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  • Journal article
    Delamare H, Ishii-Rousseau JE, Rao A, Cresta M, Vincent JP, Ségéral O, Nayagam S, Shimakawa Yet al., 2024,

    Proportion of pregnant women with HBV infection eligible for antiviral prophylaxis to prevent vertical transmission: A systematic review and meta-analysis

    , JHEP Reports, Vol: 6

    Background & Aims: In 2020, the World Health Organization (WHO) recommended peripartum antiviral prophylaxis (PAP) for pregnant women infected with hepatitis B virus (HBV) with high viremia (≥200,000 IU/ml). Hepatitis B e antigen (HBeAg) was also recommended as an alternative when HBV DNA is unavailable. To inform policymaking and guide the implementation of prevention of mother-to-child transmission strategies, we conducted a systematic review and meta-analysis to estimate the proportion of HBV-infected pregnant women eligible for PAP at global and regional levels. Methods: We searched PubMed, EMBASE, Scopus, and CENTRAL for studies involving HBV-infected pregnant women. We extracted proportions of women with high viremia (≥200,000 IU/ml), proportions of women with positive HBeAg, proportions of women cross-stratified based on HBV DNA and HBeAg, and the risk of child infection in these maternal groups. Proportions were pooled using random-effects meta-analysis. Results: Of 6,999 articles, 131 studies involving 71,712 HBV-infected pregnant women were included. The number of studies per WHO region was 66 (Western Pacific), 21 (Europe), 17 (Africa), 11 (Americas), nine (Eastern Mediterranean), and seven (South-East Asia). The overall pooled proportion of high viremia was 21.27% (95% CI 17.77–25.26%), with significant regional variation: Western Pacific (31.56%), Americas (23.06%), Southeast Asia (15.62%), Africa (12.45%), Europe (9.98%), and Eastern Mediterranean (7.81%). HBeAg positivity showed similar regional variation. After cross-stratification, the proportions of high viremia and positive HBeAg, high viremia and negative HBeAg, low viremia and positive HBeAg, and low viremia and negative HBeAg were 15.24% (95% CI 11.12–20.53%), 2.70% (95% CI 1.88–3.86%), 3.69% (95% CI 2.86–4.75%), and 75.59% (95% CI 69.15–81.05%), respectively. The corresponding risks of child infection following birth dose vaccination without immune globu

  • Journal article
    Aliaga-Samanez A, Romero D, Murray K, Segura M, Real R, Olivero Jet al., 2024,

    Potential climate change effects on the distribution of urban and sylvatic dengue and yellow fever vectors.

    , Pathog Glob Health, Pages: 1-11

    Climate change may increase the risk of dengue and yellow fever transmission by urban and sylvatic mosquito vectors. Previous research primarily focused on Aedes aegypti and Aedes albopictus. However, dengue and yellow fever have a complex transmission cycle involving sylvatic vectors. Our aim was to analyze how the distribution of areas favorable to both urban and sylvatic vectors could be modified as a consequence of climate change. We projected, to future scenarios, baseline distribution models already published for these vectors based on the favorability function, and mapped the areas where mosquitoes' favorability could increase, decrease or remain stable in the near (2041-2060) and distant (2061-2080) future. Favorable areas for the presence of dengue and yellow fever vectors show little differences in the future compared to the baseline models, with changes being perceptible only at regional scales. The model projections predict dengue vectors expanding in West and Central Africa and in South-East Asia, reaching Borneo. Yellow fever vectors could spread in West and Central Africa and in the Amazon. In some locations of Europe, the models suggest a reestablishment of Ae. aegypti, while Ae. albopictus will continue to find new favorable areas. The results underline the need to focus more on vectors Ae. vittatus, Ae. luteocephalus and Ae. africanus in West and Central sub-Saharan Africa, especially Cameroon, Central Africa Republic, and northern Democratic Republic of Congo; and underscore the importance of enhancing entomological monitoring in areas where populations of often overlooked vectors may thrive as a result of climate changes.

