd-serg.github.io/serocalculat..., serofoi epiverse-trace.github.io/serofoi/ and serojump seroanalytics.org/serojump/).
ucd-serg.github.io
serocalculator
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James Hay @jameshay.bsky.social · 18/09/2026
Each one of these projects required a new feature or modification to serosolver, which I’ve finally managed (with the help of my colleague Dr. Luna GPT) to bundle together into a single stable version with comprehensive documentation and vignettes.
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James Hay @jameshay.bsky.social · 18/09/2026
Seasonal norovirus GII.4 variant serology from children in England, used to estimate annual exposures and antibody kinetics across variants: doi.org/10.64898/202...
doi.org
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James Hay @jameshay.bsky.social · 18/09/2026
SARS-CoV-2 neutralising-antibody profiles from Malawi to estimate variant=-specific antibody dynamics and urban/rural differences in infection rates: doi.org/10.64898/202...
doi.org
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James Hay @jameshay.bsky.social · 18/09/2026
Since then, serosolver has been used for multiple pathogens, including: Estimating age-specific antibody dynamics for multiple respiratory viruses in King County, USA: doi.org/10.1038/s414...
doi.org
Multiplex serology reveals age-specific immunodynamics of respiratory pathogens in the wake of the COVID-19 pandemic - Nature Communications
Non-pharmaceutical interventions for COVID-19 also reduced circulation of endemic viruses which may have led to immune waning. Here, the authors use multiplex serology data from King County, Washingto...
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James Hay @jameshay.bsky.social · 18/09/2026
This release is a long overdue documentation and interface update following multiple extensions over the past few years. serosolver was published in 2020 (doi.org/10.1371/jour...), born out of my PhD work estimating 1000s of flu infections from multi-strain serology (doi.org/10.1371/jour...).
doi.org
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James Hay @jameshay.bsky.social · 18/09/2026
serosolver's USP is that it's flexible enough to work for other antigenically variable pathogens (like SARS-CoV-2), using antigenic maps as input data to disentangle cross-reactive responses. However, it also accommodates pathogens/questions where we only need to consider a single antigen.
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James Hay @jameshay.bsky.social · 18/09/2026
What does the package do? serosolver takes individual-level serological data to jointly estimate lifetime infection histories and antibody kinetics. We originally developed the model to analyse influenza antibody landscapes, where accounting for cross-reactivity between strains is essential.
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James Hay @jameshay.bsky.social · 18/09/2026
Are you interested in using serology to detect hidden infections, model immune responses, and estimate epidemic dynamics? You may be interested in the new 1.2.0 release of the R package, serosolver: seroanalytics.org/serosolver/i...
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James Hay @jameshay.bsky.social · 18/09/2026
SARS-CoV-2 neutralising-antibody profiles from Malawi to estimate variant-specific antibody dynamics and urban/rural differences in infection rates: doi.org/10.64898/202...
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James Hay @jameshay.bsky.social · 18/09/2026
Since then, serosolver has been used for multiple pathogens, including: Estimating age-specific antibody dynamics for multiple respiratory viruses in King County, USA: doi.org/10.1038/s414...
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James Hay @jameshay.bsky.social · 18/09/2026
This release is a long overdue documentation and interface update following multiple extensions over the past few years. serosolver was published in 2020 (doi.org/10.1371/jour...), born out of my PhD work estimating 1000s of flu infections from multi-strain serology (doi.org/10.1371/jour...).
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James Hay @jameshay.bsky.social · 18/09/2026
serosolver's USP is that it's flexible enough to work for other antigenically variable pathogens (like SARS-CoV-2), using antigenic maps as input data to disentangle cross-reactive responses. However, it also accommodates pathogens/questions where we only need to consider a single antigen.
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James Hay @jameshay.bsky.social · 18/09/2026
What does the package do? serosolver takes individual-level serological data to jointly estimate lifetime infection histories and antibody kinetics. We originally developed the model to analyse influenza antibody landscapes, where accounting for cross-reactivity between strains is essential.
