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jdmunday.bsky.social
James Munday
@jdmunday.bsky.social
1.6K followers 460 following 67 posts
Infectious disease epidemiology and surveillance at Swiss TPH • jdmunday.github.io
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jdmunday.bsky.social
James Munday @jdmunday.bsky.social · 14d
New Paper🚀! Our work analysing the Swiss national SARS-CoV-2 wastewater 🚱 monitoring data is now published in PLOS Water 💧 @plos.org journals.plos.org/water/articl... (Julien Riou, @tanjastadler.bsky.social @trj2.bsky.social Christoph Ort et al)
Fig 3. (A) Adjusted time trends in SARS-CoV-2 wastewater viral load in seven regions of Switzerland (uncertainty is not shown for clarity). (B) Correlation between adjusted time trends in viral load and laboratory-confirmed SARS-CoV-2 hospitalisations in the same region. (C) Adjusted bias in viral load by wastewater treatment plant.
Reposted by James Munday
gmknght.bsky.social
How will population shifts affect the future burden of #AMR? 👶👩‍🦳 🧫

We use a new modelling framework to explore future projections of #AMR by age and by sex, as well as interventions for control, building on our earlier findings that AMR isn’t uniform across demographics.

doi.org/10.1371/jour...
Combining demographic shifts with age-based resistance prevalence to estimate future antimicrobial resistance burden in Europe and implications for targets: A modelling study
Author summary Why was this study done? Infections caused by bacteria that are resistant to antibiotics are a major and growing threat to public health. Older adults and men are at higher risk of...
doi.org
November 5, 2025 at 12:06 PM
jdmunday.bsky.social
New Paper🚀! Our work analysing the Swiss national SARS-CoV-2 wastewater 🚱 monitoring data is now published in PLOS Water 💧 @plos.org journals.plos.org/water/articl... (Julien Riou, @tanjastadler.bsky.social @trj2.bsky.social Christoph Ort et al)
Fig 3. (A) Adjusted time trends in SARS-CoV-2 wastewater viral load in seven regions of Switzerland (uncertainty is not shown for clarity). (B) Correlation between adjusted time trends in viral load and laboratory-confirmed SARS-CoV-2 hospitalisations in the same region. (C) Adjusted bias in viral load by wastewater treatment plant.
November 4, 2025 at 1:39 PM
jdmunday.bsky.social
Our paper "Forecasting the spatial spread of an Ebola epidemic in real-time: comparing predictions of mathematical models and experts" is now published as a 'version of record' in @elife.bsky.social (with @sbfnk.bsky.social Alicia Rosello and John Edmunds) doi.org/10.7554/eLif... 1/5
Forecasting the spatial spread of an Ebola epidemic in real time: Comparing predictions of mathematical models and experts
Models were more consistent than individual experts but performed comparably to ensembles of many experts and relative performance varied by month, justifying the use of combined model and expert fore...
doi.org
October 13, 2025 at 12:00 PM
jdmunday.bsky.social
New paper led by Nicolas Banholzer "Absences, Symptoms and Respiratory Viruses in a Swiss School: Longitudinal Study With Serial Saliva Sampling" Now published in *Influenza and Other Respiratory Viruses* doi.org/10.1111/irv....
Absences, Symptoms and Respiratory Viruses in a Swiss School: Longitudinal Study With Serial Saliva Sampling
Background Viral respiratory infections contribute to sick days in school children. We monitored respiratory infections, absences, and symptoms in a Swiss school. Methods Serial saliva sampling (t...
doi.org
September 30, 2025 at 12:07 PM
jdmunday.bsky.social
New Preprint 💫: *Projected sudden step-wise increase in risk of large measles outbreaks in the Netherlands as susceptible children enter secondary school in 2025/26* on MedRxiv doi.org/10.1101/2025... (NOT YET PEER REVIEWED)
Projected sudden step-wise increase in risk of large measles outbreaks in the Netherlands as susceptible children enter secondary school in 2025/26
Background Many unvaccinated children were naturally immunised through infection during the last national Measles epidemic in the Netherlands (2013/14). Over time susceptibility amongst school aged ch...
doi.org
September 4, 2025 at 7:42 AM
Reposted by James Munday
jhuisman.bsky.social
Our paper on the transmission dynamics of Noro- and Enterovirus during the COVID-19 pandemic just came out: www.sciencedirect.com/science/arti...
We measured wastewater viral loads, estimated Re and assessed the impact of non-pharmaceutical interventions on the transmission of these pathogens.
Transmission dynamics of Norovirus GII and Enterovirus in Switzerland during the COVID-19 pandemic (2021–2022) as evidenced in wastewater
Noroviruses and enteroviruses are major causes of endemic gastrointestinal disease associated with substantial disease burden. However, viral gastroen…
www.sciencedirect.com
August 22, 2025 at 3:03 PM
jdmunday.bsky.social
New Preprint! Co-led with Nicolas Banholzer *The relative contribution of close-proximity contacts, shared classroom exposure and indoor air quality to respiratory virus transmission in schools* on MedRxiv. doi.org/10.1101/2025... (YET TO BE PEER REVIEWED)
The relative contribution of close-proximity contacts, shared classroom exposure and indoor air quality to respiratory virus transmission in schools.
Close-proximity interactions are considered a key risk factor for respiratory virus transmission, but their importance relative to shared space and air quality remains unclear. We conducted a six-week...
doi.org
August 22, 2025 at 9:24 AM
jdmunday.bsky.social
Just when you think you are beginning to understand a sport...
July 12, 2025 at 10:27 AM
Reposted by James Munday
edmhill.bsky.social
📣 Funded 3.5yr PhD opportunity (UK tuition fee rate) in @hpruezi.bsky.social @liverpooluni.bsky.social. #PhDSky