  • Journal article
    Silhol R, Maheu-Giroux M, Soni N, Fotso AS, Rouveau N, Vautier A, Doumenc-Aïdara C, Geoffroy O, Nguessan KN, Sidibé Y, Kabemba OK, Gueye PA, Ndeye PD, Mukandavire C, Vickerman P, Keita A, Ndour CT, Ehui E, Larmarange J, Boily M-Cet al., 2024,

    The impact of past HIV interventions and diagnosis gaps on new HIV acquisitions, transmissions, and HIV-related deaths in Côte d’Ivoire, Mali, and Senegal

    , AIDS, ISSN: 0269-9370

    <jats:sec> <jats:title>Objectives:</jats:title> <jats:p>To estimate the epidemiological impact of past HIV interventions and the magnitude and contribution of undiagnosed HIV among different risk groups on new HIV acquisitions in Côte d’Ivoire, Mali and Senegal.</jats:p> </jats:sec> <jats:sec> <jats:title>Design:</jats:title> <jats:p>HIV transmission dynamic models among the overall population and key populations [female sex workers (FSW), their clients, and MSM].</jats:p> </jats:sec> <jats:sec> <jats:title>Methods:</jats:title> <jats:p>Models were independently parameterized and calibrated for each set of country-specific demographic, behavioural, and epidemiological data. We estimated the fraction of new HIV infections over 2012–2021 averted by condom use and antiretroviral therapy (ART) uptake among key population and nonkey population, the direct and indirect contribution of specific groups to new infections [transmission population-attributable fraction (tPAF)] over 2012–2021 due to prevention gaps, and the distribution of undiagnosed PWH by risk group in January 2022 and their tPAF over 2022–2031.</jats:p> </jats:sec> <jats:sec> <jats:title>Results:</jats:title> <jats:p>Condom use and ART may have averted 81–88% of new HIV infections over 2012–2021 across countries, mostly because of condom use by key population. The tPAF of all key populations combined over 2012–2021 varied between 27% (Côte d’Ivoire) and 79% (Senegal). Male key population (clients of FSW and MSM) contributed most to new infections (&gt;60% in Mali and Senegal) owing to their higher HIV prevalence and larger prevention gaps. In 2022, men represented 56% of all

  • Journal article
    Grassly N, Shaw AG, Owusu M, 2024,

    Global wastewater surveillance for pathogens with pandemic potential: opportunities and challenges

    , The Lancet Microbe, ISSN: 2666-5247

    Wastewater surveillance (WS) holds promise as a sensitive method to detect spillover of zoonotic infections and early pandemic emergence, thereby informing risk mitigation and public health response. Known pandemic-risk viruses are shed in human stool and/or urine and recent experience with SARS-CoV-2, mpox and Zika highlights the feasibility of community-based WS for pandemic viruses with different transmission routes. We review human shedding and WS data for prototype viruses representing viral families of concern to determine its likely sensitivity compared with clinical surveillance. We examine how data on WS detection together with virus genetic sequences and animal faecal biomarkers could be used to identify spillover infections or early human transmission and adaptation. The opportunities and challenges facing global WS for pandemic prevention are described, focusing on low- and middle-income countries where risk is highest. We propose a research and public agenda to ensure an equitable and sustainable solution to these challenges

  • Journal article
    Barnsley G, Olivera Mesa D, Hogan A, Winskill P, Torkelson AA, Walker DG, Ghani A, Watson Oet al., 2024,

    Impact of the 100 Days Mission for vaccines on COVID-19: a mathematical modelling study

    , The Lancet Global Health, ISSN: 2214-109X
  • Journal article
    Jorgensen D, Grassly NC, Pons Salort M, 2024,

    Global age-stratified seroprevalence of Enterovirus D68: a systematic literature review

    , The Lancet Microbe, ISSN: 2666-5247

    First isolated in 1962, enterovirus D68 (EV-D68) emerged in 2014, causing outbreaksof severe respiratory infections and acute flaccid myelitis. We conducted a systematicliterature review to compile all available EV-D68 age-stratified seroprevalenceestimates . Ten studies from six countries were retained, all using microneutralizationassays, although protocols and challenge viruses varied widely. Seroprevalence age profiles were similar across time and space, with seroprevalence increasing quicklywith age, reaching ~100% by 20 years old, and remaining high throughout adulthood.This suggests continuous or frequent exposure of the populations to the virus, orpossible cross-reactivity with other viruses. Studies with two or more cross-sectionalsurveys showed consistently higher seroprevalence at later time points, suggesting aglobal increase in transmission over time. Standardizing serological protocols,understanding the contribution of cross-reactivity with other pathogens to high reportedseroprevalence, and quantifying individual exposure to EV-D68 over time are mainresearch priorities.