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Reposted by James Hay
James Hay @jameshay.bsky.social · 22/06/2026
Are you a computational immunologist or bioinformatician interested in impactful vaccine research? We're hiring a postdoc to join @psioxford.bsky.social work in vaccine immunology and evaluation, working on the ChAdOx1 Nipah vaccine. Please get in touch! my.corehr.com/pls/uoxrecru...
my.corehr.com
Job Details
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James Hay @jameshay.bsky.social · 22/06/2026
Are you a computational immunologist or bioinformatician interested in impactful vaccine research? We're hiring a postdoc to join @psioxford.bsky.social work in vaccine immunology and evaluation, working on the ChAdOx1 Nipah vaccine. Please get in touch! my.corehr.com/pls/uoxrecru...
my.corehr.com
Job Details
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James Hay @jameshay.bsky.social · 30/04/2026
It was absolutely wonderful to write something again with @skissler.bsky.social, @danlarremore.bsky.social and Aishani Aatresh. Here's our new review/perspective on the value of measuring and modelling viral kinetics as part of routine surveillance: royalsocietypublishing.org/rstb/article...
royalsocietypublishing.org
Integrating viral kinetics into routine outbreak surveillance: challenges, opportunities and lessons from COVID-19
Abstract. Viral kinetics provide crucial insights into the biology and epidemiology of infections, with direct implications for basic science, therapeutics
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James Hay @jameshay.bsky.social · 17/04/2026
Delighted to share the (preprint) output of @mhairijan.bsky.social's Oxford visit: SARS-CoV-2 Neutralising Antibody Profiles Reveal Variant Specific Antibody Dynamics and Regional Differences in Infection Histories in Malawi. dx.doi.org/10.2139/ssrn...
ssrn.com
SARS-CoV-2 Neutralising Antibody Profiles Reveal Variant Specific Antibody Dynamics and Regional Differences in Infection Histories in Malawi
Background: Serological data provide important insights into SARS-CoV-2 transmission and immunity, particularly in regions with limited routine surveillance suc
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Reposted by James Hay
Megan O'Driscoll @meganodris.bsky.social · 18/12/2025
The final piece of my PhD work is now published in Science Translational Medicine! We present a new framework to jointly infer epidemiological and antigenic parameters from multi-pathogen population serological studies🦠 www.science.org/stoken/autho...
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James Hay @jameshay.bsky.social · 11/12/2025
Totally agree! We did a quick analysis and some scenario models a few weeks ago and came to a similar conclusion -- fast and early but not unprecedented. An early start may also lead to earlier susceptible depletion. zenodo.org/records/1770... Similar from WHO: www.who.int/emergencies/...
zenodo.org
Evaluation of the epidemiological outlook of the influenza A/H3N2 clade K in England during the 2025-26 season
Key findings England is currently experiencing a high growth rate of infections caused by the influenza A/H3N2 K clade. Antigenic change from the previously dominant clade, a rapid selective sweep evi...
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James Hay @jameshay.bsky.social · 11/12/2025
Great take. We looked at the data a few weeks ago and concluded that other than starting early, this year's dynamics are comparable to previous bad seasons. Our scenario models suggest a peak in infections (not hospitalisations which lag 1/2 weeks) in early/mid December. zenodo.org/records/1770...
zenodo.org
Evaluation of the epidemiological outlook of the influenza A/H3N2 clade K in England during the 2025-26 season
Key findings England is currently experiencing a high growth rate of infections caused by the influenza A/H3N2 K clade. Antigenic change from the previously dominant clade, a rapid selective sweep evi...
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Reposted by James Hay
Prof Christina Pagel @chrischirp.bsky.social · 11/12/2025
🧵 Is it a super flu year? Who knows, but I think the current reporting is stupid. A pissed off thread using data. Firstly - here are today's headlines and some from the last 3 years... spot the difference. 1/10
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Reposted by James Hay
Ian M. Mackay, PhD (he/him) 🦠🤧🧬📑🦟🧀 @mackayim.bsky.social · 10/12/2025
WHO Disease Update Notification: Seasonal influenza 🦠Since August 2025, there's been a rapid increase of A(H3N2) J.2.4.1 subclade K driving early & prolonged seasons 🦠Vaccine helps against hospitalisation, unclear about milder impact 🦠K induces "normal" disease spectrum www.who.int/emergencies/...
who.int
Seasonal influenza - Global situation
Seasonal influenza (‘the flu’) is an acute respiratory infection caused by influenza viruses that circulate globally and year-round. It can cause illness ranging from mild to severe, sometimes resulti...
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Reposted by James Hay
NetScience @netscience.bsky.social · 05/12/2025
Random time-shift approximation enables hierarchical Bayesian inference of mechanistic within-host viral dynamics models on large datasets journals.plos.org/ploscompbiol...
journals.plos.org
Random time-shift approximation enables hierarchical Bayesian inference of mechanistic within-host viral dynamics models on large datasets
Author summary Understanding how viruses reproduce within an infected host is crucial for predicting disease progression and evaluating treatments. One way to study this is by using mathematical model...
