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

Towards the establishment of new genetic resistances to potyviruses by exploiting susceptibility factors in Arabidopsis thaliana

Les résistances génétiques constituent un moyen de lutte efficace pour combattre les virus, lesquels présentent une menace pour la production agricole. Les facteurs cellulaires que ces pathogènes utilisent pour accomplir leur cycle dans la plante, les facteurs de sensibilité (S), peuvent être supprimés ou modifiés pour produire des résistances génétiques. De telles résistances sont présentes dans la diversité naturelle des plantes, mais limités. Les alternatives d’identification de facteur S sont le criblage de mutants pour la résistance ou les études interactionnelles avec les facteurs viraux. Le but de ce travail est d’identifier de nouvelles résistances génétiques aux potyvirus chez Arabidopsis thaliana. Il s’articule autour de 2 axes : Le premier vise à trouver de nouvelles résistances au TuMV par une approche de génétique directe en poursuivant la caractérisation de la résistance de 2 plantes candidates mutées à l’EMS. Les analyses effectuées sur les F2 et le séquençage NGS devraient permettre d’identifier les mutations causales des phénotypes étudiés. Le deuxième axe de ma thèse vise à valider de nouvelles résistances génétiques aux potyvirus en ciblant les deux facteurs de sensibilité que sont la cPGK2 et HVA22a. Des mutants affectant ces deux gènes S ont été obtenus par édition du génome, mais aucun à lui seul ne suffit à générer de résistance aux potyvirus. Ces travaux illustrent que la redondance génique constitue un frein à la mise en place de résistances génétiques associées aux gène S. La co-édition de gènes homologues pourrait être une alternative permettant de générer des résistances génétiques efficaces basées sur ces facteurs S de familles multigéniques.The development of genetic resistance is an effective strategy to combat viruses, a major threat to agricultural production. These pathogens hijack host cellular factors to complete their cycle in the plant. These so-called susceptibility factors (S) can be inactivated or engineered to produce genetic resistances. Such resistances can be found in plant natural diversity, but are limited. Alternative strategies for S-factor identification are screening of mutants for virus resistance or interaction studies between cellular and viral factors. The purpose of this study is to identify new genetic resistances to potyviruses in Arabidopsis thaliana. We structured it on two main axes: The first axis of this study aims to find new resistances to a TuMV isolate by a forward genetic approach. It consists to pursue the characterization of resistance of two plants EMS candidates. Analyses carried out on F2 populations from these two plants and NGS sequencing should allow the identification of the causal mutations of the studied phenotypes. The second axis of this study aims to validate new genetic resistances to potyviruses by targeting two susceptibility factors that are cPGK2, and HVA22a. Mutants affecting these two S genes have been obtained by genome editing approach, are not sufficient alone to induce resistance to potyvirus. This work illustrates that gene redundancy is an important barrier to the development of resistance based on S-gene knock-out. The co-editing of homologous genes could be an alternative approach to generate efficient genetic resistances based on these S-factors encoded by multigene families

Exploring New Routes for Genetic Resistances to Potyviruses: The Case of the Arabidopsis thaliana Phosphoglycerates Kinases (PGK) Metabolic Enzymes

International audienceThe development of recessive resistance by loss of susceptibility is a consistent strategy to combat and limit damages caused by plant viruses. Susceptibility genes can be turned into resistances, a feat that can either be selected among the plant’s natural diversity or engineered by biotechnology. Here, we summarize the current knowledge on the phosphoglycerate kinases (PGK), which have emerged as a new class of susceptibility factors to single-stranded positive RNA viruses, including potyviruses. PGKs are metabolic enzymes involved in glycolysis and the carbon reduction cycle, encoded by small multigene families in plants. To fulfil their role in the chloroplast and in the cytosol, PGKs genes encode differentially addressed proteins. Here, we assess the diversity and homology of chloroplastic and cytosolic PGKs sequences in several crops and review the current knowledge on their redundancies during plant development, taking Arabidopsis as a model. We also show how PGKs have been shown to be involved in susceptibility—and resistance—to viruses. Based on this knowledge, and drawing from the experience with the well-characterized translation initiation factors eIF4E, we discuss how PGKs genes, in light of their subcellular localization, function in metabolism, and susceptibility to viruses, could be turned into efficient genetic resistances using genome editing techniques

