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

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

About optimal architecture of plant fibre textile composite for mechanical and sorption properties

International audienceThe aim of this work is to establish simple rules to optimise the architecture of plant woven fabric reinforcement for structural composite applications (sorption and mechanic aspects). For that, the influence of architectural parameters of reinforcement such as the frame, the yarn diameter, the pick count, and the filling rate, was studied from six different flax fabrics (2 quasi-unidirectionals and 4 balanced twills) and two processing techniques (autoclave and hot platen press). On the one hand, in order to normalise the effects of fibre fraction, porosity fraction and architectural parameters, a model was developped to analyse the mechanical properties at the level of the yarn. On the other hand, after demonstrating that the classical model of Fick does not properly fit the sorption of plant fibre textile composite, a two-phase Fick’s diffusion model was applied. It results that the best fabric architecture concerning mechanical and sorption properties is a compromise mixing high filling rate of woven fabrics, small shrinkage of yarns, and small yarn diameter

Polymer reinforced by flax fibres as a viscoelastoplastic material

International audienceFlax fibre reinforced polymers are at the heart of current scientific and societal concerns. However their mechanical behaviour is still poorly known despite significant scientific efforts, in particular the non-linear behaviour observed under tensile tests. In this paper, results of hardening, creep and repeated progressive tests under uniaxial loading performed on various quasi-unidirectional flax fibre reinforced composites are analysed in terms of the volume fraction of fibre, the titration of yarn reinforcement and temperature testing. To identify the respective parts of pure elastic, viscoelastic and viscoplastic components in the global mechanical response, a phenomenological model is built based on eight independentparameters. The parameter identification based on experimental data and checked by a sensitivity analysis shows that the viscoelastic effects are non-significant at room temperature. The non-linear behaviour can mainly be attributed to viscoplastic effects. Viscoplastic modelling is based on a combination of two hardenings; the first classical (linear) one describes the translation of the elastic domain ; the second (non-linear) one describes a translation coupled with a contraction of the elastic domain during loading that improves the unloading behaviour during repeated progressive loading tests

Polymer reinforced by flax fibres as a viscoelastoplastic material

International audienceFlax fibre reinforced polymers are at the heart of current scientific and societal concerns. However their mechanical behaviour is still poorly known despite significant scientific efforts, in particular the non-linear behaviour observed under tensile tests. In this paper, results of hardening, creep and repeated progressive tests under uniaxial loading performed on various quasi-unidirectional flax fibre reinforced composites are analysed in terms of the volume fraction of fibre, the titration of yarn reinforcement and temperature testing. To identify the respective parts of pure elastic, viscoelastic and viscoplastic components in the global mechanical response, a phenomenological model is built based on eight independentparameters. The parameter identification based on experimental data and checked by a sensitivity analysis shows that the viscoelastic effects are non-significant at room temperature. The non-linear behaviour can mainly be attributed to viscoplastic effects. Viscoplastic modelling is based on a combination of two hardenings; the first classical (linear) one describes the translation of the elastic domain ; the second (non-linear) one describes a translation coupled with a contraction of the elastic domain during loading that improves the unloading behaviour during repeated progressive loading tests