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James Hay @jameshay.bsky.social · 25/11/2025
Many thanks also to @stevenriley.bsky.social @scauchemez.bsky.social @neher.io @eales96.bsky.social, and Ben Cowling, Freya Shearer and Juliette Paireau for helpful discussion. (18/18)
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James Hay @jameshay.bsky.social · 25/11/2025
Coauthors: @punya-alahakoon.bsky.social @mishkendall.bsky.social @mghafari.bsky.social @chriswymant.bsky.social @christophraser.bsky.social and Alex Greenshields Watson, Rob Hinch, Luca Ferretti and Jasmina Panovska-Griffiths not on bsky. (17/18)
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James Hay @jameshay.bsky.social · 25/11/2025
Thanks to the @christophraser.bsky.social team for immense work in a very short time, particularly to @punya-alahakoon.bsky.social and Alex Greenshields-Watson who made great contributions under pressure. (16/18)
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James Hay @jameshay.bsky.social · 25/11/2025
Caution is needed – we looked only at data from England, whereas other countries might see quite different trends (e.g., bsky.app/profile/cmye...). Historical experience with early H3N2 seasons is also worth bearing in mind: pmc.ncbi.nlm.nih.gov/articles/PMC... (1989/90 season). (15/18)
pmc.ncbi.nlm.nih.gov
Lessons from 40 years' surveillance of influenza in England and Wales
The influenza virus continues to pose a significant threat to public health throughout the world. Current avian influenza outbreaks in humans have heightened the need for improved surveillance and planning. Despite recent advances in the development ...
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James Hay @jameshay.bsky.social · 25/11/2025
Overall, the K clade seems to have higher growth than dominant strains in prior seasons, but not total immune escape (antibody escape != all immune escape). For England, the earlier season might have interacted with half-term to dampen the peak burden (but not necessarily overall burden). (14/18)
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James Hay @jameshay.bsky.social · 25/11/2025
Our plan is to update this analysis again with cleaner data as things continue to unfold. The most current data are presented by UKHSA here: www.gov.uk/government/s... (13/18)
gov.uk
National flu and COVID-19 surveillance reports: 2025 to 2026 season
National influenza (flu) and COVID-19 report, monitoring COVID-19 activity, seasonal flu and other seasonal respiratory illnesses.
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James Hay @jameshay.bsky.social · 25/11/2025
Another key limitation is the omission of vaccination. The K clade seems to have drifted away from this season’s vaccine strains, but preliminary data from the UKHSA suggest that vaccine efficacy is in line with previous seasons. www.eurosurveillance.org/content/10.2... (12/18)
eurosurveillance.org
Early influenza virus characterisation and vaccine effectiveness in England in autumn 2025, a period dominated by influenza A(H3N2) subclade K
Influenza A(H3N2) subclade K (J.2.4.1) has dominated the 2025/26 season start in England. Post-infection ferret antisera raised against northern hemisphere 2025/26 vaccine strains showed reduced reactivity to subclade K viruses in England, aligning with World Health Organization reports. Nevertheless, early post-vaccination, vaccine effectiveness against influenza-related emergency department attendances and hospital admissions remained within typical ranges, at 72–75% in children and adolescents (< 18 years) and 32–39% in adults. Hence, vaccination remains effective against clinical disease caused by influenza A(H3N2) viruses.