AtHVA22a, a plant-specific homologue of Reep/DP1/Yop1 family proteins is involved in turnip mosaic virus propagation

The movement of potyviruses, the largest genus of single-stranded, positive-sense RNA viruses responsible for serious diseases in crops, is very complex. As potyviruses developed strategies to hijack the host secretory pathway and plasmodesmata (PD) for their transport, the goal of this study was to identify membrane and/or PD-proteins that interact with the 6K2 protein, a potyviral protein involved in replication and cell-to-cell movement of turnip mosaic virus (TuMV). Using split-ubiquitin membrane yeast two-hybrid assays, we screened an Arabidopsis cDNA library for interactors of TuMV6K2. We isolated AtHVA22a (Hordeum vulgare abscisic acid responsive gene 22), which belongs to a multigenic family of transmembrane proteins, homologous to Receptor expression-enhancing protein (Reep)/Deleted in polyposis (DP1)/Yop1 family proteins in animal and yeast. HVA22/DP1/Yop1 family genes are widely distributed in eukaryotes, but the role of HVA22 proteins in plants is still not well known, although proteomics analysis of PD fractions purified from Arabidopsis suspension cells showed that AtHVA22a is highly enriched in a PD proteome. We confirmed the interaction between TuMV6K2 and AtHVA22a in yeast, as well as in planta by using bimolecular fluorescence complementation and showed that TuMV6K2/AtHVA22a interaction occurs at the level of the viral replication compartment during TuMV infection. Finally, we showed that the propagation of TuMV is increased when AtHVA22a is overexpressed in planta but slowed down upon mutagenesis of AtHVA22a by CRISPR-Cas9. Altogether, our results indicate that AtHVA22a plays an agonistic effect on TuMV propagation and that the C-terminal tail of the protein is important in this process.</p

Assessing the Response of Small RNA Populations to Allopolyploidy Using Resynthesized Brassica napus Allotetraploids

Associate editor: Juliette de MeauxInternational audienceAllopolyploidy, combining interspecific hybridization with whole genome duplication, has had significant impact on plant evolution. Its evolutionary success is related to the rapid and profound genome reorganizations that allow neoallopolyploids to form and adapt. Nevertheless, how neoallopolyploid genomes adapt to regulate their expression remains poorly understood. The hypothesis of a major role for small noncoding RNAs (sRNAs) in mediating the transcriptional response of neoallopolyploid genomes has progressively emerged. Generally, 21-nt sRNAs mediate posttranscriptional gene silencing by mRNA cleavage, whereas 24-nt sRNAs repress transcription (transcriptional gene silencing) through epigenetic modifications. Here, we characterize the global response of sRNAs to allopolyploidy in Brassica, using three independently resynthesized Brassica napus allotetraploids originating from crosses between diploid Brassica oleracea and Brassica rapa accessions, surveyed at two different generations in comparison with their diploid progenitors. Our results suggest an immediate but transient response of specific sRNA populations to allopolyploidy. These sRNA populations mainly target noncoding components of the genome but also target the transcriptional regulation of genes involved in response to stresses and in metabolism; this suggests a broad role in adapting to allopolyploidy. We finally identify the early accumulation of both 21- and 24-nt sRNAs involved in regulating the same targets, supporting a posttranscriptional gene silencing to transcriptional gene silencing shift at the first stages of the neoallopolyploid formation. We propose that reorganization of sRNA production is an early response to allopolyploidy in order to control the transcriptional reactivation of various noncoding elements and stress-related genes, thus ensuring genome stability during the first steps of neoallopolyploid formation

Land, Climate, Energy, Agriculture and Development in the Sahel: Synthesis paper of case studies under the Sudano-Sahelian Initiative for Regional Development, Jobs, and Food Security

