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

Drought Stress Tolerance Screening of Elite American Breeding Rice Genotypes Using Low-Cost Pre-Fabricated Mini-Hoop Modules

Drought is a major abiotic stress factor affecting the growth and development of plants at all stages. Developing a screening tool for identifying drought stress tolerance during seedling establishment is important in the deployment of rice varieties suited to water-limited growing environments. An experiment was conducted to evaluate 100 rice genotypes, mostly belonging to the tropical japonica subspecies, for drought stress tolerance using low-cost, pre-fabricated mini-hoop structures. The rice seedlings were subjected to two different soil moisture regimes- control pots managed at 100% and drought pots at 50% field capacity, from 12 to 30 days after sowing (DAS). Several morpho-physiological parameters including root traits were measured to assess the response of genotypes to drought stress. Significant moisture stress × genotype interactions were found for most of the parameters measured. A cumulative drought stress response index (CDSRI) was developed by adding the individual response indices of all cultivars. Based on CDSRI and standard deviation values, 5 and 28 genotypes were identified as highly sensitive and sensitive to drought, respectively, and 45 as moderately sensitive. On the other hand, 16 and 6 genotypes were classified as tolerant and highly tolerant to drought, respectively. Cheniere, a released cultivar, and RU1402174, an experimental breeding line, were identified as the least and most tolerant to drought among the 100 genotypes tested. Significant linear correlation coefficients were obtained between CDSRI and root growth parameters (R2 = 0.91, n = 100) and CDSRI with shoot growth parameters (R2 = 0.48, n = 100), revealing the importance of root traits in studying and identifying drought tolerant lines during the seedling establishment stages in rice. The tolerant rice genotypes identified will be valuable for rice scientists in studying the mechanism for early season drought as well as for rice breeders for developing new genotypes best suited under growing environments prone to early-season drought

Genetic Variability Assessment of Tropical Indica Rice (Oryza sativa L.) Seedlings for Drought Stress Tolerance

Drought stress is one of the most devastating abiotic factors limiting plant growth and development. Devising an efficient and rapid screening method at the seedling stage is vital in identifying genotypes best suited under drought conditions. An experiment was conducted to assess 74 rice genotypes for drought tolerance using specially designed mini-hoop structures. Two treatments were imposed on rice seedlings, including 100% moisture and a 50% moisture regime. Several shoot morpho-physiological traits and root traits were measured and analyzed. The genotypes exhibited a wide range of variability for the measured traits, with the leaf area showing the most significant variation, followed by plant height, tiller number, and shoot dry weight. In contrast, the drought did not significantly affect most root traits. The germplasm was classified into different categories using cumulative drought stress response indices (CDSRI); 19 genotypes (26%) were identified as drought sensitive, and 33 (45%), 15 (20%), and 7 (9%) were determined as low, moderately, and highly drought-tolerant, respectively. Genotypes IR86638 and IR49830 were the most and least drought-tolerant, respectively. Overall, a poor correlation was observed between CDSRI, total shoot traits (R2 = 0.36), and physiological parameters (R2 = 0.10). A strong linear correlation was found between CDSRI and root traits (R2 = 0.81), suggesting that root traits are more crucial and better descriptors in screening for drought tolerance. This study can help rice breeders and scientists to accelerate breeding by adopting a mini-hoop rapid screening method. The tolerant genotypes could serve as appropriate donor parents, progenies, and potential genotypes for developing drought-tolerant commercial cultivars