Review Article : Heat stress and poultry: Adaptation to climate change, challenges and opportunities for genetic breeding in Kenya

The Earth’s ambient climatic factors, such as temperature, humidity, solar radiation, and precipitation, vary through time and space due to climate change. Heat stress, one of the major factors affecting poultry production, is a direct result of climate change, resulting in enormous losses for the poultry sector. As a result of heat stress, several physiological changes such as suppressed immunecompetence, oxidative stress, and acid-base balance lead to reduced feed intake, feed efficiency, body weight, meat, egg quality, and sometimes mortality. Adverse effects have necessitated several adjustments in animal husbandry practices such as housing and feeding regimes to be implemented. Modifying the environment in poultry production systems can cushion exposure and compensate for losses in poultry fitness in heat-stressed environments. Some of the modifications that have been tested and shown to be successful in attenuating heat stress in poultry include shade, sprinkling cold water on their bodies, and adjusting diets to reduce metabolic heat production. The extensive genetic diversity of indigenous poultry is essential for climate change adaptation and the continuous enhancement of the genetic stock through breeding adaptive features like heat stress tolerance. The naked neck (Na) and frizzle (gene F) gene have been given attention in recent times in their role to withstand heat stress in poultry. A better understanding of indigenous poultry acclimatization to severe environments, together with methods and tools available for the selection, breeding, and matching indigenous poultry ecotypes to suitable environments, should help to minimize the effects of heat stress on indigenous poultry genetic resource growth, production, and reproduction to sustain food security

Review Article : A review of the distribution, nutritional value and conservation status of wild harlequin quails (Coturnix delegorguei delegorguei) in Kenya

Wild harlequin quails are a traditional source of protein in many parts of Sub-Saharan Africa. Nonetheless, they are greatly underutilized to combat malnutrition and ensure food security. The current status of quail populations in Kenya is mostly unknown, especially after introducing numerous exotic quails during the quail ‘bubble’ of years 2013-2015. Besides, the ongoing uncontrolled harvesting of wild harlequin quails and its effect on wild quail populations has not been examined either. The aim of this review is to discuss and reveal the emerging issues associated with the opportunities, utilization challenges and conservation status of wild harlequin quails in Kenya. This review will focus on peer-reviewed research articles, published books, review articles and internet resources on wild quails and commercial quail farming. It is essential to point out that quails are already considered as emerging poultry, and increased consumption of their products is highly encouraged, thus contributing to food security in Kenya. However, wild harlequin quail conservation concerns need to be addressed regarding their uncontrolled harvesting, destruction of their habitats, and climate change

Multi-locus sequence typing of African swine fever viruses from endemic regions of Kenya and Eastern Uganda (2011–2013) reveals rapid B602L central variable region evolution

The central variable region (CVR) within the B602L gene of the African swine fever virus (ASFV) is highly polymorphic within the 23 ASFV genotypes defined by sequencing of the C-terminal end of the p72 locus. Sequencing the p54 gene further discriminates ASFV genotypes that are conserved at the p72 locus. Variation in the thymidine kinase locus is a novel additional tool for ASFV genotyping whose application for this purpose is described for the first time herein. We evaluated genetic variation at these four polymorphic loci in 39 ASFV isolates obtained from outbreaks in Kenya and a region of Eastern Uganda between 2011 and 2013. Analysis of the p72 and p54 loci revealed high genetic conservation among these isolates; all clustered within p72 genotype IX and were similar to isolates associated with earlier outbreaks in East Africa. The thymidine kinase gene of the Kenyan isolates in this study were distinct relative to Southern African isolates and synonymous substitutions were observed among viruses from central Kenya. Analysis of the CVR within the B602L gene revealed two previously unknown polymorphisms that were restricted to Western Kenya and Eastern Uganda. A novel variant was revealed within CVR subgroup XXIV and a novel CVR subgroup XXIVa that contains tetrameric repeat F which has previously only been associated with p72 genotype I, was also identified for the first time in East Africa. Phylogeographic analysis of isolates based on CVR polymorphisms revealed rapid evolution and dissemination of variants present within ASFV genotype IX in East Africa

Multi-locus sequence typing of African swine fever viruses from endemic regions of Kenya and Eastern Uganda (2011–2013) reveals rapid B602L central variable region evolution

