A global alliance declaring war on cassava viruses in Africa

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Lassa Fever Infection among Healthcare Workers during the 2018 Outbreak in Nigeria

Introduction: Healthcare workers (HCWs) are potentially exposed to infection during viral hemorrhagic fever outbreaks. In the wake of 2018, Nigeria experienced an unprecedented surge in cases of Lassa fever (LF), which affected HCWs. To guide infection prevention and control (IPC) strategies in similar settings, we characterize HCWs' infection and describe the gaps in IPC standards and practices during the outbreak. Methods: Data was collected using a structured questionnaire, interview, and review of case notes of 21 HCW with laboratory-confirmed Lassa fever who were treated at the Irrua Specialist Teaching Hospital (ISTH) Irrua and the Alex-Ekwemen Federal Teaching Hospital, Abakaliki (AEFETHA), between 1st January and 27th May 2018. Information collected was the patients' socio-demographic characteristics, date of potential exposure and onset of illness, nature, and type of exposure, clinical features, outcome, use of personal protective equipment (PPE), and personnel IPC training and were analyzed using descriptive statistics with Microsoft Excel. Results: The study included 21 HCWs, and 12 (57.14%) were doctors. The case fatality rate was 23%. Nearly two-thirds (62%) of the HCWs could describe a likely procedure leading to their exposure and infection. Among 13 HCWs, 85% had multiple blood and body fluids exposure, while 15% had needle stick injury or scalpel cut. About one-fifth of the participants had received some IPC training. Conclusion: Limited IPC adherence and inappropriate risk assessment were identified as factors leading to Lassa fever exposure and infection among HCWs. There is an urgent need to provide IPC training for all HCWs and to ensure an adequate supply of IPC materials to all healthcare facilities as part of emergency preparedness, especially in LF endemic areas

High-resolution linkage map and chromosome-scale genome assembly for cassava (Manihot esculenta Crantz) from 10 populations

Cassava (Manihot esculenta Crantz) is a major staple crop in Africa, Asia, and South America, and its starchy roots provide nourishment for 800 million people worldwide. Although native to South America, cassava was brought to Africa 400–500 years ago and is now widely cultivated across sub-Saharan Africa, but it is subject to biotic and abiotic stresses. To assist in the rapid identification of markers for pathogen resistance and crop traits, and to accelerate breeding programs, we generated a framework map for M. esculenta Crantz from reduced representation sequencing [genotyping-by-sequencing (GBS)]. The composite 2412-cM map integrates 10 biparental maps (comprising 3480 meioses) and organizes 22,403 genetic markers on 18 chromosomes, in agreement with the observed karyotype. We used the map to anchor 71.9% of the draft genome assembly and 90.7% of the predicted protein-coding genes. The chromosome-anchored genome sequence will be useful for breeding improvement by assisting in the rapid identification of markers linked to important traits, and in providing a framework for genomic selectionenhanced breeding of this important crop.Bill and Melinda Gates Foundation (BMGF) Grant OPPGD1493. University of Arizona. CGIAR Research Program on Roots, Tubers, and Bananas. Next Generation Cassava Breeding grant OPP1048542 from BMGF and the United Kingdom Department for International Development. BMGF grant OPPGD1016 to IITA. National Institutes of Health S10 Instrumentation Grants S10RR029668 and S10RR027303.http://www.g3journal.orghb201

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.

The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants

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

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

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

Genetic analysis and QTL mapping of early root bulking in an F1 population of non-inbred parents in cassava (Manihot esculenta Crantz)

The genetic basis of early bulking in cassava was studied in a replicated, multi-locational trial using 144 F1 progeny derived from an intra-specific cross between two non-inbred parents. A second, sequential harvest experiment examined the relative importance of eight yield-related traits on early bulking and their QTLs during the crop growth cycle. Our objectives were to identify traits, and genes controlling them, strongly associated with early yield as a first step to marker-assisted improvement of the trait. Multiple linear regression analysis and stepwise regression of early yield on eight yield-related traits revealed harvest index, dry foliage weight and root diameter as the most important factors associated with early yield. A total of 18 QTLs controlling early yield were identified in the first and second experiments and 27 QTLs, 2 for dry foliage weight, 8 for harvest index and 17 for root diameter, in the second experiment. The individual effects of alleles at these QTLs identified ranged from 7% to 33% of the phenotypic variance explained. Seven of 18 QTLs found for early yield (39%) coincided with QTLs associated with one or more traits with significant influence on early yield. The results show that sink and source capacities are very important in determining early yield. The identification of a number of QTLs with positive effect for increased early yield provides an opportunity for marker-assisted selection and improvement of early bulking potential in cassava