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

LIDA: the Leiden ice database for astrochemistry

Context. High-quality vibrational spectra of solid-phase molecules in ice mixtures and for temperatures of astrophysical relevance are needed to interpret infrared observations toward protostars and background stars. Such data are collected worldwide by several laboratory groups in support of existing and upcoming astronomical observations. Over the last 25 yr, the Laboratory for Astrophysics at Leiden Observatory has provided more than 1100 (high-resolution) spectra of diverse ice samples. Aims. In time with the recent launch of the James Webb Space Telescope, we have fully upgraded the Leiden Ice Database for Astrochemistry (LIDA) adding recently measured spectra. The goal of this paper is to describe what options exist regarding accessing and working with a large collection of infrared (IR) spectra, and the ultraviolet-visible (UV/vis) to the mid-infrared refractive index of H2O ice. This also includes astronomy-oriented online tools to support the interpretation of IR ice observations. Methods. This ice database is based on open-source Python software, such as Flas

Laboratory data in support of JWST observations of interstellar ices

Laboratory astrophysics and astrochemistr

Apoptose na maturação placentária de vacas em diferentes estágios de gestação: evidenciação imuno-histoquímica e bioquímica

Apoptose tem um papel importante na manutenção da homeostase placentária, e o desequilíbrio desse processo pode comprometer a gestação. O objetivo do presente estudo foi avaliar a ocorrencia de apoptose em amostras de placenta de vacas em diferentes fases de gestação. Amostras de placentomos de 15 vacas saudáveis com 4 (n=5), 6 (n=5) e 9 (n=5) meses de gestação foram colhidas e processadas rotineiramente para a histologia, imuno-histoquímica e isolamento de DNA. As lâminas obtidas foram coradas em HE, ou submetidas à análise imuno-histoquímica das proteínas pró-apoptóticas caspase-3 e Bax, e da proteína anti-apoptótica Bcl-2. O DNA isolado foi submetido à eletroforese em gel de agarose para detecção da fragmentação internucleossômica do genoma. Os resultados de histomorfometria revelaram que as células apoptóticas aumentaram progressivamente com o avanço da gestação. Confirmou-se a apoptose pela fragmentação característica do DNA genômico, visualizada pelo clássico "padrão em escada" na eletroforese em gel de agarose. Adcionalmente, a imunoexpressão de caspase-3, Bax e Bcl-2 foram observadas em todas as amostras. Entretanto, a proteína caspase-3 apresentou marcação mais intensa em todos os tempos gestacionais, quando comparada com a marcação das proteínas Bcl-2 e Bax. Esses resultados confirmam e reforçam a importância da apoptose na maturação placentária. Além disto, indica que caspase-3, Bax e Bcl-2 estão envolvidas nos mecanismos de ativação da apoptose pela via intrínseca mitocondrial ao longo da gestação, contribuindo para o equilíbrio fisiológico da celularidade e renovação celular na placenta bovina

Variações fenológicas das espécies do cerrado em Emas - Pirassununga, SP Phenological variations of the cerrado species in Emas (Pirassununga, SP)

Foi estudada a flora vascular de uma área de cerrado, situada no distrito de Emas, município de Pirassununga, Estado de São Paulo (aproximadamente, 22º02'S e 47º30'W). Entre abril de 1994 e abril de 1995, realizou-se um levantamento florístico, em que foram amostradas 358 espécies. A partir dos dados deste levantamento, estudaram-se as variações fenológicas das espécies, procurando analisá-las como estratégias adaptativas. Os componentes herbáceo-subarbustivo e arbustivoarbóreo comportaram-se de maneira distinta. As espécies arbustivo-arbóreas floresceram principalmente no início da estação chuvosa, enquanto que as herbáceo-subarbustivas produziram flores, de modo geral, apenas no final da estação úmida, após período de acúmulo de carboidratos. As espécies do componente herbáceo-subarbustivo tiveram pico de frutificação no final da estação chuvosa, qualquer que fosse a síndrome de dispersão de seus diásporos. Já as espécies do componente arbustivo-arbóreo apresentaram comportamentos distintos, conforme a síndrome de dispersão. As espécies zoocóricas frutificaram ao longo de toda estação úmida, enquanto que as anemocóricas e autocóricas produziram frutos, principalmente no início da estação seca.<br>The vascular flora of the cerrado in Emas district, Pirassununga municipality, São Paulo State (approximately 22º02'S and 47º30'W) was studied. Between April 1994 and April 1995 a floristic survey was carried out, when 358 species, representing 227 genera and 78 families, were found. During this survey, the phenologycal variations were observed and analysed as adaptive strategies. The woody and herbaceous components had distinct behaviours. The woody species flowered mainly at the beginning of the rainy season, while the herbaceous ones produced flowers generally at the end of that season, after a period of carbohydrate accumulation. The herbaceous species produced fruits specially at the end of the rainy season whatever its dispersion syndrome was. The woody ones showed different patterns depending on its dispersion syndrome. The zoochorous species fruited along the whole rainy season, while the anemochorous and autochorous ones produced fruits principally at the beginning of the dry season