Phylogenetics and Pathogenesis of Early Avian Influenza Viruses (H5N1), Nigeria

Three highly pathogenic avian influenza subtype H5N1 and 4 Newcastle disease viruses were isolated from sick or dead chickens in southwestern Nigeria. Sequencing and phylogenetic analysis placed them within H5N1 subclade 2.2.2. Intravenous and intranasal pathogenicity tests produced systemic disease with vascular endothelial cell tropism in chickens

A Mendelian randomization study of genetic liability to post-traumatic stress disorder and risk of ischemic stroke.

Observational studies have shown an association between post-traumatic stress disorder (PTSD) and ischemic stroke (IS) but given the susceptibility to confounding it is unclear if these associations represent causal effects. Mendelian randomization (MR) facilitates causal inference that is robust to the influence of confounding. Using two sample MR, we investigated the causal effect of genetic liability to PTSD on IS risk. Ancestry-specific genetic instruments of PTSD and four quantitative sub-phenotypes of PTSD, including hyperarousal, avoidance, re-experiencing, and total symptom severity score (PCL-Total) were obtained from the Million Veteran Programme (MVP) using a threshold P value (P) of <5 × 10-7, clumping distance of 1000 kilobase (Mb) and r2 < 0.01. Genetic association estimates for IS were obtained from the MEGASTROKE consortium (Ncases = 34,217, Ncontrols = 406,111) for European ancestry individuals and from the Consortium of Minority Population Genome-Wide Association Studies of Stroke (COMPASS) (Ncases = 3734, Ncontrols = 18,317) for African ancestry individuals. We used the inverse-variance weighted (IVW) approach as the main analysis and performed MR-Egger and the weighted median methods as pleiotropy-robust sensitivity analyses. In European ancestry individuals, we found evidence of an association between genetic liability to PTSD avoidance, and PCL-Total and increased IS risk (odds ratio (OR)1.04, 95% Confidence Interval (CI) 1.007-1.077, P = 0.017 for avoidance and (OR 1.02, 95% CI 1.010-1.040, P = 7.6 × 10-4 for PCL total). In African ancestry individuals, we found evidence of an association between genetically liability to PCL-Total and reduced IS risk (OR 0.95 (95% CI 0.923-0.991, P = 0.01) and hyperarousal (OR 0.83 (95% CI 0.691-0.991, P = 0.039) but no association was observed for PTSD case-control, avoidance, or re-experiencing. Similar estimates were obtained with MR sensitivity analyses. Our findings suggest that specific sub-phenotypes of PTSD, such as hyperarousal, avoidance, PCL total, may have a causal effect on people of European and African ancestry's risk of IS. This shows that the molecular mechanisms behind the relationship between IS and PTSD may be connected to symptoms of hyperarousal and avoidance. To clarify the precise biological mechanisms involved and how they may vary between populations, more research is required

Small and Medium Enterprises and Biopharmaceutical Innovations in Africa: Challenges and Prospects

Biopharmaceuticals can be described as medicines or medicinal products manufactured through biotechnological processes with links to biological sources especially those of live organisms or their active components. The biopharmaceutical industry is presently experiencing tremendous revenue growth rates projected at more than $167 billion worldwide in 2015. There are more than 500 biopharmaceutical products that have been approved with about 400 presently marketable in the United States and European markets. The full potential of biopharmaceutical, biotechnology, genomic, genetic and biogeneric compounds is best realized in small entrepreneurial firms which have the capacity for creativity, risk, flexibility and iteration that no large biopharmaceutical entity can match. Although there are challenges facing African Small and Medium Enterprises (SMEs) in biopharmaceutical industry, the prospects on the other hand can be lucrative taking into cognizance Africa’s ever increasing population and the need for affordable health care. To facilitate the contribution of SMEs in Africa, this article presents a perspective on the prospects of African SMEs in biopharmaceutical innovations such as new products, processes and services. The roles of SMEs in the global biopharmaceutical industry are reviewed. Additionally, selected critical factors to accelerate the contribution of African SMEs in global biopharmaceutical innovation are described. Finally, the prospective areas for biopharmaceutical innovation in Africa include research and development, marketing, workforce development and contract manufacturing

Whole genome sequence-based genetic characterization of Muturu, an endangered trypanotolerant population of West African Bos Taurus

Muturu cattle, mostly found nowadays in Nigeria, have been classified as an endangered cattle population due to the rapid decline in their population size. They are among the shorthorn West African B. taurus trypanotolerance cattle. Here, we report candidate signature of positive selection obtained from whole genome re-sequencing data in a population of 10 Muturu samples from southeastern Nigeria. We present within Muturu population results in comparison with other B. taurus cattle including the trypanotolerant longhorn N’Dama and the European Holstein and Jersey dairy cattle. We identify a total of 8,937,932 single nucleotide polymorphisms (SNPs) and 1,373,437 insertion/deletions (indels) on the autosomes, of which about 11.3% and 10.2% respectively, are unique to Muturu. As revealed by the integrated haplotype score (iHS) test, 266 loci and 432 related candidate genes are under positive selection in the Muturu genome. One of the most significant regions is located on BTA 23. It includes several genes belonging to the major histocompatibility complex (MHC) with functions related to both innate and adaptive immunity. Thirty-one candidate genes including the MHC genes region were also found under selection in N'Dama. Several genes such as KIT, ZRANB3, MAP3K5, ABCGR, GHR, LAP3, SRY, RFX2, GPX5 and PRKAG3 which are related to coat colour, feed efficiency, milk production, reproduction and response to heat stress were also identified. Our results provide insights into the candidate genes under selection in Muturu paving the way for further investigations into important adaptation traits such as trypanotolerance in West African B. taurus

Data from: Signatures of selection for environmental adaptation and zebu x taurine hybrid fitness in East African Shorthorn Zebu

The East African Shorthorn Zebu (EASZ) cattle are ancient hybrid between Asian zebu × African taurine cattle preferred by local farmers due to their adaptability to the African environment. The genetic controls of these adaptabilities are not clearly understood yet. Here, we genotyped 92 EASZ samples from Kenya (KEASZ) with more than 770,000 SNPs and sequenced the genome of a pool of 10 KEASZ. We observe an even admixed autosomal zebu × taurine genomic structure in the population. A total of 101 and 165 candidate regions of positive selection, based on genome-wide SNP analyses (meta-SS, Rsb, iHS, and ΔAF) and pooled heterozygosity (Hp) full genome sequence analysis, are identified, in which 35 regions are shared between them. A total of 142 functional variants, one novel, have been detected within these regions, in which 30 and 26 were classified as of zebu and African taurine origins, respectively. High density genome-wide SNP analysis of zebu × taurine admixed cattle populations from Uganda and Nigeria show that 25 of these regions are shared between KEASZ and Uganda cattle, and seven regions are shared across the KEASZ, Uganda, and Nigeria cattle. The identification of common candidate regions allows us to fine map 18 regions. These regions intersect with genes and QTL associated with reproduction and environmental stress (e.g., immunity and heat stress) suggesting that the genome of the zebu × taurine admixed cattle has been uniquely selected to maximize hybrid fitness both in terms of reproduction and survivability

HD_SNP

SNP genotypes data from Illumina BovineHD Genotyping BeadChip of the examined cattle population

HD_SNP

map file of the high density SNP data ped fil