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

Student Book Collection Contests in American Colleges and Universities

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Comparing Informants for Mental Health Screening at the Preschool Level

Universal screening for mental health in preschools provides the opportunity for early identification and early intervention, but guidance regarding which informants to use is needed. Preschoolers' (N = 535) parent and teacher reports across two screening forms were analyzed to determine similarities and discrepancies for classification results and screener scores. The analyses also examined if an additional rater provided incrementally valid information to the prediction of longitudinal kindergarten outcomes. Parents' and teachers' screening scores were significantly correlated across forms by rater and across raters. However, categorical classification results indicated that teachers were more likely than parents to rate preschoolers in at-risk ranges across forms. Finally, hierarchical regression analyses revealed teacher ratings were predictive of kindergarten social-emotional, cognitive, and academic outcomes, and that the addition of parent ratings did not significantly improve prediction of outcomes. Implications are discussed in the context of multiple raters within multiple-gating screening procedures

Intake, total-tract digestibility and methane emissions of Texel and Blackbelly sheep fed C4 and C3 grasses tested simultaneously in a temperate and a tropical area

International audienceThis experiment was designed to better understand the differences in enteric methane (CH4) emissions of ruminants in tropical and temperate areas. Two double 4 4 Latin squares using adult sheep were evaluated simultaneously in a temperate and a tropical site. At each site, two breeds (four Texel, temperate origin, and four Blackbelly, tropical origin) and four hay types (two C3 grasses and two C4 grasses grown, respectively, in temperate and tropical sites) were tested. High-(H) and low-quality (L) grass hays were tested within each type of grass. No difference in dry matter (DM) intake (g/kg BW/d) was observed between sites. Intake of C4 grass was lower than that of C3 grass. A breed site interaction was observed. In the tropical site, dry matter intake (g/kg BW/d) was higher in Blackbelly compared to Texel, whereas no difference was observed in the temperate site. The total-tract DM, OM (organic matter), NDF (neutral detergent fiber) and ADF (acid detergent fiber) digestibility values recorded in the temperate site were lower (P < 0.01) than those reported in the tropical site. Methane yield (g/kg DM intake) was not affected by site, whereas a breed site interaction was observed. In the tropical site, methane emission was lower for Blackbelly compared to Texel, whereas the opposite was observed in the temperate site. Differences in methane emissions between the temperate and tropical sites could only be the result of diet and breed interactions with the environment

Potential of tannin-rich plants, <em>Leucaena leucocephala</em>, <em>Glyricidia sepium</em> and <em>Manihot esculenta</em>,to reduce enteric methane emissions in sheep

International audienceAn in vivo trial was conducted in sheep to investigate the effect of three tropical tannin-rich plants (TRP) on methane emission, intake and digestibility. The TRP used were leaves of Glyricidia sepium, Leucaena leucocephala and Manihot esculenta that contained, respectively, 39, 75 and 92 g condensed tannins/kg DM. Methane was determined with the sulphur hexafluoride tracer technique. Eight rumen-cannulated sheep of two breeds (four Texel, four Blackbelly) were used in two 4 × 4 Latin square designs. Four experimental diets were tested. They consisted in a tropical natural grassland hay based on Dichanthium spp. fed alone (C) or in association with G. sepium (G), L. leucocephala (L) or M. esculenta (M) given as pellets at 44% of the daily ration. Daily organic matter intake was higher in TRP diets (686, 984, 1054 and 1186 g/day for C, G, L and M respectively; p 0.05). Methane emission was 47.1, 44.9, 33.3 and 33.5 g/kg digestible organic matter intake for C, G, L and M, respectively, and was significantly lower (p < 0.05) for L and M than for G and C. Our results confirm the potential of some TRP to reduce methane production. The strong decrease in methane and the increase in intake with TRPs may be due to their presentation as pellets