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  • Journal article
    Kwok KO, Huynh T, Wei WI, Wong SYS, Riley S, Tang Aet al., 2024,

    Utilizing large language models in infectious disease transmission modelling for public health preparedness

    , COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, Vol: 23, Pages: 3254-3257, ISSN: 2001-0370
  • Journal article
    Smith DRM, Turner J, Fahr P, Attfield LA, Bessell PR, Donnelly CA, Gibb R, Jones KE, Redding DW, Asogun D, Ayodeji OO, Azuogu BN, Fischer WA, Jan K, Olayinka AT, Wohl DA, Torkelson AA, Dinkel KA, Nixon EJ, Pouwels KB, Hollingsworth TDet al., 2024,

    Health and economic impacts of Lassa vaccination campaigns in West Africa

    , NATURE MEDICINE, Vol: 30, ISSN: 1078-8956
  • Journal article
    Doohan P, Jorgensen D, Naidoo T, McCain K, Hicks J, McCabe R, Bhatia S, Charniga K, Cuomo-Dannenburg G, Hamlet A, Nash R, Nikitin D, Rawson T, Sheppard R, Unwin H, van Elsland S, Cori A, Morgenstern C, Imai Net al., 2024,

    Lassa fever outbreaks, mathematical models, and disease parameters: a systematic review and meta-analysis

    , The Lancet Global Health, Vol: 12, Pages: e1962-e1972, ISSN: 2214-109X

    BackgroundUnderstanding the epidemiological parameters and transmission dynamics of Lassa fever, a significant public health threat in west Africa caused by the rodent-borne Lassa virus, is crucial for informing evidence-based interventions and outbreak response strategies. Therefore, our study aimed to collate and enhance understanding of the key epidemiological parameters of Lassa fever.MethodsWe conducted a systematic review, searching PubMed and Web of Science for peer-reviewed studies published from database inception up to June 13, 2024, to compile and analyse key epidemiological parameters, mathematical models, and outbreaks of Lassa fever. English-language, peer-reviewed, original research articles were included if they reported on Lassa fever outbreak sizes, transmission models, viral evolution, transmission, natural history, severity, seroprevalence, or risk factors. Non-peer-reviewed literature was excluded. Data were extracted by two independent individuals from published literature, focusing on seroprevalence, transmissibility, epidemiological delays, and disease severity. We performed a meta-analysis to calculate pooled estimates of case-fatality ratios (CFRs) and the delay from symptom onset to hospital admission. This study is registered with PROSPERO (identifier number CRD42023393345).FindingsThe database search returned 5614 potentially relevant studies, and a further 16 studies were identified from backward citation chaining. After de-duplication and exclusion, 193 publications met our inclusion criteria and provided 440 relevant parameter estimates in total. Although Lassa virus is endemic in west Africa, the spatiotemporal coverage of general-population seroprevalence estimates (ranging from 2·6% [6/232] to 58·2% [103/177]) was poor, highlighting the spatial uncertainty in Lassa fever risk. Similarly, only four basic reproduction number estimates (ranging from 1·13 to 1·40) were available. We estimated a pooled total

  • Journal article
    Atsame J, Stapley JN, Ramani A, Mourou R, Ntsame E, Efame E, Angue O-N, Obiang J-L, Pilotte N, Gass K, Basáñez M-Get al., 2024,

    Comparison of diagnostic tools to assess the feasibility of programmatic use of rapid diagnostic tests for onchocerciasis: a dataset from Gabon

    , Data in Brief, Vol: 57, ISSN: 2352-3409

    Due to the success of large-scale ivermectin mass drug administration (MDA), the aim of onchocerciasis intervention efforts have shifted from control of the disease to elimination of transmission. This has necessitated a greater understanding and comparison of the performance of diagnostic tools in hypoendemic (low prevalence) settings which had not been incorporated into large-scale MDA programmes before the goal switched from onchocerciasis elimination as a public health problem to elimination (interruption) of transmission (EOT). Data on age, sex and duration of residence were collected, prior to ivermectin treatment, across Gabon in 2015 from 5,829 participants in 67 communities from 14 districts. Skin-snip samples (for detection of Onchocerca volvulus microfilariae) were obtained from 4,350 (75 %) and blood samples (for detection of presence of IgG4 antibodies against the O. volvulus Ov16 antigen) from 4,257 of those skin-snip tested (98 %).Whole blood was tested in the field using the SD Ov16 Rapid Diagnostic Test Prototype (Ov16 RDT). Dried blood spots (DBS) were prepared for all blood-sampled individuals. After assessing DBS quality, 2,990 (70 %) samples underwent valid analysis in the lab using horseradish peroxidase (HRP) Ov16 enzyme-linked immunosorbent assay (Ov16 ELISA). The number of positive individuals varied between diagnostic tools with skin-snip microscopy, Ov16 RDT and Ov16 ELISA detecting 337/4,350 (8 %, 95 % CI =7 %–9 %), 383/4,257 (9 %, 8 %–10 %) and 348/2,990 (12 %, 10 %–13 %), respectively. Data were analysed to understand the age profiles of microfilarial and IgG4 antibody prevalence by diagnostic and mapped across Gabon.These data have reuse potential for policy makers, test manufacturers and country programmes when making determinations at community level of the suitability of using Ov16 RDT for conducting delineation mapping or evaluating the current stage of a community or, more generally, an evaluation unit along the

