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

Morfo-anatomia do envoltório seminal de espécies brasileiras de Indigofera L. (Leguminosae, Papilionoideae)

RESUMO O grande número de espécies e a complexidade do gênero Indigofera geram controvérsias taxonômicas de difícil resolução. Para contribuir com a taxonomia do gênero, foram levantados caracteres diagnósticos do envoltório seminal de sete espécies brasileiras de Indigofera, utilizando técnicas de exame de superfície e histológicas. As sementes são pequenas, em sua maioria rombóides mas também cúbicas ou cilíndricas, variando de verde-claras a castanho-escuras, exotestais, albuminosas, com hilo mediano, circular a ovado, de coloração conspícua. O envoltório apresentou microescultura micro a macrorreticulada, sendo constituído por macroesclereídes (com conteúdo fenólico em cinco espécies) e osteosclereídes. Embora a anatomia do envoltório da semente não tenha apresentado diferenças marcantes entre as espécies, a combinação de caracteres provenientes da microescultura da superfície seminal, da forma e do tamanho do hilo e da semente, e do número de camadas de osteosclereídes, permitiu a identificação das espécies estudadas neste trabalho. Foi concluído que a anatomia é uma ferramenta bastante útil para subsidiar a taxonomia do gênero

Investigation of metallo-β-lactamase-producing Acinetobacter sp and Pseudomonas aeruginosa at an emergency hospital in Porto Alegre, State of Rio Grande do Sul, Brazil

Introdução: O aparecimento de Pseudomonas aeruginosa e Acinetobacter sp produtores de metalo-β-lactamases (MBLs) é um desafio para os hospitais. Métodos: Verificou-se a produção de MBL em cepas clínicas de Pseudomonas aeruginosa e Acinetobacter sp de um hospital de emergência de Porto Alegre pelo método de aproximação de disco e E-test MBL. Os genes bla foram pesquisados pela PCR. Resultados: Duas cepas de Pseudomonas aeruginosa e oito Acinetobacter sp demonstraram fenótipo de MBLs. A amplificação do gene blaSPM-1 confirmou a enzima em P. aeruginosa.. Conclusões: Deve-se ter cautela ao avaliar testes fenotípicos utilizados na detecção rotineira de metalo-enzima.Introduction: The appearance of metallo-β-lactamase (MBL)-producing Pseudomonas aeruginosa and Acinetobacter sp. is a challenge for hospitals. Methods: The production of MBL in clinical isolates of Pseudomonas aeruginosa and Acinetobacter sp. From an emergency hospital in Porto Alegre was investigated using the disk approximation test and MBL E-test. The bla genes were determined using PCR. Results: Two strains of Pseudomonas aeruginosa and eight of Acinetobacter sp were shown to be MBL phenotypes. Amplification of the blaSPM-1 gene confirmed the presence of the enzyme in P. aeruginosa. Conclusions: Caution is needed in evaluating phenotype tests used for routine detection of metallo-β-lactamases