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Journal articleTamayo Cuartero C, Carnegie AC, Cucunuba ZM, et al., 2025,
From the 100 Day Mission to 100 lines of software development: how to improve early outbreak analytics.
, Lancet Digit Health, Vol: 7, Pages: e161-e166Since the COVID-19 pandemic, considerable advances have been made to improve epidemic preparedness by accelerating diagnostics, therapeutics, and vaccine development. However, we argue that it is crucial to make equivalent efforts in the field of outbreak analytics to help ensure reliable, evidence-based decision making. To explore the challenges and key priorities in the field of outbreak analytics, the Epiverse-TRACE initiative brought together a multidisciplinary group of experts, including field epidemiologists, data scientists, academics, and software engineers from public health institutions across multiple countries. During a 3-day workshop, 40 participants discussed what the first 100 lines of code written during an outbreak should look like. The main findings from this workshop are summarised in this Viewpoint. We provide an overview of the current outbreak analytic landscape by highlighting current key challenges that should be addressed to improve the response to future public health crises. Furthermore, we propose actionable solutions to these challenges that are achievable in the short term, and longer-term strategic recommendations. This Viewpoint constitutes a call to action for experts involved in epidemic response to develop modern and robust data analytic approaches at the heart of epidemic preparedness and response.
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Journal articlePeeling RW, Fongwen NT, Guzman MG, et al., 2025,
Specimen and data sharing to advance research and development on Zika virus
, The Lancet Microbe, Pages: 101057-101057, ISSN: 2666-5247 -
Journal articleScachetti GC, Forato J, Claro IM, et al., 2025,
Re-emergence of Oropouche virus between 2023 and 2024 in Brazil: an observational epidemiological study.
, Lancet Infect Dis, Vol: 25, Pages: 166-175BACKGROUND: Oropouche virus is an arthropod-borne virus that has caused outbreaks of Oropouche fever in central and South America since the 1950s. This study investigates virological factors contributing to the re-emergence of Oropouche fever in Brazil between 2023 and 2024. METHODS: In this observational epidemiological study, we combined multiple data sources for Oropouche virus infections in Brazil and conducted in-vitro and in-vivo characterisation. We collected serum samples obtained in Manaus City, Amazonas state, Brazil, from patients with acute febrile illnesses aged 18 years or older who tested negative for malaria and samples from people with previous Oropouche virus infection from Coari municipality, Amazonas state, Brazil. Basic clinical and demographic data were collected from the Brazilian Laboratory Environment Management System. We calculated the incidence of Oropouche fever cases with data from the Brazilian Ministry of Health and the 2022 Brazilian population census and conducted age-sex analyses. We used reverse transcription quantitative PCR to test for Oropouche virus RNA in samples and subsequently performed sequencing and phylogenetic analysis of viral isolates. We compared the phenotype of the 2023-24 epidemic isolate (AM0088) with the historical prototype strain BeAn19991 through assessment of titre, plaque number, and plaque size. We used a plaque reduction neutralisation test (PRNT50) to assess the susceptibility of the novel isolate and BeAn19991 isolate to antibody neutralisation, both in serum samples from people previously infected with Oropouche virus and in blood collected from mice that were inoculated with either of the strains. FINDINGS: 8639 (81·8%) of 10 557 laboratory-confirmed Oropouche fever cases from Jan 4, 2015, to Aug 10, 2024, occurred in 2024, which is 58·8 times the annual median of 147 cases (IQR 73-325). Oropouche virus infections were reported in all 27 federal units, with 8182 (77·5%) of
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Journal articleSchmit N, Topazian H, Pianella M, et al., 2025,
Quantifying the potential value of entomological data collection for programmatic decision-making on malaria control in sub-Saharan African settings
, Malaria Journal, ISSN: 1475-2875 -
Journal articlePenn MJ, Scheidwasser N, Donnelly CA, et al., 2025,
Bayesian Inference of Phylogenetic Distances: Revisiting the Eigenvalue Approach.
