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

Effect of inorganic and organic trace minerals in diet on laying performance, egg quality and yolk mineral contents in broiler breeder hens

Two hundred and twenty (20 male and 200 female) 39 weeks old Ross-308 broiler breeder hens were used in this experiment. Birds were placed in a complete randomized design with 4 dietary treatments (A: 100% inorganic, B: 50% organic + 50% inorganic, C: 50% organic, and D: 100% organic source of trace minerals) and 5 replications containing 1 male + 10 females in each having similar body weight and egg production. Results indicated that inclusion of organic and inorganic trace minerals in broiler breeders’ diet did not have a significant effect on body weight change, feed intake, feed conversion ratio, and egg production. However, the diets containing organic and/ or inorganic trace minerals had a significant effect on some egg quality parameters such as albumin weight (%), egg shell weight, yolk weight, yolk index, shell strength, shell thickness, and yolk colour. Inclusion of organic and inorganic trace minerals in broiler breeders’ diet also affected yolk trace minerals content. It was concluded that egg quality and yolk trace minerals content in broiler breeders can be affected by source of trace minerals in diet. © 2019 Indian Council of Agricultural Research. All rights reserved

Effect of omega-3 and omega-6 fatty acid inclusion in broiler breeder's diet on laying performance, egg quality, and yolk fatty acids composition

The present study was conducted to evaluate the effect of different dietary oil sources (omega-3 and omega-6 fatty acid) in female broiler breeders' diets on laying performance, egg quality and yolk fatty acids composition. Ross-308 breeders (220; 25 weeks old) were used in this experiment for 6 weeks. Birds were placed in a complete randomized design with 4 dietary treatments (containing 2% soybean oil, 2% sunflower oil, 2% flaxseed oil, and 2% fish oil) and 5 replications containing 1 male + 10 females in each pen having a similar body weight (3,424 g) and egg production (86%). Results indicated that different sources of dietary oil had no significant effect on body weight gain, feed conversion ratio, and egg production but had a significant effect on egg weight. Also feeding the diets containing 2% of different fatty acids had a significant effect on some egg quality parameters and egg yolk fatty acids composition. It was concluded that inclusion of 2% flaxseed oil can improve laying performance, egg quality, and egg yolk fatty acids composition parameters in broiler breeders. © 2018 Indian Council of Agricultural Research. All rights reserved.Türkiye Bilimsel ve Teknolojik Araştirma Kurumu: 114O749 British Association for Psychopharmacology: ZF2013D12We acknowledge TÜBITAK (Project no: 114O749) and BAP (Project no: ZF2013D12) centers for providing financial support for this research study

Effect of multi-enzyme produced by a single fungus on growth performance and some carcass parameters of broiler chicks fed on maize-soya based diets [Bir mantar tarafından üretilen multi-enzimin mısır-soya bazlı rasyonla beslenen broyler civcivlerinin büyüme performansı ve karkas parametrelerine etkisi]

The present study was conducted to test whether a multi-enzyme produced by a fungus would keep performance of broiler chicks receiving a diet with almost 3% less nutrients (energy, protein, amino acids, calcium and phosphor) under two different housing density. In both experiments, positive control received standard broiler diet, negative control received a diet with 3% less nutrients than standard broiler diet and enzyme group received the negative control diet+supplemental enzyme. In the first trial with 1000, day-old chicks housed 10 birds/m 2 , only 1% improvement in feed conversion efficiency and body growth was achieved with enzyme supplementation in contrast to the negative control at the end of 35 days feeding period. In the second trial with 1200, day-old-chicks accommodated 16 birds/m 2 . The results showed that enzyme improved broiler performance almost 3.5% in contrast to the performance obtained from the negative control. In conclusion, supplementing broiler diets based on maize/soya with a multi-enzyme produced by a single fungus provides a great potential to gain the gap created by formulating almost 3% nutrients reduction in broilers housed with 16 birds/m 2 density. However, providing high comfort and better rearing condition as the birds at 10 birds/m 2 density, positive effects of the enzyme was limited. © 2019, Veteriner Fakultesi Dergisi. All rights reserved

Effect of form of selenium used in broiler breeders’ diet on egg production, egg quality, hatchability and chicks growth performance

The present study was conducted to evaluate two different sources (Sehydroxy-4-methylselenobutanoic acid, HMSeBA vs. selenium yeast) of organic selenium in female broiler breeder’s diets on egg production, fertility, egg quality, hatchability and chicks’ growth performance. Two hundred and twenty, 54 weeks old Ross-308 male (20) and female (200) breeders were used in the experiment for 9 weeks. Standard breeder (female) diet based on corn and soya were used. Birds were placed in a completely randomized design with 2 dietary treatments (HMSeBA and Selenium yeast) groups with 10 replicates each including 10 females and 1 male per pen. Feed intake, feed conversion ratio, egg production, egg yield, hen-day egg production were recorded. Hatching and progeny performances were run twice. Form of selenium did not have any significant effects on body weight changes, egg production, egg weight, egg mass, feed efficiency and hatching performance (P>0.05). Chicks of the first hatching from the maternal receiving HMSeBA had higher body weight gain at 7 and 14 days of age (P?0.05). At 35 days of age, the chicks obtained from the breeder receiving HMSeBA had numerically higher (P>0.05) body weight, feed intake and better feed efficiency (P>0.05) than those of maternal receiving selenium yeast. Chicks of the second hatching from the maternal receiving HMSeBA had attained numerically (P>0.05) better growth performance than the group fed Se-Yeast. Additionally, the performance values of the chicks obtained from the both hatching were found to be greatly higher than breeder’s expectation in the both trials. © 2019, Pakistan Agricultural Scientists Forum. All rights reserved