  • Journal article
    Daniels BC, Buddhari D, Hunsawong T, Iamsirithaworn S, Farmer AR, Cummings DAT, Anderson KB, Dorigatti Iet al., 2024,

    Predicting the infecting dengue serotype from antibody titre data using machine learning

    , PLOS COMPUTATIONAL BIOLOGY, Vol: 20, ISSN: 1553-734X
  • Journal article
    Mills C, Donnelly CA, 2024,

    Climate-based modelling and forecasting of dengue in three endemic departments of Peru

    , PLOS NEGLECTED TROPICAL DISEASES, Vol: 18, ISSN: 1935-2735
  • Journal article
    Huong NHT, Toan ND, Thien TB, Khanh TH, Tuan NM, Truc TT, Nghia NA, Thinh LQ, Thoa NTK, Nhan LNT, Minh NNQ, Turner HC, Thwaites CL, Hung NT, Van Tan L, Irani SR, Quy DTet al., 2024,

    In children, N-Methyl-D-Aspartate receptor antibody encephalitis incidence exceeds that of Japanese encephalitis in Vietnam

    , Open Forum Infectious Diseases, Vol: 11, ISSN: 2328-8957

    BackgroundThe recognition of autoimmune causes of encephalitis has led to epidemiological shifts in the worldwide characteristics. N-Methyl-D-Aspartate receptor antibody encephalitis leads to well-established complex neuropsychiatric manifestations. In low- and middle-income countries, including Vietnam, its relative incidence, especially in children, is unknown and most neurologists currently consider infectious encephalitis prior to autoimmune etiologies.MethodsThe study was prospectively conducted at Children’s Hospital 1 in Ho Chi Minh City between March 2020 and December 2022. Any child admitted to the Department of Infectious Diseases and Neurology fulfilling the case definition of encephalitis, was eligible to participate. Cerebrospinal fluid samples were collected alongside meta-clinical data for analysis.ResultsWe recruited 164 children with a clinical diagnosis of encephalitis. Etiologies were determined as N-Methyl-D-Aspartate receptor antibody encephalitis in 23/164 cases (14.0%), Japanese Encephalitis Virus in 14/164 (8.5%) and Herpes Simplex Virus in 4/164 (2.4%). Clinical categorizations suggested idiopathic viral encephalitis in another 71 (43.3%), and autoimmune encephalitis of unknown origin in the remaining 52. Factors including demographics, specific clinical features, cerebrospinal fluid and electroencephalogram findings, and length of hospital stay were significantly different between N-Methyl-D-Aspartate receptor antibody encephalitis and Japanese encephalitis.ConclusionsAt a tertiary children’s hospital in Vietnam, the prevalence of N-Methyl-D-Aspartate receptor antibody encephalitis exceeds that of Japanese encephalitis, the most common infectious encephalitis cause in Southeast Asia. N-Methyl-D-Aspartate receptor antibody encephalitis is associated with long hospital stay and poor outcomes. These findings should change paediatric diagnostics, to earlier consider autoimmune treatments in this clinical setting.

  • Journal article
    Peak CM, Lyons H, Voorman A, Gray EJ, Cooper LV, Blake IM, Hawes KM, Bandyopadhyay ASet al., 2024,

    Monitoring the risk of type-2 circulating vaccine-derived poliovirus emergence during roll-out of type-2 novel oral polio vaccine

    , Vaccines, Vol: 12, ISSN: 2076-393X

    Background/Objectives: Although wild poliovirus type 2 has been eradicated, the prolonged transmission of the live- attenuated virus contained in the type-2 oral polio vaccine (OPV2) in under-immunized populations has led to the emergence of circulating vaccine-derived poliovirus type 2 (cVDPV2). The novel OPV2 (nOPV2) was designed to be more genetically stable and reduce the chance of cVDPV2 emergence while retaining comparable immunogenicity to the Sabin monovalent OPV2 (mOPV2). This study aimed to estimate the relative reduction in the emergence risk due to the use of nOPV2 instead of mOPV2. Methods: Data on OPV2 vaccination campaigns from May 2016 to 1 August 2024 were analyzed to estimate type-2 OPV-induced immunity in children under 5 years of age. Poliovirus surveillance data were used to estimate seeding dates and classify cVDPV2 emergences as mOPV2- or nOPV2-derived. The expected number of emergences if mOPV2 was used instead of nOPV2 was estimated, accounting for the timing and volume of nOPV2 doses, the known risk factors for emergence from mOPV2, and censoring due to the incomplete observation period for more recent nOPV2 doses. Results: As of 1 August 2024, over 98% of the approximately 1.19 billion nOPV2 doses administered globally were in Africa. We estimate that approximately 76 (95% confidence interval 69–85) index isolates of cVDPV2 emergences would be expected to be detected by 1 August 2024 if mOPV2 had been used instead of nOPV2 in Africa. The 18 observed nOPV2-derived emergences represent a 76% (74–79%) lower risk of emergence by nOPV2 than mOPV2 in Africa. The crude global analysis produced similar results. Key limitations include the incomplete understanding of the drivers of heterogeneity in emergence risk across geographies and variance in the per-dose risk of emergence may be incompletely captured using known risk factors. Conclusions: These results are consistent with the accumulating clinical and field evidence showing the en