🧪 On "Optimising testing & control strategies in the early stages of infectious disease outbreaks" #IDSky #EpiSky

⏳ Deadline to apply: 07 Jul 2025

🔗: www.liverpool.ac.uk/courses/opti...
Optimising testing and control strategies in the early stages of infectious disease outbreaks Supervisors: Dr Emily Nixon, Professor Christl Donnelly, Dr Richard Vipond, Dr Emily Adams, Dr Chris Overton. Subject area: Mathematics Stipend Amount: Funded studentship Study mode: Full-time Duration: 3.5 years Application deadline: 07 July 2025 Start date: 01 October 2025 Overview Develop models to help make decisions early in a major disease outbreak when availability of new tests is limited, on where and how best to use them for maximum impact in controlling spread, e.g. in low versus high areas of transmission, in hospitals or in the community. These will depend on the pathogen type, its mode of transmission, reproduction number, etc. About this opportunity In the early stages of a major disease outbreak, the availability of suitable diagnostic tests is often limited, however, timely interventions are critical for controlling the spread of disease. In this PhD, you will develop mechanistic and statistical models to investigate the effectiveness of various diagnostic test deployment strategies for emerging and zoonotic diseases which are at risk of causing large outbreaks, such as respiratory viruses (Influenza, SARS-CoV-2, Respiratory syncytial virus), vector-borne diseases (Dengue, Tick-borne encephalitis) or viral haemorrhagic fevers (Nipah, Lassa fever and Crimean-Congo haemorrhagic fever). You will investigate the effectiveness of targeting use of tests in different settings, for example in areas of high versus low transmission, or in hospitals versus the community. The optimum strategy for diagnostic test deployment will vary depending on prevalence of disease, the sensitivity and specificity of the tests and the time it takes to receive and act on results. In addition, variation between pathogens, for example, in their mode of transmission, reproduction number and incubation period, will influence which strategy is the most effective in controlling the impact of the outbreak. These insights will inform stockpiling strategies of medical countermeasures for pandemic preparedness and in the event of a major outbreak, can be used and adapted to help inform decision making. Who is this for? Applicants must hold, in a relevant STEM subject, either a first-class honours degree, a distinction at master level, or equivalent achievements. A background in programming (such as R, Python, Julia) would be advantageous, along with a keen desire to develop those skills. Prospective applicants are encouraged to contact the primary supervisor, Dr Emily Nixon, emily.nixon@liverpool.ac.uk prior to preparation of an application to discuss the fit of the project with your background and qualifications. Funding your PhD This PhD opportunity is funded by the National Institute for Health and Care Research (NIHR) Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections (EZI). This studentship will be for a maximum of 3.5 years duration. The studentship includes tuition fees at the UK/home rate, stipend and research-related travel. International students may apply but must be able to themselves cover the additional tuition fee costs as outlined on the University website: https://www.liverpool.ac.uk/study/fees-and-funding/tuition-fees/postgraduate-research/. The supervisory team have no additional funding to support this difference in tuition fee costs for international students. The stipend amount is aligned with UK Research and Innovation rates. For the academic year 2025-2026, the rate of the UKRI Stipend is £20,780 per annum (tax free).
