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...

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...

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...

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...

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

royalsocietypublishing.org

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...

Mhairi McCormack@mhairijan.bsky.social · 2y ago

Had a wonderful time in Oxford this week filled with data modelling, presentations, meetings, and beautiful lunch spots! Huge thanks to @jameshay.bsky.social for inviting me down and all the wonderful researchers who have taken the time to speak with me #PhD #BigData @ox.ac.uk

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...

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...

Prof Christina Pagel@chrischirp.bsky.social · 10mo ago

🧵 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

🧵 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

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/...

Random time-shift approximation enables hierarchical Bayesian inference of mechanistic within-host viral dynamics models on large datasets journals.plos.org/ploscompbiol...

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...

journals.plos.org

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)

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.

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...

T.Y. Lim@tylim.bsky.social · 2y ago

How do you track an ongoing epidemic, especially without large-scale testing? We explored the use of routinely collected RT-qPCR cycle threshold values in our new preprint out now! doi.org/10.1101/2024... 1/

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

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...

bit.ly

🚨 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

Closing date tomorrow!

James Hay@jameshay.bsky.social · last yr.

We're hiring a modelling postdoc at PSI Oxford for two exciting projects: 1) modelling the early immune responses to Nipah vaccination, and 2) joining the PRESTO team working on immunobridging in vaccine evaluation studies. tinyurl.com/5abbxrjh Get in touch for more info! Deadline 4th August.

Excited to share our paper on viral load dynamics of West Nile virus in mosquitoes! Key findings: 1. Variation in pooled Ct values from mosquito traps reflect underlying biological and epidemiological mechanisms. 2. WNV prevalence estimates are improved by using Cts rather than +ve/-ve pool status.

Punya Alahakoon@punya-alahakoon.bsky.social · last yr.

New preprint! We use pooled Ct values from mosquito surveillance to estimate West Nile virus prevalence—without binarising the data. Joint work with Ian Marchinton, Joseph R. Fauver & James Hay. Check it out: www.biorxiv.org/content/10.1...

We're hiring a modelling postdoc at PSI Oxford for two exciting projects: 1) modelling the early immune responses to Nipah vaccination, and 2) joining the PRESTO team working on immunobridging in vaccine evaluation studies. tinyurl.com/5abbxrjh Get in touch for more info! Deadline 4th August.

Excited to share our paper on viral load dynamics of West Nile virus in mosquitoes! Key findings: 1. Variation in pooled Ct values from mosquito traps reflect underlying biological and epidemiological mechanisms. 2. WNV prevalence estimates are improved by using Cts rather than +ve/-ve pool status.

Punya Alahakoon@punya-alahakoon.bsky.social · last yr.

New preprint! We use pooled Ct values from mosquito surveillance to estimate West Nile virus prevalence—without binarising the data. Joint work with Ian Marchinton, Joseph R. Fauver & James Hay. Check it out: www.biorxiv.org/content/10.1...

Our latest paper www.sciencedirect.com/science/arti... shows that mass PCR testing could control a range of potential respiratory pandemics at low societal cost. We also explore logistics. Even a prototype would be really nice now with H5N1. @jameshay.bsky.social 1/9

Enhanced testing can substantially improve defense against several types of respiratory virus pandemic

Mass testing to identify and isolate infected individuals is a promising approach for reducing harm from the next acute respiratory virus pandemic. It…

sciencedirect.com

Two postdoc positions to work on virus epi & evolution in response to vaccination, with both theoretical models + data analysis. Paris/Montpellier. With Sylvain Gandon, Sébastien Lion, François Blanquart, Katrina Lythgoe, & Troy Day emploi.cnrs.fr/Offres/CDD/U... emploi.cnrs.fr/Offres/CDD/U...

Hello influenza enthusiasts! You may be interested in our recent publication linked below. We used multi-strain serology to figure out who got infected with which A/H3N2 influenza strain and when, allowing us to reconstruct epidemiological patterns back to 1968 stratified by time, age and location.

James Hay@jameshay.bsky.social · 2y ago

Reconstructed influenza A/H3N2 infection histories using multistrain serology, paper out in PLOS Biology plos.io/3YIDQpt! We inferred lifetime infections and antibody levels for 1130 individuals in Guangzhou, China, giving insights into long-term influenza incidence and immunity. Thread below:

Are you interested in analysing serological data for infectious disease epidemiology? Check out our new review article on serodynamics! With Saki Takahashi at JHU and Isobel Routledge at UCSF. (See next comment if you're into serology modeling) www.sciencedirect.com/science/arti...

Serodynamics: A primer and synthetic review of methods for epidemiological inference using serological data

We present a review and primer of methods to understand epidemiological dynamics and identify past exposures from serological data, referred to as ser…

sciencedirect.com

Are you interested in analysing serological data for infectious disease epidemiology? Check out our new review article on serodynamics! With Saki Takahashi at JHU and Isobel Routledge at UCSF. (See next comment if you're into serology modeling) www.sciencedirect.com/science/arti...

Serodynamics: A primer and synthetic review of methods for epidemiological inference using serological data

We present a review and primer of methods to understand epidemiological dynamics and identify past exposures from serological data, referred to as ser…

sciencedirect.com

New study tracking epidemic dynamics using cycle threshold values (a proxy for viral load) from routine hospital and community testing. This is the next step of our work from 2021 showing that the population distribution of Ct values over time is related to SARS-CoV-2 epidemic growth rates.

T.Y. Lim@tylim.bsky.social · 2y ago

How do you track an ongoing epidemic, especially without large-scale testing? We explored the use of routinely collected RT-qPCR cycle threshold values in our new preprint out now! doi.org/10.1101/2024... 1/

New study tracking epidemic dynamics using cycle threshold values (a proxy for viral load) from routine hospital and community testing. This is the next step of our work from 2021 showing that the population distribution of Ct values over time is related to SARS-CoV-2 epidemic growth rates.

T.Y. Lim@tylim.bsky.social · 2y ago

How do you track an ongoing epidemic, especially without large-scale testing? We explored the use of routinely collected RT-qPCR cycle threshold values in our new preprint out now! doi.org/10.1101/2024... 1/

NEW EPISODE #ScienceInContext! This week Dr @eonore.bsky.social speaks with Dr @jameshay.bsky.social of the Big Data Institute about influenza: who, where and when influenza infections are likely to occur using antibody profiles and individual infection histories 👇 youtu.be/Ux6yDWO_c8I

Reconstructed influenza A/H3N2 infection histories using multistrain serology, paper out in PLOS Biology plos.io/3YIDQpt! We inferred lifetime infections and antibody levels for 1130 individuals in Guangzhou, China, giving insights into long-term influenza incidence and immunity. Thread below:

Reconstructed influenza A/H3N2 infection histories reveal variation in incidence and antibody dynamics over the life course

How do repeated influenza infections generate such a complex immunological landscape? This study of influenza A/H3N2 in humans estimated lifetime infection histories for 1,130 individuals, reconstruct...

plos.io

James Hay@jameshay.bsky.social · 2y ago

New preprint: Reconstructed influenza A/H3N2 infection histories reveal variation in incidence and antibody dynamics over the life course www.medrxiv.org/content/10.1...

New preprint: Reconstructed influenza A/H3N2 infection histories reveal variation in incidence and antibody dynamics over the life course www.medrxiv.org/content/10.1...

Reconstructed influenza A/H3N2 infection histories reveal variation in incidence and antibody dynamics over the life course

medRxiv - The Preprint Server for Health Sciences

medrxiv.org