189 research outputs found

    The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

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    INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

    Genome-wide association analyses reveal the genetic basis of biomass accumulation under symbiotic nitrogen fixation in African soybean

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    Published online: 10 Dec 2019Symbiotic nitrogen fixation (SNF) increases sustainability by supplying biological nitrogen for crops to enhance yields without damaging the ecosystem. A better understanding of this complex biological process is critical for addressing the triple challenges of food security, environmental degradation, and climate change. Soybean plants, the most important legume worldwide, can form a mutualistic interaction with specialized soil bacteria, bradyrhizobia, to fix atmospheric nitrogen. Here we report a comprehensive genome-wide association study of 11 SNF-related traits using 79K GBS-derived SNPs in 297 African soybeans. We identified 25 QTL regions encompassing 40 putative candidate genes for SNF-related traits including 20 genes with no prior known role in SNF. A line with a large deletion (164 kb), encompassing a QTL region containing a strong candidate gene (CASTOR), exhibited a marked decrease in SNF. This study performed on African soybean lines provides fundamental insights into SNF-related traits and yielded a rich catalog of candidate genes for SNF-related traits that might accelerate future efforts aimed at sustainable agriculture

    Impacts of Nitrogen Deposition on Forest Ecosystem Services and Biodiversity

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    Nitrogen deposition has a beneficial or adverse effect on the provision of several forest ecosystem services, depending on the level of nitrogen deposition and the service considered. Biodiversity and water quality regulation are much more sensitive to increasing nitrogen deposition levels than wood production and carbon sequestration. Beyond a certain threshold, however, effects of nitrogen deposition on forest ecosystem services are always negative. This threshold is currently exceeded in much of Central Europe, eastern US and China. Estimates of the contribution of nitrogen to global forest carbon sequestration indicate that elevated nitrogen deposition is responsible for approximately 10–20% of the global terrestrial carbon sink. In areas with persisting high levels of nitrogen deposition forests can become saturated with nitrogen, which represents a risk to the permanence of this service in those areas

    Mechanical behavior of carbon fibers polyphenylene sulfide composites exposed to radiant heat flux and constant compressive force

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    International audienceThe thermo-mechanical behavior of carbon/PPS laminates under a constant compressive stress and radiant heat flux has been studied in the case of a quasi-isotropic layup. Though lots of studies focus on the time-to-failure, the present work is aimed at investigating the influence of thermal and mechanisms phenomena on the fire behavior of composite structures. The mechanical response is studied at different scales. From the total macroscopic strain standpoint, the response is divided into three stages, referred to as transient, stationary and failure stages. During these stages, different thermal and mechanical mechanisms compete and prevail depending on the applied compressive stress: thermal and thermo-chemical expansion, decomposition, changes in the mechanical properties, etc. With the measurement of macroscopic thermal strains, the mechanical strain is calculated, enabling the calculation of a macroscopic damage factor describing only the mechanical phenomena. Other quantitative indicators are also used to study the competition between thermally-and mechanically-induced mechanisms: maximal expansion, strain rate, etc. It is shown that under a low compressive force, the thermal expansion is a strain-driven mechanism. Failure is studied at the meso scale. The formation and development of porosities associated with the transition liquid-gas (due to the PPS matrix decomposition) leads to micro-buckling in matrix-rich areas and ultimately , to the formation and propagation in the transverse direction of plastic kink bands. Post-failure observations show that this macroscopic kinking propagates specifically according to the decomposition state of the material

    Mechanical behavior of carbon fibers polyphenylene sulfide composites exposed to radiant heat flux and constant compressive force

    No full text
    International audienceThe thermo-mechanical behavior of carbon/PPS laminates under a constant compressive stress and radiant heat flux has been studied in the case of a quasi-isotropic layup. Though lots of studies focus on the time-to-failure, the present work is aimed at investigating the influence of thermal and mechanisms phenomena on the fire behavior of composite structures. The mechanical response is studied at different scales. From the total macroscopic strain standpoint, the response is divided into three stages, referred to as transient, stationary and failure stages. During these stages, different thermal and mechanical mechanisms compete and prevail depending on the applied compressive stress: thermal and thermo-chemical expansion, decomposition, changes in the mechanical properties, etc. With the measurement of macroscopic thermal strains, the mechanical strain is calculated, enabling the calculation of a macroscopic damage factor describing only the mechanical phenomena. Other quantitative indicators are also used to study the competition between thermally-and mechanically-induced mechanisms: maximal expansion, strain rate, etc. It is shown that under a low compressive force, the thermal expansion is a strain-driven mechanism. Failure is studied at the meso scale. The formation and development of porosities associated with the transition liquid-gas (due to the PPS matrix decomposition) leads to micro-buckling in matrix-rich areas and ultimately , to the formation and propagation in the transverse direction of plastic kink bands. Post-failure observations show that this macroscopic kinking propagates specifically according to the decomposition state of the material

    Data from: Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems

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    Using massively parallel sequencing data from two species with different life history traits, American lobster (Homarus americanus) and Arctic Char (Salvelinus alpinus), we highlight how an unbalanced sex ratio in the samples and a few sex-linked markers may lead to false interpretations of population structure and thus to potentially erroneous management recommendations. Here, multivariate analyses revealed two genetic clusters separating samples by sex instead of by expected spatial variation; inshore and offshore locations in lobster, or east and west locations in Arctic Char. To further investigate this, we created several subsamples artificially varying the sex ratio in the inshore/offshore and east/west groups, and then demonstrated that significant genetic differentiation could be observed despite panmixia in lobster, and that Fst values were overestimated in Arctic Char. This pattern was due to 12 and 94 sex-linked markers driving differentiation for lobster and Arctic Char, respectively. Removing sex-linked markers led to non-significant genetic structure in lobster and a more accurate estimation of Fst in Arctic Char. The locations of these markers and putative identities of genes containing, or nearby the markers were determined using available transcriptomic and genomic data, and this provided new information related to sex determination in both species. Given that only 9.6% of all marine/diadromous population genomic studies to date have reported sex information, we urge researchers to collect and consider individual sex information. Sex information is therefore relevant for avoiding unexpected biases due to sex-linked markers as well as for improving our knowledge of sex determination systems in non-model species
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