, Bull Math Biol, Vol: 87Using genetic data to infer evolutionary distances between molecular sequence pairs based on a Markov substitution model is a common procedure in phylogenetics, in particular for selecting a good starting tree to improve upon. Many evolutionary patterns can be accurately modelled using substitution models that are available in closed form, including the popular general time reversible model (GTR) for DNA data. For more complex biological phenomena, such as variations in lineage-specific evolutionary rates over time (heterotachy), other approaches such as the GTR with rate variation (GTR + Γ ) are required, but do not admit analytical solutions and do not automatically allow for likelihood calculations crucial for Bayesian analysis. In this paper, we derive a hybrid approach between these two methods, incorporating Γ ( α , α ) -distributed rate variation and heterotachy into a hierarchical Bayesian GTR-style framework. Our approach is differentiable and amenable to both stochastic gradient descent for optimisation and Hamiltonian Markov chain Monte Carlo for Bayesian inference. We show the utility of our approach by studying hypotheses regarding the origins of the eukaryotic cell within the context of a universal tree of life and find evidence for a two-domain theory.
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Journal articleHan SM, Kubo Y, Robert A, et al., 2025,
Impact of Viral Co-Detection on the Within-Host Viral Diversity of Influenza Patients.
, Viruses, Vol: 17Numerous studies have documented the evidence of virus-virus interactions at the population, host, and cellular levels. However, the impact of these interactions on the within-host diversity of influenza viral populations remains unexplored. Our study identified 13 respiratory viral pathogens from the nasopharyngeal swab samples (NPSs) of influenza-like-illness (ILI) patients during the 2012/13 influenza season using multiplex RT-PCR. Subsequent next-generation sequencing (NGS) of RT-PCR-confirmed influenza A infections revealed all samples as subtype A/H3N2. Out of the 2305 samples tested, 538 (23.3%) were positive for the influenza A virus (IAV), while rhinovirus (RV) and adenoviruses (Adv) were detected in 264 (11.5%) and 44 (1.9%) samples, respectively. Among these, the co-detection of more than one virus was observed in ninety-six samples, and five samples showed co-detections involving more than two viruses. The most frequent viral co-detection was IAV-RV, identified in 48 out of the 96 co-detection cases. Of the total samples, 150 were processed for whole-genome sequencing (WGS), and 132 met the criteria for intra-host single-nucleotide variant (iSNV) calling. Across the genome, 397 unique iSNVs were identified, with most samples containing fewer than five iSNVs at frequencies below 10%. Seven samples had no detectable iSNVs. Notably, the majority of iSNVs (86%) were unique and rarely shared across samples. We conducted a negative binomial regression analysis to examine factors associated with the number of iSNVs detected within hosts. Two age groups-elderly individuals (>64 years old) and school-aged children (6-18 years old)-were significantly associated with higher iSNV counts, with incidence rate ratios (IRR) of 1.80 (95% confidence interval [CI]: 1.09-3.06) and 1.38 (95% CI: 1.01-1.90), respectively. Our findings suggest a minor or negligible contribution of these viral co-detections to the evolution of influenza viruses. However, the data available i
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Journal articleAnanth S, Adeoti AO, Ray A, et al., 2025,
Healthcare worker views on antimicrobial resistance in chronic respiratory disease
, Antimicrobial Resistance and Infection Control, Vol: 14, ISSN: 2047-2994Background and objectiveAntimicrobial resistance (AMR) is a global crisis, however, relatively little is known regarding its impact in chronic respiratory disease and the specific challenges faced by healthcare workers across the world in this field. We aimed to assess global healthcare worker views on the challenges they face regarding AMR in chronic respiratory disease.MethodsAn online survey was sent to healthcare workers globally working in chronic respiratory disease through a European Respiratory Society clinical research collaboration (AMR-Lung) focussed on AMR in chronic lung disease. Responses from different geographic regions were analysed.Results279 responses were received across 60 countries. 54.5% of respondents encountered AMR in chronic respiratory disease weekly. There were differences in perceived high-priority diseases and species with AMR burden between Europe, Asia and Africa. 76.4% of respondents thought that inappropriate antimicrobial prescribing in chronic respiratory disease was common. However, only 43.4% of respondents thought that there were adequate antimicrobial stewardship programmes in their area for chronic respiratory disease, with limited availability in outpatient (29.0%) and ambulatory settings (24.7%). Developing rapid diagnostics for antimicrobial susceptibility (59.5%) was perceived to be the most common challenge in implementing antimicrobial stewardship, with an improved understanding of regional epidemiology of AMR strains the most important factor to improve outcome (55.2%).ConclusionsAMR has significant perceived burden in chronic respiratory disease by healthcare professionals globally. However, current implementation of antimicrobial stewardship is limited, with significant challenges related to the availability of rapid diagnostics and understanding of regional epidemiology of AMR strains.
