Institut de Recherche pour le Développement

Tsunami wave observations far from the coast remain challenging due to the logistics and cost of deploying and operating offshore instrumentation on a long-term basis with sufficient spatial coverage and density. Distributed Acoustic Sensing (DAS) on submarine fiber optic cables now enables real-time seafloor strain observations over distances exceeding 100 km at a relatively low cost. Here, we evaluate the potential contribution of DAS to tsunami warning by assessing theoretically the sensitivity required by a DAS instrument to record tsunami waves. Our analysis includes signals due to two effects induced by the hydrostatic pressure perturbations arising from tsunami waves: the Poisson’s effect of the submarine cable and the compliance effect of the seafloor. It also includes the effect of seafloor shear stresses and temperature transients induced by the horizontal fluid flow associated with tsunami waves. The analysis is supported by fully coupled 3-D physics-based simulations of earthquake rupture, seismo-acoustic waves and tsunami wave propagation. The strains from seismo-acoustic waves and static deformation near the earthquake source are orders of magnitude larger than the tsunami strain signal. We illustrate a data processing procedure to discern the tsunami signal. With enhanced low-frequency sensitivity on DAS interrogators (strain sensitivity ≈ 2×10 at mHz frequencies), we find that, on seafloor cables located above or near the earthquake source area, tsunamis are expected to be observable with a sufficient signal-to-noise ratio within a few minutes of the earthquake onset. These encouraging results pave the way towards faster tsunami warning enabled by seafloor DAS.

INTRODUCTION:Mother-to-child transmission (MTCT) of HIV, syphilis, and hepatitis B virus (HBV) commonly observed in the WHO African region is associated with excess morbidity and mortality. Despite some progress, the coverage of interventions to prevent MTCT of these infections remains insufficient, particularly for syphilis and HBV. To fulfil these gaps and achieve the triple elimination of MTCT of these infections by 2030, the World Health Organization (WHO) advocates for integration of prevention of MTCT (PMTCT) activities for HBV with HIV and syphilis antenatal services. In partnership with the local governments, the TRI-MOM project, conducted in 2 phases, aims to evaluate a simplified (based on inexpensive rapid diagnostic tests), integrated (in maternal and child health services) and coordinated (between the various programs and health care workers) strategy for the triple elimination of HIV, syphilis and HBV MTCT in Burkina Faso and The Gambia. METHODS AND ANALYSIS:The strategy will be implemented in 5 rural and urban health facilities in each country and will include four activities: i) training sessions for healthcare workers working in maternal and child health services, ii) screening of pregnant women of the three infections using rapid diagnostic tests at the first antenatal visit, iii) clinical assessment and treatment of women tested positive for any of the 3 infections, and iv) raising awareness on HIV, Syphilis and HBV PMTCT among pregnant women and empowering those screened positive. 17,000 pregnant women are expected to be screened. The strategy will be evaluated through an interdisciplinary, mixed-methods approach comprising three studies: i) a quantitative and qualitative cross-sectional study conducted both before and after the implementation of the strategy to assess its impact on triple screening coverage in pregnant women; ii) a an intervention study with longitudinal follow-up of pregnant women positive for any of the three infections to assess the coverage of PMTCT measures; and iii) a cost and cost-effectiveness analysis of the project compared to the reference situation in each country, which will rely on a micro costing study to estimate the incremental cost of the strategy per mother/child couple compared with the reference situation in each country, and compare it to the number of avoided infections. ETHICS AND DISSEMINATION:The study protocol has been approved by the competent authorities of the countries participating to the research (the LSHTM/MRCUG Scientific Coordinating Committee, the Gambia Government/MRC Joint Ethics Committee, the LSHTM ethics committee, the Burkinabe National Ethical Committee for Research in Health and the French Commission on Information Technology and Liberties). Results on the feasibility and acceptability of the triple elimination strategy will be disseminated using different media including policy briefs, posters and articles. TRIAL REGISTRATION NUMBER:ClinicalTrials.gov NCT05951751.

