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

Imunodiagnóstico da esquistossomose mansônica com baixa carga parasitária

Atualmente, a esquistossomose mansônica com baixa carga parasitária é freqüente, e desta forma, ensaios imunológicos de interesse ao diagnóstico populacional de infecção leve por Schistosoma mansoni foram aqui avaliados. Incluíram-se neste estudo ensaios anteriormente não avaliados (grupo I) e pouco avaliados (grupo II) para triagem de infecções leves. No grupo I, destacaram-se as reações de inunofluorescência destinadas à detecção de anticorpos IgM antiverme (RIFv IgM), e de anticorpos IgG anti-ovo (RIFo IgG) por apresentarem níveis elevados de sensibilidade, especificidade, eficiência e valor preditivo positivo. Todavia, os ensaios imunoenzimáticos para a detecção de anticorpos IgM, antiverme (ELISAv IgM) e anti- ovo (ELISAo IgM) revelaram níveis menores que as reações acima. Os ensaios do grupo II, namaioria utilizada para detecção de anticorpos IgG contra os mesmos antígenos, demonstraram desempenhos diagnósticos satisfatórios. Os dados aqui obtidos contribuíram para evidenciar pelo menos três categorias de ensaios imunológicos, e concluímos que os de categoria I são apropriados para estudos soroepidemiológicos de infecção leve por S. mansoni, em vista de suas características diagnosticas permanecerem inalteradas mesmo que a intensidade de infecção por S. mansoni varie significativamente

Aplicações da curva de resistência no controle da qualidade física de um solo sob pastagem Applications of the resistance curve in the control of the physical quality of soils under grass

A degradação da qualidade física do solo pode estar associada com a compactação causada pelo pisoteio dos animais. A resistência do solo à penetração (RP) é um parâmetro físico utilizado para estabelecer o grau de compactação do solo. Contudo, esta varia com a umidade (teta) e densidade do solo (Ds). O objetivo deste trabalho foi obter a curva de resistência do solo e utilizá-la na avaliação da qualidade física do solo num sistema de pastejo intensivo rotacionado de capim-elefante. A curva de resistência do solo foi determinada por meio de 48 amostras indeformadas, obtidas na profundidade de 0-10 cm numa Terra Roxa Estruturada utilizada com pastagem em sistema intensivo de exploração. Os resultados demonstraram correlação negativa entre a RP e teta, e correlação positiva entre RP e Ds. Estimativas indicaram que no potencial de -0,01 MPa a RP não atinge valores considerados restritivos ao crescimento radicular. Entretanto, no potencial de -0,3 MPa, a RP atinge níveis limitantes em toda a área. Quanto ao sistema de manejo e a espécie estudada, os resultados sugerem que a curva de resistência do solo pode ser utilizada para orientar as práticas de manejo visando à manutenção de uma qualidade física do solo adequada para o crescimento das plantas.<br>The degradation of the physical quality of soils has been associated with the soil compaction caused by animal trampling. The soil resistance to penetration (SRP) is a soil physical parameter used to assess the soil compaction degree. However, SRP varies with soil moisture (theta) and bulk density (Db). The objective of this research was to quantify the soil resistance curve and use it to evaluate the physical quality of a soil under short duration grazing system of elephant grass. The soil resistance curve was measured using forty-eight undisturbed cores taken at the 0-10 cm depth of a Kandiudalfic Eutrudox used with elephant grass in intensive system of exploration. The results indicated a negative correlation among SRP and theta as well as a positive correlation between SRP and Db. Predictions indicated that at soil matric potential equal to -0.01 MPa the SRP did not reach critical values to root growth. Nevertheless, at the soil matric potential equal to -0.3 MPa, the SRP reached limiting values in the whole area. For the management system and the studied species, the results suggest that soil resistance curve may be used to guide soil management practices for maintaining a good soil physical quality for grass growth

Brazilian Flora 2020: Leveraging the power of a collaborative scientific network

International audienceThe shortage of reliable primary taxonomic data limits the description of biological taxa and the understanding of biodiversity patterns and processes, complicating biogeographical, ecological, and evolutionary studies. This deficit creates a significant taxonomic impediment to biodiversity research and conservation planning. The taxonomic impediment and the biodiversity crisis are widely recognized, highlighting the urgent need for reliable taxonomic data. Over the past decade, numerous countries worldwide have devoted considerable effort to Target 1 of the Global Strategy for Plant Conservation (GSPC), which called for the preparation of a working list of all known plant species by 2010 and an online world Flora by 2020. Brazil is a megadiverse country, home to more of the world's known plant species than any other country. Despite that, Flora Brasiliensis, concluded in 1906, was the last comprehensive treatment of the Brazilian flora. The lack of accurate estimates of the number of species of algae, fungi, and plants occurring in Brazil contributes to the prevailing taxonomic impediment and delays progress towards the GSPC targets. Over the past 12 years, a legion of taxonomists motivated to meet Target 1 of the GSPC, worked together to gather and integrate knowledge on the algal, plant, and fungal diversity of Brazil. Overall, a team of about 980 taxonomists joined efforts in a highly collaborative project that used cybertaxonomy to prepare an updated Flora of Brazil, showing the power of scientific collaboration to reach ambitious goals. This paper presents an overview of the Brazilian Flora 2020 and provides taxonomic and spatial updates on the algae, fungi, and plants found in one of the world's most biodiverse countries. We further identify collection gaps and summarize future goals that extend beyond 2020. Our results show that Brazil is home to 46,975 native species of algae, fungi, and plants, of which 19,669 are endemic to the country. The data compiled to date suggests that the Atlantic Rainforest might be the most diverse Brazilian domain for all plant groups except gymnosperms, which are most diverse in the Amazon. However, scientific knowledge of Brazilian diversity is still unequally distributed, with the Atlantic Rainforest and the Cerrado being the most intensively sampled and studied biomes in the country. In times of “scientific reductionism”, with botanical and mycological sciences suffering pervasive depreciation in recent decades, the first online Flora of Brazil 2020 significantly enhanced the quality and quantity of taxonomic data available for algae, fungi, and plants from Brazil. This project also made all the information freely available online, providing a firm foundation for future research and for the management, conservation, and sustainable use of the Brazilian funga and flora

Growing knowledge: an overview of Seed Plant diversity in Brazil

Abstract An updated inventory of Brazilian seed plants is presented and offers important insights into the country's biodiversity. This work started in 2010, with the publication of the Plants and Fungi Catalogue, and has been updated since by more than 430 specialists working online. Brazil is home to 32,086 native Angiosperms and 23 native Gymnosperms, showing an increase of 3% in its species richness in relation to 2010. The Amazon Rainforest is the richest Brazilian biome for Gymnosperms, while the Atlantic Rainforest is the richest one for Angiosperms. There was a considerable increment in the number of species and endemism rates for biomes, except for the Amazon that showed a decrease of 2.5% of recorded endemics. However, well over half of Brazillian seed plant species (57.4%) is endemic to this territory. The proportion of life-forms varies among different biomes: trees are more expressive in the Amazon and Atlantic Rainforest biomes while herbs predominate in the Pampa, and lianas are more expressive in the Amazon, Atlantic Rainforest, and Pantanal. This compilation serves not only to quantify Brazilian biodiversity, but also to highlight areas where there information is lacking and to provide a framework for the challenge faced in conserving Brazil's unique and diverse flora