The central variable region (CVR) within the B602L gene of the African swine fever virus (ASFV) is highly polymorphic within the 23 ASFV genotypes defined by sequencing of the C-terminal end of the p72 locus. Sequencing the p54 gene further discriminates ASFV genotypes that are conserved at the p72 locus. Variation in the thymidine kinase locus is a novel additional tool for ASFV genotyping whose application for this purpose is described for the first time herein. We evaluated genetic variation at these four polymorphic loci in 39 ASFV isolates obtained from outbreaks in Kenya and a region of Eastern Uganda between 2011 and 2013. Analysis of the p72 and p54 loci revealed high genetic conservation among these isolates; all clustered within p72 genotype IX and were similar to isolates associated with earlier outbreaks in East Africa. The thymidine kinase gene of the Kenyan isolates in this study were distinct relative to Southern African isolates and synonymous substitutions were observed among viruses from central Kenya. Analysis of the CVR within the B602L gene revealed two previously unknown polymorphisms that were restricted to Western Kenya and Eastern Uganda. A novel variant was revealed within CVR subgroup XXIV and a novel CVR subgroup XXIVa that contains tetrameric repeat F which has previously only been associated with p72 genotype I, was also identified for the first time in East Africa. Phylogeographic analysis of isolates based on CVR polymorphisms revealed rapid evolution and dissemination of variants present within ASFV genotype IX in East Africa.Supplementary Fig. 1 Phylogenetic tree based on the C-terminal end of the p72 protein comparing the Kenyan and Eastern Uganda ASFV isolates collected in this study (●) between 2011 and 2013 with other African swine fever virus isolates belonging to ASFV genotypes IX and X. A total of 91 distinct taxa were used to infer a Minimum Evolution tree and the percentage of replicate trees in which the associated taxa clustered together in a bootstrap analysis (1000 replicates) are shown adjacent to the branches. The tree is drawn to scale; with branch lengths represented using the same units as the evolutionary distances used to infer the phylogenetic tree.Supplementary Fig. 2 Phylogenetic tree highlighting genetic conservation within the E183L gene within the Kenyan and Eastern Uganda ASFV isolates in comparison to reference nucleotide sequences obtained from GenBank.Supplementary Fig. 3 Amino acid sequences translated using SeqPublish highlighting synonymous substitutions within the thymidine kinase gene in the ASFV isolates obtained from Central Kenya.Supplementary Table 1 Summary of the data obtained from ASFV isolates selected for genotyping in this study and the respective GenBank accession numbers.The Australian aid (AusAID) and the Commonwealth Scientific and Industrial Research Organization (CSIRO) under the Special Africa Program.http://link.springer.com/journal/11262hj2018Mammal Research InstituteZoology and Entomolog

Metagenomic characterization reveals virus coinfections associated with Newcastle disease virus among poultry in Kenya

Newcastle disease (ND) is an endemic viral disease affecting poultry and causing massive economic losses. This cross-sectional purposive study detected coinfections that are associated with the Newcastle disease virus among poultry from selected regions in Kenya. Cloacal (n = 599) and oral-pharyngeal (n = 435) swab samples were collected and pooled into 17 and 15 samples, respectively. A total of 17,034,948 and 7,751,974 paired-end reads with an average of 200 nucleotides were generated from the cloacal and oral-pharyngeal swab samples, respectively. Analysis of the de novo assembled contigs identified 177 and 18 cloacal and oral-pharyngeal contigs, respectively with hits to viral sequences, as determined by BLASTx and BLASTn analyses. Several known and unknown representatives of Coronaviridae, Picobirnaviridae, Reoviridae, Retroviridae, and unclassified Deltavirus were identified in the cloacal swab samples. However, no Newcastle disease virus (family Paramyxoviridae) was detected in the cloacal swabs, although they were detected in the oropharyngeal swabs of chickens sampled in Nairobi, Busia, and Trans Nzoia. Additionally, sequences representative of Paramyxoviridae, Coronaviridae, and Retroviridae were identified in the oral-pharyngeal swab samples. Infectious bronchitis virus and rotavirus were chickens' most prevalent coinfections associated with the Newcastle disease virus. The detection of these coinfections suggests that these viruses are significant threats to the control of Newcastle disease as the Newcastle disease virus vaccines are known to fail because of these coinfections. Therefore, this study provides important information that will help improve disease diagnosis and vaccine development for coinfections associated with the Newcastle disease virus