June 17, 2025 at 4:06 PM
Reposted by James Munday
tanjastadler.bsky.social
In this project led by James Munday, we quantified the post-sampling degradation of viral RNA in wastewater. Taking into account this degradation is core towards unbiased quantification of epidemiological dynamics based on wastewater data.
June 17, 2025 at 11:11 AM
jdmunday.bsky.social
We have a new preprint 📝 *Post-sampling degradation of viral RNA in wastewater impacts the quality of PCR-based concentration estimates* Now on bioRxiv doi.org/10.1101/2025... with @tanjastadler.bsky.social, trj2.bsky.social, Christoph Ort and others
Post-sampling degradation of viral RNA in wastewater impacts the quality of PCR-based concentration estimates
Successful wastewater-based infectious disease surveillance programs depend on regular, reliable molecular detection of nucleic acids in municipal wastewater systems. This process is challenged by the...
doi.org
June 9, 2025 at 9:05 AM
Reposted by James Munday
sonjalehtinen.bsky.social
Come work with us! We're looking of postdoc(s) with experience in bacterial genomics and interest in mathematical modelling to work on bacterial ecology and evolution in the context of public health. tinyurl.com/n34vzszu
Opportunités de carrière : Postdoctoral researcher in bacterial genomics (22209)
tinyurl.com
April 28, 2025 at 5:54 PM
jdmunday.bsky.social
New preprint 📝. We used a bayesian time-series model to quantify contributions of various factors to variation in the SARS-CoV-2 concentration in 🇨🇭 wastewater. We then analyse geographic correlations in adjusted conc. using DTW distances. doi.org/10.1101/2025...
Determinants and spatio-temporal structure of variability in wastewater SARS-CoV-2 viral load measurements in Switzerland: key insights for future surveillance efforts
Background: Wastewater-based surveillance (WBS) has emerged as a valuable tool for monitoring the circulation of infectious pathogens in the population, offering a complement to classical surveillance...
doi.org
May 12, 2025 at 8:31 AM
jdmunday.bsky.social
Check out our new perspective in Epidemics on wastewater surveillance and pandemic prep. It came out of a workshop spearheaded by Kath O'Reilly and @leondanon.bsky.social. What can we do? what could we do better? And when is it most likely to be useful? doi.org/10.1016/j.ep...
Redirecting
doi.org
April 4, 2025 at 2:31 PM
Reposted by James Munday
iddjobs.org
Other (Barcelona, Spain)
We seek a highly motivated data scientist to co-create harmonised datasets and dashboards for decision-support.
More details: http://iddjobs.org/jobs/we-seek-a-highly-motivated-data-scientist-to-co-create-harmonised-datasets-and-dashboards-for-decision-support
December 21, 2024 at 8:42 AM
Reposted by James Munday
edmhill.bsky.social
📣 #fundedPhD in "Modelling salivo-surveillance for detecting population immunity, transmission dynamics & changes in vaccine effectiveness" #IDsky #EpiSky #PhDSky 🧪