  • Journal article
    Carter A, et al, 2024,

    Global, regional, and national burden of HIV/AIDS, 1990–2021, and forecasts to 2050, for 204 countries and territories: the Global Burden of Disease Study 2021

    , The Lancet HIV, Vol: 11, Pages: e807-e822, ISSN: 2352-3018

    BackgroundAs set out in Sustainable Development Goal 3.3, the target date for ending the HIV epidemic as a public health threat is 2030. Therefore, there is a crucial need to evaluate current epidemiological trends and monitor global progress towards HIV incidence and mortality reduction goals. In this analysis, we assess the current burden of HIV in 204 countries and territories and forecast HIV incidence, prevalence, and mortality up to 2050 to allow countries to plan for a sustained response with an increasing number of people living with HIV globally.MethodsWe used the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2021 analytical framework to compute age-sex-specific HIV mortality, incidence, and prevalence estimates for 204 countries and territories (1990–2021). We aimed to analyse all available data sources, including data on the provision of HIV programmes reported to UNAIDS, published literature on mortality among people on antiretroviral therapy (ART) identified by a systematic review, household surveys, sentinel surveillance antenatal care clinic data, vital registration data, and country-level case report data. We calibrated a mechanistic simulation of HIV infection and natural history to available data to estimate HIV burden from 1990 to 2021 and generated forecasts to 2050 through projection of all simulation inputs into the future. Historical outcomes (1990–2021) were simulated at the 1000-draw level to support propagation of uncertainty and reporting of uncertainty intervals (UIs). Our approach to forecasting utilised the transmission rate as the basis for projection, along with new rate-of-change projections of ART coverage. Additionally, we introduced two new metrics to our reporting: prevalence of unsuppressed viraemia (PUV), which represents the proportion of the population without a suppressed level of HIV (viral load <1000 copies per mL), and period lifetime probability of HIV acquisition, which quantifies the

  • Journal article
    Churcher TS, Stopard IJ, Hamlet A, Dee DP, Sanou A, Rowland M, Guelbeogo MW, Emidi B, Mosha JF, Challenger JD, Denz A, Glover A, Charles GD, Russell EL, Fitzjohn R, Winskill P, Fornadel C, Mclean T, Digre P, Wagman J, Mosha F, Cook J, Akogbéto MC, Djogbenou LS, Ranson H, McCall P, Manjurano A, NFalé S, Protopopoff N, Accrombessi M, Ngufor C, Foster G, Sherrard-Smith Eet al., 2024,

    The epidemiological benefit of pyrethroid–pyrrole insecticide treated nets against malaria: an individual-based malaria transmission dynamics modelling study

    , The Lancet Global Health, Vol: 12, Pages: e1973-e1983, ISSN: 2214-109X

    BackgroundInsecticide treated nets (ITNs) are the most important malaria prevention tool in Africa but the rise of pyrethroid resistance in mosquitoes is likely impeding control. WHO has recommended a novel pyrethroid–pyrrole ITN following evidence of epidemiological benefit in two cluster-randomised, controlled trials (CRTs). It remains unclear how effective more costly pyrethroid–pyrrole ITNs are compared with other tools, or whether they should be deployed when budgets are limited. We aimed to compare the epidemiological impact and cost-effectiveness of the mass distribution of pyrethroid–pyrrole ITNs relative to other ITNs over 3 years in different African settings.MethodsIn this individual-based malaria transmission dynamics modelling study we characterise the entomological impact of ITNs using data from a systematic review of experimental hut trials from across Africa. This African entomological data was used to inform an individual-based malaria transmission dynamics model, which was validated against CRT results from Benin and Tanzania. The full impact of new ITNs was quantified for trial sites and simulation was used to project impact in different settings which were included within an accessible interface (the Malaria Intervention Tool) to support National Malaria Programmes to explore how vector control tools and budgets could be allocated across regions to avert the most cases.FindingsThe model projects that distributing pyrethroid–pyrrole ITNs averted 65% (95% credible interval 48–74) of cases over 3 years in Tanzania, and 75% (28–93) in Benin. The model indicates that trials might have underestimated the benefits of switching ITNs by 12–16% over 3 years because participants stopped using trial-allocated nets. In moderate endemicity non-trial settings, pyrethroid–pyrrole ITNs are projected to reduce malaria prevalence by 25–60% and switching from pyrethroid-only ITNs is probably highly cost-effective

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