Quantitative Outcomes of a One Health Approach to Investigate the First Outbreak of African Swine Fever in the Republic of Sierra Leone

African swine fever (ASF) outbreaks have been reported in Sub-Saharan countries, including West Africa states, but has never been notified in the Republic of Sierra Leone. This is the first report describing field epidemiological and laboratory investigations into the outbreak of fatal pig disease in western rural and urban districts, Freetown. A preliminary finding indicated that pigs exhibited clinical and necropsy signs suggestive of ASF. Serological (ELISA) and molecular (qRT-PCR) methods used to confirm and investigate the outbreak yielded three positive results for the ASF antibody and all negative for Swine flu; thus, confirming ASF as the etiology agent

Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation

Over the last several hundred years, donkeys have adapted to high-altitude conditions on the Tibetan Plateau. Interestingly, the kiang, a closely related equid species, also inhabits this region. Previous reports have demonstrated the importance of specific genes and adaptive introgression in divergent lineages for adaptation to hypoxic conditions on the Tibetan Plateau. Here, we assessed whether donkeys and kiangs adapted to the Tibetan Plateau via the same or different biological pathways and whether adaptive introgression has occurred. We assembled a de novo genome from a kiang individual and analyzed the genomes of five kiangs and 93 donkeys (including 24 from the Tibetan Plateau). Our analyses suggested the existence of a strong hard selective sweep at the EPAS1 locus in kiangs. In Tibetan donkeys, however, another gene, i.e., EGLN1, was likely involved in their adaptation to high altitude. In addition, admixture analysis found no evidence for interspecific gene flow between kiangs and Tibetan donkeys. Our findings indicate that despite the short evolutionary time scale since the arrival of donkeys on the Tibetan Plateau, as well as the existence of a closely related species already adapted to hypoxia, Tibetan donkeys did not acquire adaptation via admixture but instead evolved adaptations via a different biological pathway

Detection of rift valley Fever virus interepidemic activity in some hotspot areas of kenya by sentinel animal surveillance, 2009-2012

Rift Valley fever virus causes an important zoonotic disease of humans and small ruminants in Eastern Africa and is spread primarily by a mosquito vector. In this region, it occurs as epizootics that typically occur at 5–15-year intervals associated with unusual rainfall events. It has hitherto been known that the virus is maintained between outbreaks in dormant eggs of the mosquito vector and this has formed the basis of understanding of the epidemiology and control strategies of the disease. We show here that seroconversion and sporadic acute disease do occur during the interepidemic periods (IEPs) in the absence of reported cases in livestock or humans. The finding indicates that previously undetected low-level virus transmission during the IEPs does occur and that epizootics may also be due to periodic expansion of mosquito vectors in the presence of both circulating virus and naïve animals

Review Article : Antimicrobial drug resistance in poultry pathogens: Challenges and opportunities

Antimicrobial resistance (AMR) is widely considered a global public health threat, with the use of antimicrobials in poultry production considered one of the contributing factors. Antimicrobial agents are used for growth promotion, prevention, and treatment of poultry diseases. They are also used to prevent and treat human diseases. This unchecked dependence on antimicrobials results in their unregulated use and abuse in human and animal health, resulting in AMR. Previously, AMR was investigated using antimicrobial susceptibility testing using the disc diffusion method (for bacteria and fungi) and phenotypic fluorescence-based inhibition assay (for viruses). This was done after culturing the bacteria and fungi in growth media or propagating viruses in embryonic chicken eggs or specific cell lines. Recent studies utilizing metagenomics and next generation sequencing (NGS) platforms have also identified a large array of antimicrobial resistance genes that had not been discovered earlier. In this study, a systematic review of different studies focusing on AMR in some poultry pathogens was conducted using different databases, such as MEDLINE, EMBASE, and CINAHL library sources for relevant studies. These sources were screened against the protocol eligibility criteria, where 103 studies met the inclusion criteria. We wish to review the current state of antimicrobial resistance in bacteria, fungi and viruses in poultry and also explore alternative approaches for preventing and treating diseases and promoting growth in food animals such as poultry. This is essential in enhancing efforts of harmonizing testing practices and facilitating free access to information and data on AMR with the aim of enhancing treatment measures, along with monitoring the advancement of AMR in poultry pathogens