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Journal articleLansbury L, McKeever TM, Lawrence H, et al., 2025,
Pneumococcal pneumonia trends in adults hospitalised with community-acquired pneumonia over 10 years (2013-2023) and the role of serotype 3.
, Thorax, Vol: 80, Pages: 86-96BACKGROUND: With higher valency pneumococcal vaccines on the horizon and new adult immunisation strategies under discussion, we aimed to evaluate the contribution of individual pneumococcal serotypes to the burden of pneumococcal community-acquired pneumonia (CAP). Over 10 years, trends in pneumococcal pneumonia epidemiology in adults hospitalised with CAP were assessed. The risk factors and severity associated with serotype 3 were examined. METHODS: We conducted a prospective cohort study of adults hospitalised with CAP between September 2013 and May 2023. Pneumococcal serotypes were identified using a serotype-specific 24-valent urinary-antigen assay. Trends in the proportion of CAP due to pneumococcus and causative serotypes were compared prepandemic and postpandemic. Risk factors and severity of serotype 3 pneumonia were compared with other serotypes using logistic regression. RESULTS: Of 5186 patients with CAP, 2193 (42.2%) had pneumococcal pneumonia. The proportion of CAP due to pneumococcus increased across all ages between 2013 and 2023 (36.4%-66.9%, p<0.001). The proportion due to serotype 3 increased significantly from 13.4% (2013) to 48.8% (2023). Serotype 3 pneumonia in adults was associated with older age (p<0.001), male sex (adjusted OR (aOR) 2.22, 95% CI 1.64 to 3.01) and chronic renal disease (aOR 1.81, 95% CI 1.09 to 3.02). Serotype 3 pneumonia was not observed to be associated with severity, critical care requirement, mortality or readmission. INTERPRETATION: Serotype 3 is the predominant serotype in adult pneumococcal CAP and has been increasing despite a mature infant pneumococcal immunisation programme, consistent with a lack of herd protection for this serotype.
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Journal articleNikitin D, Whittles LK, Imai-Eaton JW, et al., 2025,
Cost-effectiveness of 4CMenB vaccination against gonorrhea: importance of dosing schedule, vaccine sentiment, targeting strategy, and duration of protection
, Journal of Infectious Diseases, Vol: 231, Pages: 71-83, ISSN: 0022-1899BackgroundObservational evidence suggests the 4CMenB meningococcal vaccine may partially protect against gonorrhea, with 1 dose being two-thirds as protective as 2 doses. We examined the cost-effectiveness of vaccinating men who have sex with men (MSM) in England, with 1- or 2-dose primary vaccination.MethodsIntegrated transmission-dynamic health-economic modeling explored the effects of targeting strategy, first- and second-dose uptake levels, and duration of vaccine protection, using observational estimates of vaccine protection.ResultsVaccination with 1 or 2 primary doses is always cost-saving, irrespective of uptake, although vaccine sentiment is an important determinant of impact and cost-effectiveness. The most impactful and cost-effective targeting is offering “vaccination according to risk” (VaR), to all patients with gonorrhea plus those reporting high numbers of sexual partners. If VaR is not feasible to implement then the more restrictive strategy of “vaccination on diagnosis” (VoD) with gonorrhea is cost-effective, but much less impactful. Under conservative assumptions, VaR (2-dose) saves £7.62M (95% credible interval [CrI], 1.15–17.52) and gains 81.41 (95% CrI, 28.67–164.23) quality-adjusted life-years (QALYs) over 10 years; VoD (2-dose) saves £3.40M (95% CrI, .48–7.71) and gains 41.26 (95% CrI, 17.52–78.25) QALYs versus no vaccination. Optimistic versus pessimistic vaccine-sentiment assumptions increase net benefits by approximately 30% (VoD) or approximately 60% (VaR).ConclusionsAt UK costs, targeted 4CMenB vaccination of MSM gains QALYs and is cost-saving at any uptake level. Promoting uptake maximizes benefits and is an important role for behavioral science.
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Journal articleMurray KA, 2025,
Keep it in the ground: climate change could prompt the reemergence of zombie pathogens.
, BMJ, Vol: 388
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