9 research outputs found

    The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

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    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

    Influence of adding fibrolytic enzymes on the ruminal fermentation of date palm by-products

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    This study was conducted in order to assess the influence of four doses (0, 0.5, 1, and 2 mg (g dry matter)1 of commercial fibrolytic enzymes (MAXFIBER-Ir, SHAUMANN GmbH, Wahlstedt, Germany) on in vitro fermentation of date palm (Phoenix dactylifera) by-products: date kernels, wasted dates, floral stems, and palm fronds. Rumen contents were obtained from two non-lactating Holstein cows. Enzyme supplementation to by-products was carried out 12 h prior to incubation. Compared to the control, the enzymatic supplementation quadratically increased the extent but not the gasproduction rate of date kernel fermentation. Indeed, the potential gas production increased notably by 14.8% with the lowest enzymes dose following recorded gas production after 48, 72, and 96 h of incubation. The estimated organic-matter digestibility, metabolisable energy, and total volatile fatty acids in the incubation fluid tended to be increased with the lowest dose by 7.8 %, 8.4 %, and 13.9% respectively. For the wasted dates, this feed additive tended to linearly increase the gas production rate of fermentation with the highest dose. On the other hand, this supplementation had no effect on the ruminal fermentation of the floral stems and palm fronds. The exogenous fibrolytic enzymes were more effective on fibrous but not on lignified date palm by-products

    Effect of treating olive cake with fibrolytic enzymes on feed intake, digestibility and performance in growing lambs

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    8 páginas, 4 tablas.This research evaluated the effects of the addition of a blend of exogenous fibrolytic enzymes composed of a mixture of cellulase and xylanase (CX) to a high-fibre diet on growth performance of meat lambs. The diet contained olive cake (OC), and CX was added to this fibrous by-product at 0 (control, no addition of CX), 4 (CX04) or 16 (CX16) ml of the enzyme preparation per kg OC dry matter. The study was planned according to a quintuplicated 3 × 3 Latin square design, with three experimental treatments (control, CX04, CX16), three 21-day periods (14-day adaptation plus 7-day collection period) and 15 weaned male lambs (Queue Fine de l'Ouest) randomly assigned to the 5 replicates (3 lambs in each replicate). Intake of both dry matter and organic matter were increased (P 0.05) by CX, except cholesterol concentration that was increased (P < 0.05). As compared with lambs fed the control diet, average daily weight gain was increased (P < 0.05) by 6 and 10 % when lambs were fed CX04 and CX16 diets, respectively. These results indicate that the supplementation of OC-based lamb diets with CX, even at relative low concentrations, improves lamb growth performance as a result of increasing feed intake and enhancing fibre digestibility with no adverse effects on animal health.The authors are grateful to Prof. Ben Ramdon Najib, Head of biochemistry department (Ecole Nationale de Médecine Vétérinaire, Sidi Thabet, Tunisia) for his fruitful assistance on the analysis of blood serum samples

    Poster session 4: Friday 5 December 2014, 08:30-12:30Location: Poster area.

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