  • Journal article
    He J, Flaxman A, Imai-Eaton JW, Aravkin A, Zheng P, Sorensen R, Mittal S, Kyu HHet al., 2024,

    Association between early sexual debut and new HIV infections among adolescents and young adults in 11 African countries

    , AIDS and Behavior, Vol: 28, Pages: 2444-2453, ISSN: 1090-7165

    We investigated the association between early sexual debut and HIV infection among adolescents and young adults. Analyzing data from nationally representative Population-Based HIV Impact Assessment (PHIA) surveys in 11 African countries, the research employed a multivariate logistic regression model to assess the relationship between the early sexual debut and new HIV infections in the age group of 10–24 years. The results revealed a significant and robust association, indicating that young individuals who experienced early sexual debut were approximately 2.65 times more likely to contract HIV than those who did not, even after accounting for other variables. These findings align with prior research suggesting that early initiation of sexual activity may increase vulnerability to HIV infection due to factors such as biological susceptibility and risky behaviors like low condom use and multiple sexual partners. The implications of these findings for HIV prevention strategies are substantial, suggesting that interventions aimed at delaying sexual debut could be an effective component in reducing HIV risk for this population. Targeted sex education programs that address the risks of early sexual debut may play a pivotal role in these prevention efforts. By employing a comprehensive approach, there is a possibility to advance efforts towards ending AIDS by 2030.

  • Journal article
    Turner HC, 2024,

    Cost-effectiveness of a Wolbachia-based replacement strategy for dengue control in Brazil

    , The Lancet Regional Health. Americas, Vol: 35, ISSN: 2667-193X
  • Journal article
    Silhol R, Maheu-Giroux M, Soni N, Simo Fotso A, Rouveau N, Vautier A, Doumenc-Aïdara C, Geoffroy O, N'Guessan KN, Sidibé Y, Kabemba OK, Gueye PA, Ndeye PD, Mukandavire C, Vickerman P, Keita A, Ndour CT, Larmarange J, Boily M-C, Amani EG, Badiane K, Bayac C, Bekelynck A, Boily M-C, Boye S, Breton G, d'Elbée M, Desclaux A, Desgrées du Loû A, Diop PM, Ehui E, Medley G, Jean K, Keita A, Kouassi AK, Ky-Zerbo O, Larmarange J, Maheu-Giroux M, Moh R, Mosso R, Ndour CT, Paltiel D, Pourette D, Rouveau N, Silhol R, Simo Fotso A, Terris-Prestholt F, Traoré MM, Doumenc-Aïdara C, Geoffroy O, Kabemba OK, Vautier A, Abokon A, Anoma C, Diokouri A, Kouamé B, Kouakou V, Koffi O, Kpolo A, Tety J, Traore Y, Bagendabanga J, Berthé D, Diakité D, Diakité M, Diallo Y, Daouda M, Hessou S, Kanambaye S, Kanouté AK, Dembélé Keita B, Koné D, Koné M, Maiga A, Saran Keita A, Sidibé F, Tall M, Yattassaye Camara A, Sanogo A, Bâ I, Diallo PAN, Fall F, NGom Guèye NF, Ndiaye SM, Niang AM, Samba O, Thiam S, Turpin NME, Bouaré S, Camara CS, Kouadio BA, Sarrassat S, Sow S, Eponon Ehua A, Kouvahe A, Montaufray M-A, Ndeye PDet al., 2024,

    Potential population-level effects of HIV self-test distribution among key populations in Côte d'Ivoire, Mali, and Senegal: a mathematical modelling analysis

    , The Lancet HIV, ISSN: 2352-3018
  • Journal article
    Penn MJ, Scheidwasser N, Khurana MP, Duchêne DA, Donnelly CA, Bhatt Set al., 2024,

    Phylo2Vec: a vector representation for binary trees.

    , Syst Biol

    Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes in a tree is computationally expensive. State-of-the-art methods rely on carefully designed heuristics for tree search, using different data structures for easy manipulation (e.g., classes in object-oriented programming languages) and readable representation of trees (e.g., Newick-format strings). Here, we present Phylo2Vec, a parsimonious encoding for phylogenetic trees that serves as a unified approach for both manipulating and representing phylogenetic trees. Phylo2Vec maps any binary tree with n leaves to a unique integer vector of length n - 1. The advantages of Phylo2Vec are fourfold: i) fast tree sampling, (ii) compressed tree representation compared to a Newick string, iii) quick and unambiguous verification if two binary trees are identical topologically, and iv) systematic ability to traverse tree space in very large or small jumps. As a proof of concept, we use Phylo2Vec for maximum likelihood inference on five real-world datasets and show that a simple hill-climbing-based optimisation scheme can efficiently traverse the vastness of tree space from a random to an optimal tree.

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