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

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Not AvailableNot AvailableDepartment of Agriculture and CooperationGovernment of Telangana, HyderabadDepartment of Agriculture, Cooperation and Farmers Welfare, GoI, New Delh

Performance of potato (Solanum tuberosum L.) genotypes under hill zone of Karnataka.

An experiment was conducted to study the performance of nine genotypes of potato under hill zone of Karnataka. Among nine genotypes, maximum tuber sprout percentage was observed in Kufri Jyoti (100) followed by TT7011 (98.75) and least percentage was in C-28 (89.16). Kufri Jyoti performed better for most of the characters such as plant height(68.04 cm), number of leaves(42.21), leaf area (154.88 cm2), tuber weight (116.42 g), tuber length (8.20 cm), tuber diameter (5.88 cm), chlorophyll content (1.26 mg/g) and which was found to be significantly superior over other genotypes. Number of tubers per plant (4.43), total tuber yield per plot (18.98 kg), total tuber yield per hectare (26.36 t), marketable yield per plot (10.21 kg), marketable yield per hectare (14.18 t), dry matter (19.88 %), total sugars (2.55 %) was observed in genotype TT7011 compared to the rest of the genotypes. The genotype C-28 recorded highest starch content (24.10 %) followed by TT7007 (22.92 %) and the least starch content (19.05 %) was observed in MCIP-9-1. Genotype TT7011 realized maximum gross returns (283600.00 per ha) and net returns (193457.00 per ha) followed by TT7010 (Gross returns 190200.00 per ha and net returns 100057.00 per ha)

Correlation and path analysis for yield and yield-related traits of potato (Solanum tuberosum L.) in Karnataka

Correlation and path analyses study on total tuber yield and yield attributing traits of nine CIP advance potato genotypes revealed that total tuber yield per plot had highly significant and positive association with marketable yield per plot, number of tubers per plant, dry matter and number of stems at 60 DAP both at genotypic and phenotypic level indicating the possibility of simultaneous selection for these traits to improve the tuber yield. It revealed that numbers of tubers per plant, marketable yield per plot, number of stems at 60 DAP and tuber weight were the most influencing factors to improve the tuber yield. Thus, these characters deserve greater weightage during selection for yield performance attribute

Effect of lesion morphology on microwave signature in ultra-wideband breast imaging: A preliminary two-dimensional investigation

10.1109/APS.2007.4395957IEEE Antennas and Propagation Society, AP-S International Symposium (Digest)2168-217

Castor wilt

The technical bulletin on "castor wilt" contains information on distribution, economic importance, symptoms, variability of pathogen, nematode –fungus interaction, disease cycle, screening of castor germ plasm for identification of resistant sources and management of wilt disease.Not AvailableDirectorate of Oilseeds Research, Hyderaba

Collagen-related genes influence the glaucoma risk factor, central corneal thickness

10.1093/hmg/ddq511Human Molecular Genetics204649-658HMGE

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ABCC5, a Gene That Influences the Anterior Chamber Depth, Is Associated with Primary Angle Closure Glaucoma

10.1371/journal.pgen.1004089PLoS Genetics103e100408

Publisher Correction: Whole-genome sequencing of a sporadic primary immunodeficiency cohort (Nature, (2020), 583, 7814, (90-95), 10.1038/s41586-020-2265-1)

An amendment to this paper has been published and can be accessed via a link at the top of the paper