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James Hay @jameshay.bsky.social · 25/11/2025
This analysis was done quickly with many limitations (see preprint!) – we merged imperfect ILI+ datasets from past seasons, combined H3N2 and other subtypes, made many assumptions for our scenario model, and some growth trends might be masked by smoothing introduced through the models. (11/18)
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James Hay @jameshay.bsky.social · 25/11/2025
Also compatible but perhaps less plausible are a 10-20% higher R0, or an earlier seed date. In almost all scenarios, an earlier and faster epidemic growth rate leads to depletion of susceptibles before the Christmas period with a dampening effect due to the half term school holiday. (10/18)
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James Hay @jameshay.bsky.social · 25/11/2025
The scenarios suggest substantial immune escape is unlikely given current trends. Only a small drop in population immunity is needed to generate an early peak and faster growth. Current data are compatible with small levels of immune escape in all ages, or greater escape in children. (9/18)
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James Hay @jameshay.bsky.social · 25/11/2025
However, it’s tricky to translate immune escape from antibodies in the lab to overall immune escape in human populations, where other immune mechanisms will play a key role. (8/18)
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James Hay @jameshay.bsky.social · 25/11/2025
A key concern for the season has been immune escape of the new clade. Antibodies generated in response to infection from other recent H3N2 viruses, including the vaccine strain, do not appear to recognise K clade viruses very well: youtu.be/jKlthy3YYNQ?.... (7/18)
youtu.be
WHO Information Meeting - Influenza virus vaccines composition for 2026 Southern Hemisphere
YouTube video by World Health Organization Regional Office for the Western Pacific
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James Hay @jameshay.bsky.social · 25/11/2025
Alex Greenshields-Watson put the model online as a webtool for others to explore: hay-idd.shinyapps.io/ModelFluUk-H.... *We particularly encourage users to tailor scenarios for Scotland, Wales and NI, as the season timing has been quite different to England so far.* (6/18)
hay-idd.shinyapps.io
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James Hay @jameshay.bsky.social · 25/11/2025
We developed an age-stratified SIR model, visually calibrated to 2022/23 data (an H3N2 season). We ran scenarios varying intrinsic transmissibility, loss of immunity overall or in children, and the season start date. We accounted for changes in contacts over school holidays and Christmas. (5/18)
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James Hay @jameshay.bsky.social · 25/11/2025
Rapid spread in children – the usual culprits driving seasonal flu transmission. Compared to the past 2 seasons, there has been a larger difference in growth rate between <14 yos and adults. Half term caused a drop in growth and may have acted as a circuit break for the early season. (4/18)
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James Hay @jameshay.bsky.social · 25/11/2025
Case numbers and epi dynamics don’t look too unusual when you align the curves by date of peak growth rate (* to date*). The flu season has started very early but is otherwise not completely unprecedented (at least in terms of symptomatic cases). (3/18)
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James Hay @jameshay.bsky.social · 25/11/2025
We analysed public data sources (Resp DataMart, RGCP, WHO FluNet) from England to compare growth rates and reproduction numbers to previous seasons. So far, peak growth rates have been higher than the past 10 seasons, but Rt estimates are in line with the upper end of previous seasons. (2/18)
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James Hay @jameshay.bsky.social · 25/11/2025
H3N2 preprint: there are concerns of a severe incoming influenza season due to the drifted H3N2 K clade. We at @psioxford.bsky.social analysed epi data and ran scenario models to see what we could discern about K clade transmission dynamics: zenodo.org/records/1770.... (1/18)
zenodo.org
Evaluation of the epidemiological outlook of the influenza A/H3N2 clade K in England during the 2025-26 season
Key findings England is currently experiencing a high growth rate of infections caused by the influenza A/H3N2 K clade. Antigenic change from the previously dominant clade, a rapid selective sweep evi...
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Reposted by James Hay
Caitlin Rivers @cmyeaton.bsky.social · 20/11/2025
In Texas' public health region 6/5S, which includes Houston, the number of emergency department visits for influenza is already almost on par with the *peak* of last year.
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Reposted by James Hay
Yonatan Grad @yhgrad.bsky.social · 20/11/2025
Now out in @natcomms.nature.com Kudos to @tylim.bsky.social and @jameshay.bsky.social for a huge effort and thanks to all the collaborators for their hard work. See the final version here: www.nature.com/articles/s41...
nature.com
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Reposted by James Hay
CCDD @ccdd-hsph.bsky.social · 21/11/2025
New study shows that shifts in SARS‑CoV‑2 Ct value distributions can help nowcast epidemic trends, revealing both strong potential and key real‑world limitations for Ct‑based surveillance. From CCDD alumni TY Lim & @jameshay.bsky.social and faculty @yhgrad.bsky.social at bit.ly/4o37EaN
bit.ly
Nowcasting epidemic trends using hospital- and community-based virologic test data - Nature Communications
Population-level distributions of SARS-CoV-2 viral load can correlate with epidemic trends. Here, the authors use viral loads to nowcast epidemic growth rates over two-week periods and investigate how...
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Reposted by James Hay
David Hodgson @dchodge.bsky.social · 23/09/2025
🚨 New paper out in PLOS Computational Biology! 🚨 We're excited to share our new paper, serojump, a new probabilistic framework and R package for inferring infections and antibody kinetics from longitudinal serological data. 📄 Full paper: tinyurl.com/re7du3t2 R package: seroanalytics.org/serojump
seroanalytics.org
A serological inference package using reversible jump mcmc
The `serojump` package provides tools for fitting serological models to antibody kinetics data using reversible-jump Markov Chain Monte Carlo (RJ-MCMC). It enables researchers to model the dynamics of...
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James Hay @jameshay.bsky.social · 03/08/2025
Closing date tomorrow!
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