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Journal articleDaniels BC, Buddhari D, Hunsawong T, et al., 2024,
Predicting the infecting dengue serotype from antibody titre data using machine learning
, PLOS COMPUTATIONAL BIOLOGY, Vol: 20, ISSN: 1553-734X -
Journal articleMills 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 articleHuong NHT, Toan ND, Thien TB, et 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: 2328-8957BackgroundThe 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.
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Journal articlePeak CM, Lyons H, Voorman A, et 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: 2076-393XBackground/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
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Journal articleCarter 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: 2352-3018BackgroundAs 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
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Journal articleChurcher TS, Stopard IJ, Hamlet A, et 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: 2214-109XBackgroundInsecticide 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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Journal articlede Villiers MJ, de Villiers E, Nayagam S, et al., 2024,
Direct and indirect effects of hepatitis B vaccination in four low- and middle-income countries
, Epidemics, Vol: 49, ISSN: 1755-4365Population-level vaccination effects of the hepatitis B vaccine were investigated in four low- and middle-income countries with different levels of vertical and horizontal transmission. Indirect vaccination effects constitute a large proportion of overall vaccination effects of the vaccination programmes in all four countries (over 70% by 2030 in all four countries). However, countries with higher levels of vertical transmission benefit less from indirect vaccination effects from the infant hepatitis B vaccine series during the first decades of the vaccination programme, making the birth dose vaccine more important in these countries. Vaccination, even at levels that do not fully control transmission, has a great effect on the development of disease as it also increases the average age of infection, thereby causing a decrease in the number of chronic infections relative to the number of acute infections.
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Journal articleCordeiro AA, Moorhouse L, Dadirai T, et al., 2024,
Correction: Intimate partner violence, behaviours associated with risk of HIV acquisition and condom use in married women in Manicaland, East Zimbabwe: an HIV prevention cascade analysis
, BMC Women's Health, Vol: 24, ISSN: 1472-6874 -
Journal articleScott TA, Baker KS, Trotter C, et al., 2024,
Shigella sonnei: epidemiology, evolution, pathogenesis, resistance and host interactions.
, Nat Rev MicrobiolShigella sonnei is a major cause of diarrhoea globally and is increasing in prevalence relative to other Shigella because of multiple demographic and environmental influences. This single-serotype species has traditionally received less attention in comparison to Shigella flexneri and Shigella dysenteriae, which were more common in low-income countries and more tractable in the laboratory. In recent years, we have learned that Shigella are highly complex and highly susceptible to environmental change, as exemplified by epidemiological trends and increasing relevance of S. sonnei. Ultimately, methods, tools and data generated from decades of detailed research into S. flexneri have been used to gain new insights into the epidemiology, microbiology and pathogenesis of S. sonnei. In parallel, widespread adoption of genomic surveillance has yielded insights into antimicrobial resistance, evolution and organism transmission. In this Review, we provide an overview of current knowledge of S. sonnei, highlighting recent insights into this globally disseminated antimicrobial-resistant pathogen and assessing how novel data may impact future vaccine development and implementation.
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Journal articleDerqui N, Blake IM, Gray EJ, et al., 2024,
Timeliness of 24 childhood immunisations and evolution of vaccination delay: analysis of data from 54 low- and middle-income countries
, PLOS Global Public Health, Vol: 4, ISSN: 2767-3375Vaccination timeliness is often not considered among standard performance indicators of routine vaccination programmes, such as vaccination coverage, yet quantifying vaccination delay could inform policies to promote in-time vaccination and help design vaccination schedules. Here, we analysed vaccination timeliness for 24 routine childhood immunisations for 54 countries. We extracted individual vaccination status and timing from Demographic and Health Surveys data from 54 countries with surveys from 2010 onwards. Individual data was used to estimate age at vaccination for <5 year-old children. Recommended age of vaccination for each country and vaccine was compared to the age at vaccination to determine vaccination delay. The evolution of vaccination delay over time was described using estimates from different birth cohorts. To identify socio-demographic indicators associated with delayed vaccination, we used multivariable Cox regression models with country as random effect and estimated the Hazard Ratio for vaccination with each vaccine-dose for each week post recommended vaccination age. Vaccine coverage at the recommended age was highest for birth and first doses (e.g. 50.5% BCG, 18.5% DTP-D1) and lowest for later doses (e.g. 5.5% DTP-D3, 16.3% MCV-D1, 8.2% MCV-D2). Median delay was lowest for birth doses, e.g. BCG (1 week (IQR: 0 to 4)), and it increased with later doses in vaccination courses: 1 (0, 4) week for DTP-D1 versus 4 (2, 9) weeks for DTP-D3. Although the median delay for each vaccine-dose remained largely constant over time, the range of delay estimates moderately decreased. Children living in rural areas, their countries’ poorer wealth quintiles and whose mothers had no formal education were more likely to received delayed vaccinations. Although we report most children are vaccinated within the recommended age window, we found little reduction on routine immunisation delays over the last decade and that children from deprived socioeconomic b
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