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

Modelos de ajuste e métodos para a determinação da curva de retenção de água de um Latossolo-vermelho-amarelo Adjustment models and methods for determining the soil water retention curve of a red-yellow Latosol

A caracterização da capacidade de retenção de água de um solo é fundamental para a descrição do fluxo de água através dele e para o adequado manejo da irrigação. São apresentadas comparações entre curvas de retenção de água do solo: ajustadas pelos modelos propostos por van Genuchten e por Hutson & Cass; obtidas pelo método do WP4 usando processo de umedecimento e de secagem; obtidas pelo método da centrífuga utilizando amostras deformadas e indeformadas; e obtidas pelo WP4 e centrífuga, usando um processo de secagem e amostra deformada. Amostras deformadas e indeformadas foram coletadas com trados específicos em um Latossolo Vermelho-Amarelo (LVA), textura argilosa. Foram determinadas as propriedades hídricas do solo necessárias à elaboração das curvas de retenção de água obtidas por análise de regressão. O modelo de van Genuchten possibilitou o melhor ajuste nas diversas situações estudadas. Considerando o processo de secagem, o teor de água útil obtido superou em 13 % o resultado do processo de umedecimento e evidenciou reduzido efeito de histerese. A amostra deformada apresentou-se com um teor de água útil superior 61,7 % ao valor obtido para a amostra indeformada. Entre os métodos estudados, verificou-se que aquele que usa o WP4 subestimou os dados obtidos pela centrífuga. Verificou-se que há diferenças entre amostra deformada e indeformada e os métodos utilizados na obtenção da curva de retenção.<br>The characterization of the soil water retention capacity is fundamental for an adequate irrigation management and water flow description. We present comparisons of soil water retention curves adjusted in distinct ways: by the models proposed by van Genuchten and by Hutson & Cass; by the WP4 method in a wetting and drying process; by the centrifuge method using disturbed as well as undisturbed soil samples; and by the WP4 and centrifuge using a drying process and disturbed soil samples. Disturbed and undisturbed samples were collected with a specific sampler in a Red-Yellow Latosol (Oxisol). Important soil water properties to establish the soil water retention curves, which were then determined by regression analysis. The van Genuchten model led to the best adjustment in the different studied situations. Based on the drying process, the available water content was 13 % higher than by the wetting process, evidencing a reduced hysteresis effect. The available water content in the disturbed sample was 61.7 % higher than in undisturbed samples. It was verified that among the studied methods the WP4 underestimated the data obtained by the centrifuge method. Differences were observed among procedures based on disturbed and undisturbed soil samples as well as the methods used to establish the retention curve