👥 Supervised by @3113n.bsky.social + colleagues at Uni. of Bristol & UKHSA

🗓️ Closes 27 Jan 2025. Interviews Mar 2025. Start Sep 2025.
About the Project. Vaccination is a highly effective public health intervention that prevents morbidity and mortality. The UK vaccination programme evolves in response to vaccine developments and emerging evidence. This may include the addition of new vaccines, or removal of old vaccines or booster doses. Following a modification to the vaccine schedule, there is a delay before the impact on key indicators such as diagnosed cases, hospital admissions and deaths is observed. This delay hampers the responsiveness of public health action. We are developing saliva-based tests that will facilitate rapid, repeated sampling to measure both carriage of respiratory pathogens and mucosal immunocorrelates, and thus detect changes in population immunity before disease cases present. The aim of these tests is to develop a surveillance programme that will provide an early warning system for lapses in population-level protection and allow for adaptive management of the UK vaccine schedule. Project aims: The aim of this PhD is to use data analytics, data linkage and mathematical models to inform the use and necessary test characteristics of saliva-based tests for vaccination evaluation. The aims of the project are to: - Develop transmission models for vaccine-preventable respiratory pathogens (Streptococcus pneumoniae and Respiratory Syncytial Virus) and emerging threats (Group A Streptococcus) in the UK. - Identify opportunities for early identification of changes in population immunity that would provide a rapid assessment of vaccine effectiveness and coverage. - Explore the trade-offs involved in detecting population protection. Methods: This PhD will use data analysis, statistical and mathematical modelling to inform the use of a rapid and scalable test to measure changes in vaccine coverage and population protection. The methods will involve data analysis, visualisation and code development using software such as R, describing immunological process of transmission mathematically, reviewing and interpreting the literature and working with and maintaining an inter-disciplinary network of collaborators. In year 1, you will work with immunologists to use immunological data to develop data-driven mathematical models of the dynamics of transmission, carriage and infection for respiratory infectious diseases. In year 2, you will design models that link vaccination, disease transmission, carriage and healthcare usage. In year 3, you will explore the impact of changes to the vaccine schedule on population immunity and subsequently invasive disease and determine the necessary test uptake and characteristics needed to provide an early indication of changes to population immunity. There will be scope for the successful candidate to shape the research. Supervisors: Professor Ellen Brooks-Pollock, Dr Anu Goenka, Dr Mary Ramsay (UKHSA) & Dr Bassam Hallis (UKHSA). Advisory team: Dr Rajeka Lazarus, Dr Clare French, Dr Amy Thomas, Dr Leon Danon, Dr Alice Halliday. Candidate requirements: This is a unique opportunity for a quantitative scientist to join a multi-disciplinary team and work closely with clinicians, lab scientists and policymakers. Applications are sought from high performing individuals who have, or are expected to obtain, at least a 2.1 degree (or equivalent) in a quantitative subject (e.g. maths, statistics, physics, computer science, biological sciences) together with an interest in public health and multi-disciplinary research. Possession of a relevant Master's degree or research experience would be advantageous but is not required. We welcome applications from those with non-standard qualifications who can demonstrate knowledge, experience and skills developed in the workplace, or elsewhere, relevant to the programme of study. How to apply: When applying, candidates must search for and select the ‘Population Health Sciences PhD’ programme and enter supervisor names as listed under the project title for which they are applying. Please state Health Protection Research Unit in Evaluation and Behavioural Science in the funding box. Full details on what to include in your application can be found in the Admissions Statement. Personal statement: Please provide a personal statement that describes your training and experience so far, your motivation for doing a PhD, your motivations for applying to the University of Bristol, and why you think we should select you. We are keen to support applicants from minority and under-represented backgrounds (based on protected characteristics) and those who have experienced other challenges or disadvantages. We encourage you to use your personal statement to ensure we can take these factors into account. Funding Notes: The studentship is fully funded by Health Protection Research Unit in Evaluation and Behavioural Science (HPRU-EBS) for three years. The funding covers tuition fees for home students and a stipend at the UKRI rate (£19,237 in 2024/2025). Overseas students are very welcome to apply, please include in your application if you are able pay the difference between the home and overseas fees. If you are unable to cover these costs, we can look into other options to cover these. Deadline: Applications for this project will close at 16:00 GMT on Monday 27th January 2025. Interviews will be in March 2025 . The anticipated start date is September 2025. Contact: If you have questions about the project, please contact the supervisors. If you need help with your application, contact admissions at fohs-pgadmissions@bristol.ac.uk.
December 11, 2024 at 7:34 PM
Reposted by James Munday
iddjobs.org
Postdoc (Berlin, Germany)
Vaccine or outbreak modelling. With Stefan Flasche
at @cmmid
More details: http://iddjobs.org/jobs/experienced-postdoc-in-vaccine-or-outbreak-modelling
December 11, 2024 at 6:39 PM
Reposted by James Munday
justinlessler.bsky.social
Congrats to team member Carl Pearson and his co-authors @lucygoodfellow.bsky.social and @mert0248.bsky.social. An important tool for a pervasive problem in modeling infectious disease data www.medrxiv.org/content/10.1...
paramix : An R package for parameter discretisation in compartmental models, with application to calculating years of life lost
Compartmental infectious disease models are used to calculate disease transmission, estimate underlying rates, forecast future burden, and compare benefits across intervention scenarios. These models ...
www.medrxiv.org
December 6, 2024 at 4:03 PM
Reposted by James Munday
pathoplexus.org
We're incredibly honoured to be winners of the Swiss Academies of Arts & Sciences National Prize for Open Research Data 2024! 🎉🎊