The advent of multiplexing technologies, allowing antibodies to hundreds of antigens to be measured in a single test, has led to enormous increases in the amount of data generated by serological surveys. New modelling methods are required to exploit this data. This study extends serocatalytic models to consider up to three antibody responses targeting the same pathogen simultaneously. These models were fitted to data from cross-sectional serological surveys of Plasmodium falciparum malaria in the Senegalese villages of Dielmo and Ndiop, and model predictions were validated against 22 years of longitudinal epidemiological data. The most accurate reconstruction of historical clinical incidence of P. falciparum was provided by a combination of antibodies to Apical Membrane Antigen 1 (PfAMA1) and Glutamate-Rich Protein (PfGlurpR2). This model estimated a 76% (95% CrI: 61% - 86%) drop in transmission in 2004 (95% CrI: 2001 - 2008) coinciding with changing anti-malarial treatment. Multiplex serocatalytic models provided more accurate estimates of past clinical incidence than singleplex serocatalytic models, with the most accurate multiplex model (PfAMA1 + PfGlurpR2) outperforming all singleplex models (KruskalWallis p < 0.01). Finally, models with three antigens did not provide more accurate estimation than models with two antigens.

The Amazon River plume generates strong hydrographic gradients that shape pelagic ecosystem functioning in the tropical Atlantic. We quantify the relative influence of key environmental drivers on copepod biomass and diversity and identify indicator taxa across contrasting plume regions. Using data from the AMAZOMIX expedition, we sampled three hydrographic zones, the coastal plume [Shelf Amazon River Plume (SARP)], oceanic plume (Ocean Amazon River Plume) and oligotrophic ocean (Non-Amazon River Plume). Twenty-five copepod families were recorded, reflecting high biodiversity across plume-influenced and oceanic environments. Hierarchical Bayesian models were used to assess environmental effects and to derive a Latent Ecosystem Functioning Index (LIFE), defined as a shared ecological state integrating biomass and diversity along environmental gradients. Copepod biomass peaked in the plume-influenced SARP (mean = 1 585 mu g C m-3) and was positively associated with fluorescence (beta = 392) and salinity (beta = 257), indicating strong bottom-up control. In contrast, diversity showed weak environmental responses, suggesting stronger dependence on habitat heterogeneity than on productivity. LIFE was strongly correlated with biomass (r = 0.93) but not with diversity (r = 0.03), revealing a spatial decoupling between productivity and community structure. These findings emphasize key environmental drivers of copepod biomass and propose a latent ecosystem functioning index as an integrative tool for plume-affected ecosystems.

Purpose: We introduce GraNPA, standing for Graph Node-Phenotype Associa- tion, a method performing a GWAS-like analysis on a pangenome variation graph (PVG) built using a small number of individual genome sequences, without the need for additional population materials or kinship information for qualitative phenotypes. This method reduces the number of individuals required for associ- ation studies and prevents reference bias from variant calling in these types of analyses. Background: A PVG represents the multiple alignment of a set of complete genomes. It contains all variations, from single nucleotide polymorphisms (SNPs) to large structural variations (SVs), which are represented as nodes in the graph. By integrating phenotype information within nodes, we can assign a Phenotype Score (PS) to each node in the PVG and identify phenotype-related regions directly within it. These regions represent statistically significant shifts in PS distribution, highlighting their implication in the phenotype. Finally, GraNPA provides their positions and scores for further analysis. Results: This method was tested using simulated data and two publicly available datasets: the Sub1A gene locus for Oryza sativa in a 13 indi- viduals PVG, and the insertion responsible for the white-headed cattle with a PVG of 24 individuals. Source code of GraNPA is available here https://forge.ird.fr/diade/graphgwas/granpa under GNU GPLv3. Conclusion: GraNPA was able to identify the expected area in two simulated datasets and the responsible loci for these two known traits using only a few 1 dozen complete genomes in these PVGs. While currently limited to qualitative phenotypes, this method opens the way to more efficient ones relying on PVGs and few individuals.