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

<i>In vitro</i> antioxidant and antibacterial efficacy of <i>Feronia elephantum</i> Correa fruit

301-305The present investigation was formulated to screen the in vitro antioxidant and antibacterial potential of ethanolic extract of Wood apple, Feronia elephantum Correa fruit. Antioxidant ability of the fruit extract was assessed by estimating total phenols, flavonoids, tannins, total antioxidant capacity and iron chelating activity. The extract was also examined for its antibacterial efficacy against the bacterial isolates of clinical significance. The results suggested that the extract exhibited dose-dependent antioxidant ability and broad-spectrum antibacterial activity which might possibly be due to the presence of phenolic constituents of the fruit

Cultural Characteristics and Molecular Confirmation of Ustilaginoidea virens the Incitant of False Smut of Rice

Aims: Ustilaginoidea virens, which causes false smut of rice (synonyms: green smut or pseudo smut), is an emerging grain disease around the world. The main aim of the study is to find out suitable culturable medium, carbon sources and pH for the growth of false smut pathogen and molecular confirmation of U. virens isolates. Place and Duration of Study: The in vitro studies were conducted in the Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, between December 2020 to April 2021. Methodology: To study the growth pattern of U.virens, five different carbon sources and mediums were used. Standardization of pH was done using a PSA medium amended with different pH levels. DNA extraction of all 13 isolates were done using the CTAB method. The phylogenetic tree was constructed using MEGA 12 software. Results: It is a slow-growing pathogen and grew well in the potato sucrose agar medium with a mycelial growth of about (54.00 mm) after 30 days and sucrose was found to be a good carbon source. The pH of 5 was found to be optimum. PCR reaction was carried out to further validate 13 isolates using three sets of primer pairs ITS 1/ITS 4, US1-5/US3-3, and US 2-5/US 4-3 with amplified products of 560 bp, 380 bp and 260 bp. Accession numbers were obtained for all the isolates