This paper synthesizes a set of national case studies conducted in the Sahelian countries during 2019-2020 as a collaboration between national universities and research institutes, and the Center for Development Research (ZEF), University of Bonn, with contributions from the Agrhymet Regional Centre, Permanent Interstate Committee for Drought Control in the Sahel (CILSS). These case studies provide up-to-date knowledge and critical insights on the nexus of land degradation, climate change and energy in the Sahel. The current synthesis paper highlights their major findings and provides crosscutting and cross-regional analytical conclusions. First, the synthesis paper explores current trends in the Sahel region on land use and land degradation, energy use and supply, climate change projections and impacts, as well as their interactions and links to agricultural growth, food security, poverty reduction, and peace in the region. Second, technological, socio-economic and policy solutions at the nexus of land, water, energy and climate challenges that enable environmentally sustainable and socially inclusive rural development in the Sahel are discussed, including their interactions and implications for peace and stability in the region. The findings show that such socio-economic solutions as improving access to markets, strengthening social safety nets, increasing investments to transport and energy infrastructures, promoting land tenure security, expanding off-farm employment opportunities can greatly contribute to rural development in the Sahel, particularly by aiding climate change resilience and sustainable land management. Key technological innovations highlighted across the case studies include expanding irrigation and adopting water use efficient irrigation techniques, crop diversification, expanding agricultural mechanization, investing into restoring and rehabilitating degraded lands through reforestation, afforestation and agroforestry practices. The key lessons learnt from ongoing national policy initiatives for sustainable development highlight the importance of active stakeholder consultation and participation in policy formulation, institution of effective policy monitoring and assessment mechanisms, and avoiding of excessive reliance on external sources of funding for the successful implementation of sustainable development policies and programs. Based on these findings, the synthesis paper proposes an agenda for applied research to provide guidance to and accompany promising development strategies in and for the region

Partnership for Research on Ebola VACcination (PREVAC): protocol of a randomized, double-blind, placebo-controlled phase 2 clinical trial evaluating three vaccine strategies against Ebola in healthy volunteers in four West African countries

International audienceAbstract Introduction The Ebola virus disease (EVD) outbreak in 2014–2016 in West Africa was the largest on record and provided an opportunity for large clinical trials and accelerated efforts to develop an effective and safe preventative vaccine. Multiple questions regarding the safety, immunogenicity, and efficacy of EVD vaccines remain unanswered. To address these gaps in the evidence base, the Partnership for Research on Ebola Vaccines (PREVAC) trial was designed. This paper describes the design, methods, and baseline results of the PREVAC trial and discusses challenges that led to different protocol amendments. Methods This is a randomized, double-blind, placebo-controlled phase 2 clinical trial of three vaccine strategies against the Ebola virus in healthy volunteers 1 year of age and above. The three vaccine strategies being studied are the rVSVΔG-ZEBOV-GP vaccine, with and without a booster dose at 56 days, and the Ad26.ZEBOV,MVA-FN-Filo vaccine regimen with Ad26.ZEBOV given as the first dose and the MVA-FN-Filo vaccination given 56 days later. There have been 4 versions of the protocol with those enrolled in Version 4.0 comprising the primary analysis cohort. The primary endpoint is based on the antibody titer against the Ebola virus surface glycoprotein measured 12 months following the final injection. Results From April 2017 to December 2018, a total of 5002 volunteers were screened and 4789 enrolled. Participants were enrolled at 6 sites in four countries (Guinea, Liberia, Sierra Leone, and Mali). Of the 4789 participants, 2560 (53%) were adults and 2229 (47%) were children. Those < 18 years of age included 549 (12%) aged 1 to 4 years, 750 (16%) 5 to 11 years, and 930 (19%) aged 12–17 years. At baseline, the median (25th, 75th percentile) antibody titer to Ebola virus glycoprotein for 1090 participants was 72 (50, 116) EU/mL. Discussion The PREVAC trial is evaluating—placebo-controlled—two promising Ebola candidate vaccines in advanced stages of development. The results will address unanswered questions related to short- and long-term safety and immunogenicity for three vaccine strategies in adults and children. Trial registration ClinicalTrials.gov NCT02876328 . Registered on 23 August 2016