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

Características de carcaça e da carne de suínos machos castrados e imunocastrados alimentados com diferentes níveis nutricionais Carcass characteristics and meat of surgically castrated and immunocastrated pigs fed different nutritional levels

O trabalho foi realizado para avaliar as características de carcaça e carne de suínos machos castrados e imunocastrados alimentados com dietas contendo diferentes níveis nutricionais. O delineamento experimental foi inteiramente casualizado com quatro tratamentos principais (T1-suínos machos castrados alimentados com dieta basal; T2-machos imunocastrados alimentados com dieta basal; T3-machos imunocastrados alimentados com dieta basal+3% aminoácidos e energia; T4-machos imunocastrados alimentados com dieta basal+5% aminoácidos e energia) e dois tratamentos secundários com ou sem ractopamina dentro de cada tratamento principal. Os suínos machos castrados apresentaram peso de abate 3,3% inferior (P<0,05), peso de carcaça fria 1,4% superior (P<0,05) e peso de carré 13% superior (P<0,05) em relação aos machos imunocastrados. Suínos machos imunocastrados suplementados com 5% a mais de aminoácidos e energia apresentaram costela 19% mais (P<0,05) pesada e valores superiores (P<0,05) na coloração b* (amarelo-azul) na carne aos 45min e às 24h pós-abate em relação aos machos castrados alimentados com a dieta basal. A suplementação com 5% de aminoácidos e energia aumenta o peso e rendimento de costela e altera o valor da coloração b* (amarelo-azul) na carne aos 45min e às 24h pós-abate de suínos machos imunocastrados.<br>The study was carried out to evaluate the carcass characteristics and meat of surgically castrated and immunocastrated pigs fed with different nutritional levels. The animals were distribuited in a completely randomized experimental design with four main treatments (T1-surgically castrated pigs fed with basal diet; T2-immunocastrated pigs fed with basal diet; T3-immunocastrated pigs fed with basal diet+3% amino acids and energy; T4-immunocastrated pigs fed with basal diet+5% amino acids and energy) and two secondary treatments with or without ractopamine within each main treatment. The surgically castrated pigs had slaughter weight 3.3% lower (P<0.05), cold carcass weight 1.4% higher (P<0.05) and loin chop weight 13% higher (P<0.05) compared to immunocastred pigs. The immunocastrated pigs supplemented with 5% more amino acids and energy had rib 19% more heavier (P<0.05) and higher values (P<0.05) in the color b* (yellow-blue) in the meat to 45min and 24h post-slaughter compared with surgically castrated pigs fed with basal diet. Supplementation with 5% amino acids and energy increases weight and yield of rib and changes the value of color b* (yellow-blue) in the meat to 45min and 24h post-slaughter male pigs immunocastrated

Comparison between gradient-dependent hydraulic conductivities of roots using the root pressure probe: the role of pressure propagations and implications for the relative roles of parallel radial pathways

The definitive version is available at www.blackwell-synergy.comHydrostatic pressure relaxations with the root pressure probe are commonly used for measuring the hydraulic conductivity (Lpr) of roots. We compared the Lpr of roots from species with different root hydraulic properties (Lupinus angustifolius L. ‘Merrit’, Lupinus luteus L. ‘Wodjil’, Triticum aestivum L. ‘Kulin’ and Zea mays L. ‘Pacific DK 477’) using pressure relaxations, a pressure clamp and osmotic gradients to induce water flow across the root. Only the pressure clamp measures water flow under steady-state conditions. Lpr determined by pressure relaxations was two- to threefold greater than Lpr from pressure clamps and was independent of the direction of water flow. Lpr (pressure clamp) was two- to fourfold higher than for Lpr (osmotic) for all species except Triticum aestivum where Lpr (pressure clamp) and Lpr (osmotic) were not significantly different. A novel technique was developed to measure the propagation of pressure through roots to investigate the cause of the differences in Lpr. Root segments were connected between two pressure probes so that when root pressure (Pr) was manipulated by one probe, the other probe recorded changes in Pr. Pressure relaxations did not induce the expected kinetics in pressure in the probe at the other end of the root when axial hydraulic conductance, and probe and root capacitances were accounted for. An electric circuit model of the root was constructed that included an additional capacitance in the root loaded by a series of resistances. This accounted for the double exponential kinetics for intact roots in pressure relaxation experiments as well as the reduced response observed with the double probe experiments. Although there were potential errors with all the techniques, we considered that the measurement of Lpr using the pressure clamp was the most unambiguous for small pressure changes, and provided that sufficient time was allowed for pressure propagation through the root. The differences in Lpr from different methods of measurement have implications for the models describing water transport through roots and the potential role of aquaporins.Helen Bramley, Neil C. Turner, David W. Turner and Stephen D. Tyerma

Euclid. I. Overview of the Euclid mission

The current standard model of cosmology successfully describes a variety of measurements, but the nature of its main ingredients, dark matter and dark energy, remains unknown. Euclid is a medium-class mission in the Cosmic Vision 2015-2025 programme of the European Space Agency (ESA) that will provide high-resolution optical imaging, as well as near-infrared imaging and spectroscopy, over about 14,000 deg^2 of extragalactic sky. In addition to accurate weak lensing and clustering measurements that probe structure formation over half of the age of the Universe, its primary probes for cosmology, these exquisite data will enable a wide range of science. This paper provides a high-level overview of the mission, summarising the survey characteristics, the various data-processing steps, and data products. We also highlight the main science objectives and expected performance

Euclid. I. Overview of the Euclid mission

International audienceThe current standard model of cosmology successfully describes a variety of measurements, but the nature of its main ingredients, dark matter and dark energy, remains unknown. Euclid is a medium-class mission in the Cosmic Vision 2015-2025 programme of the European Space Agency (ESA) that will provide high-resolution optical imaging, as well as near-infrared imaging and spectroscopy, over about 14,000 deg^2 of extragalactic sky. In addition to accurate weak lensing and clustering measurements that probe structure formation over half of the age of the Universe, its primary probes for cosmology, these exquisite data will enable a wide range of science. This paper provides a high-level overview of the mission, summarising the survey characteristics, the various data-processing steps, and data products. We also highlight the main science objectives and expected performance

Euclid. I. Overview of the Euclid mission

International audienceThe current standard model of cosmology successfully describes a variety of measurements, but the nature of its main ingredients, dark matter and dark energy, remains unknown. Euclid is a medium-class mission in the Cosmic Vision 2015-2025 programme of the European Space Agency (ESA) that will provide high-resolution optical imaging, as well as near-infrared imaging and spectroscopy, over about 14,000 deg^2 of extragalactic sky. In addition to accurate weak lensing and clustering measurements that probe structure formation over half of the age of the Universe, its primary probes for cosmology, these exquisite data will enable a wide range of science. This paper provides a high-level overview of the mission, summarising the survey characteristics, the various data-processing steps, and data products. We also highlight the main science objectives and expected performance