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  • Journal article
    Li A, Coffey LL, Mohr EL, Raper J, Chahroudi A, Ausderau KK, Aliota MT, Friedrich TC, Mitzey AM, Koenig MR, Golos TG, Jaeger HK, Roberts VHJ, Lo JO, Smith JL, Hirsch AJ, Streblow DN, Newman CM, OConnor DH, Lackritz EM, Van Rompay KKA, Adams Waldorf KM, Adams Waldorf KM, Barrett ADT, Beasley DWC, Bennie JB, Bourne N, Brault AC, Cehovin A, Coelho C, Diamond MS, Emperador D, Faria NR, Fay PC, Golding JP, Harris E, Hasanin N, Jaenisch T, Ko AI, Lackritz EM, Leighton T, Leo Y-S, Mehr AJ, Memish ZA, Méndez-Rico JA, Moore KA, Mura M, Ng L-C, Osterholm MT, Ostrowsky JT, Peeling RW, Rabe IB, Salje H, Staples JE, Thomas SJ, Ulrich AK, Vanhomwegen J, Wongsawat Jet al., 2025,

    Role of non-human primate models in accelerating research and developing countermeasures against Zika virus infection

    , The Lancet Microbe, Pages: 101030-101030, ISSN: 2666-5247
  • Journal article
    Ostrowsky JT, Katzelnick LC, Bourne N, Barrett ADT, Thomas SJ, Diamond MS, Beasley DWC, Harris E, Wilder-Smith A, Leighton T, Mehr AJ, Moua NM, Ulrich AK, Cehovin A, Fay PC, Golding JP, Moore KA, Osterholm MT, Lackritz EM, Adams Waldorf KM, Barrett ADT, Beasley DWC, Bennie JYB, Bourne N, Brault AC, Cehovin A, Coelho C, Diamond MS, Emperador D, Faria NR, Fay PC, Golding JP, Harris E, Hasanin N, Jaenisch T, Ko AI, Lackritz EM, Leighton T, Leo Y-S, Mehr AJ, Memish ZA, Méndez-Rico JA, Moore KA, Mura M, Ng L-C, Osterholm MT, Ostrowsky JT, Peeling RW, Rabe IB, Salje H, Staples JE, Thomas SJ, Ulrich AK, Vanhomwegen J, Wongsawat Jet al., 2025,

    Zika virus vaccines and monoclonal antibodies: a priority agenda for research and development

    , The Lancet Infectious Diseases, ISSN: 1473-3099
  • Journal article
    Schmit N, Topazian H, Pianella M, Charles G, Winskill P, Hancock P, Sherrard-Smith E, Hauck K, Churcher T, Ghani Aet 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 article
    Han SM, Kubo Y, Robert A, Baguelin M, Ariyoshi Ket al., 2025,

    Impact of Viral Co-Detection on the Within-Host Viral Diversity of Influenza Patients.

    , Viruses, Vol: 17

    Numerous 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
  • Journal article
    Penn MJ, Scheidwasser N, Donnelly CA, Duchêne DA, Bhatt Set al., 2025,

    Bayesian Inference of Phylogenetic Distances: Revisiting the Eigenvalue Approach.

    , Bull Math Biol, Vol: 87

    Using 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.
  • Journal article
    Ananth S, Adeoti AO, Ray A, Middleton PG, Ekkelenkamp M, Thee S, Shah Aet al., 2025,

    Healthcare worker views on antimicrobial resistance in chronic respiratory disease

    , Antimicrobial Resistance and Infection Control, ISSN: 2047-2994
  • Journal article
    Laufer Halpin A, Mathers AJ, Walsh TR, Zingg W, Okeke IN, McDonald LC, Elkins CA, Harbarth S, Peacock SJ, Srinivasan A, Bell M, Pittet D, Cardo D, 3rd Geneva Infection Prevention and Control Think Tanket al., 2025,

    A framework towards implementation of sequencing for antimicrobial-resistant and other health-care-associated pathogens.

    , Lancet Infect Dis

    Antimicrobial resistance continues to be a growing threat globally, specifically in health-care settings in which antimicrobial-resistant pathogens cause a substantial proportion of health-care-associated infections (HAIs). Next-generation sequencing (NGS) and the analysis of the data produced therein (ie, bioinformatics) represent an opportunity to enhance our capacity to address these threats. The 3rd Geneva Infection Prevention and Control Think Tank brought together experts to identify gaps, propose solutions, and set priorities for the use of NGS for HAIs and antimicrobial-resistant pathogens. The major deliverable recommendation from this meeting was a proposed framework for implementing the sequencing of HAI pathogens, specifically those harbouring antimicrobial-resistance mechanisms. The key components of the proposed framework relate to wet laboratory quality, sequence data quality, database and tool selection, bioinformatic analyses, data sharing, and NGS data integration, to support public health and actions for infection prevention and control. In this Personal View we detail and discuss the framework in the context of global implementation, specifically in low-income and middle-income countries.
  • Journal article
    Lansbury L, McKeever TM, Lawrence H, Pick H, Baskaran V, Edwards-Pritchard R, Matthews L, Bailey H, Ashton D, Bendall L, Rodrigo C, Daniel P, Litt D, Eletu S, Parmar H, Sheppard C, Ladhani SN, Trotter C, Lim WSet 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: 86-96

    BACKGROUND: 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.
  • Journal article
    Nikitin D, Whittles LK, Imai-Eaton JW, White PJet 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: 0022-1899

    BackgroundObservational 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.
  • Journal article
    Murray KA, 2025,

    Keep it in the ground: climate change could prompt the reemergence of zombie pathogens.

    , BMJ, Vol: 388

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