"Pathoplexus ensures open access and provides a cutting-edge infrastructure for interactive and programmable data exploration"

akademien-schweiz.ch/en/medien/pr...

1/2
November 28, 2024 at 4:50 PM
Reposted by James Munday
rozeggo.bsky.social
Position with @mert0248.bsky.social and me in modelling the potential impact of next generation flu vaccines: iddjobs.org/jobs/modelli...
IDDjobs — Modelling the potential impact and value of developing a new generation of influenza vaccines, and their potential utility during a pandemic. — LSHTM
Find infectious disease dynamics modelling jobs, studentships, and fellowships.
iddjobs.org
November 26, 2024 at 4:23 PM
Reposted by James Munday
anne-cori.bsky.social
A group of us have been working on creating a repository of models and epidemiological parameters ready-to-use in future epidemics, with a focus on high-threat pathogens. Today our Lassa review is out: www.sciencedirect.com/science/arti.... More on the overall project here: bit.ly/imperial-PERG
Lassa fever outbreaks, mathematical models, and disease parameters: a systematic review and meta-analysis
Understanding the epidemiological parameters and transmission dynamics of Lassa fever, a significant public health threat in west Africa caused by the…
www.sciencedirect.com
November 21, 2024 at 11:33 AM
Reposted by James Munday
chaoranchen.de
Our new GenSpectrum.org dashboard has finally launched! Using Influenza H5N1, RSV and SARS-CoV-2 data from INSDC and West Nile virus data from @pathoplexus.org, it enables fast and interactive analyses of genome sequencing data similar to CoV-Spectrum. 1/5
November 25, 2024 at 12:55 PM
Reposted by James Munday
jameshay.bsky.social
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.
November 20, 2024 at 5:31 PM
Reposted by James Munday
sbfnk.bsky.social
If there are any users of the socialmixr R package for estimating contact matrices here: we're planning some substantial changes to the user interface and would love to hear your thoughts/views. Please feel free to comment at github.com/epiforecasts...
November 22, 2024 at 10:57 AM