Prevalence of Human Papillomavirus infection by age and cervical cytology in Thika, Kenya

Human papillomavirus (HPV) infections cause cervical cancer and premalignant dysplasia. Data on HPV and cervical cancer in Kenya are scarce. Type-specific HPV prevalence data provides a basis for assessing the impact of HPV vaccination programs on cervical cytology and how HPV based screening will influence cervical cancer prevention. To investigate HPV infections in a population in Kenya, we obtained cervical cells specimen from 498 women in a population in Thika district. We report HPV type specific prevalence and distribution data for 498 women (age range 18-74 years; mean age 36 years) recruited into the study in relation to age and cervical cytology. The study was conducted between January to May 2010. Pap smears were performed, HR HPV DNA were detected by Digene Hybrid capture 2® (hc2) test and HPV genotyping was performed with Multiplex Luminex HPV genotyping kit (Multimetrix, Progen, Germany). Samples from 106 women (21.3%) tested positive for HPV. Multiple HPV types were detected in 40 (37.7% of HC2-positive samples) and the rest had infection with single HPV type. The most common HR HPV type at all ages was HPV16, 52, 56, 66, and 18. There was a marked decline in the prevalence of HR-HPV with age. The pattern of HR HPV distribution in this population was slightly different from existing literature, which has important consequences for HPV vaccination and prevention programs

Characterization of sheep populations of Kenya using microsatellite markers: Implications for conservation and management of indigenous sheep populations

Indigenous sheep of Kenya are very important to resource-poor farmers and pastoralists. They have over time adapted to the harsh environmental conditions of the arid and semi-arid lands where they are faced with challenges of persistent droughts, diseases, conflicts and poor nutrition, yet show resistance to gastrointestinal nematodes. In recent years, these indigenous sheep populations have been crossbred indiscriminately to exotic breeds particularly the Dorper. A study was undertaken to determine the level of genetic diversity and relatedness between the various sheep populations and breeds of Kenya. This paper reports results on the genetic diversity and admixture observed using microsatellite DNA markers

Transcriptome profile of spleen tissues from locally-adapted Kenyan pigs (Sus scrofa) experimentally infected with three varying doses of a highly virulent African swine fever virus genotype IX isolate: Ken12/busia.1 (ken-1033)

Background African swine fever (ASF) is a lethal hemorrhagic disease affecting domestic pigs resulting in up to 100% mortality rates caused by the ASF virus (ASFV). The locally-adapted pigs in South-western Kenya have been reported to be resilient to disease and harsh climatic conditions and tolerate ASF; however, the mechanisms by which this tolerance is sustained remain largely unknown. We evaluated the gene expression patterns in spleen tissues of these locally-adapted pigs in response to varying infective doses of ASFV to elucidate the virus-host interaction dynamics. Methods Locally adapted pigs (n = 14) were experimentally infected with a high dose (1x106HAD50), medium dose (1x104HAD50), and low dose (1x102HAD50) of the highly virulent genotype IX ASFV Ken12/busia.1 (Ken-1033) isolate diluted in PBS and followed through the course of infection for 29 days. The in vivo pig host and ASFV pathogen gene expression in spleen tissues from 10 pigs (including three from each infective group and one uninfected control) were analyzed in a dual-RNASeq fashion. We compared gene expression between three varying doses in the host and pathogen by contrasting experiment groups against the naïve control. Results A total of 4954 differentially expressed genes (DEGs) were detected after ASFV Ken12/1 infection, including 3055, 1771, and 128 DEGs in the high, medium, and low doses, respectively. Gene ontology and KEGG pathway analysis showed that the DEGs were enriched for genes involved in the innate immune response, inflammatory response, autophagy, and apoptosis in lethal dose groups. The surviving low dose group suppressed genes in pathways of physiopathological importance. We found a strong association between severe ASF pathogenesis in the high and medium dose groups with upregulation of proinflammatory cytokines and immunomodulation of cytokine expression possibly induced by overproduction of prostaglandin E synthase (4-fold; p < 0.05) or through downregulation of expression of M1-activating receptors, signal transductors, and transcription factors. The host-pathogen interaction resulted in induction of expression of immune-suppressive cytokines (IL-27), inactivation of autophagy and apoptosis through up-regulation of NUPR1 [5.7-fold (high dose) and 5.1-fold (medium dose) [p < 0.05] and IL7R expression. We detected repression of genes involved in MHC class II antigen processing and presentation, such as cathepsins, SLA-DQB1, SLA-DOB, SLA-DMB, SLA-DRA, and SLA-DQA in the medium and high dose groups. Additionally, the host-pathogen interaction activated the CD8+ cytotoxicity and neutrophil machinery by increasing the expression of neutrophils/CD8+ T effector cell-recruiting chemokines (CCL2, CXCL2, CXCL10, CCL23, CCL4, CXCL8, and CXCL13) in the lethal high and medium dose groups. The recovered pigs infected with ASFV at a low dose significantly repressed the expression of CXCL10, averting induction of T lymphocyte apoptosis and FUNDC1 that suppressed neutrophilia. Conclusions We provide the first in vivo gene expression profile data from locally-adapted pigs from south-western Kenya following experimental infection with a highly virulent ASFV genotype IX isolate at varying doses that mimic acute and mild disease. Our study showed that the locally-adapted pigs induced the expression of genes associated with tolerance to infection and repression of genes involved in inflammation at varying levels depending upon the ASFV dose administered

Integration and adoption of climate resilient management practices for enhanced productivity of sheep and goats in pastoral communities of northern Kenya

Interventions to improve productivity in pastoral livestock systems of northern Kenya focus on the management of the rangeland resources and grazing areas with few initiatives on changes related to the livestock assets. However, changing climatic conditions with high frequencies of droughts have increased the vulnerability of pastoral communities and necessitate prompt interventions in animal management practices. In 2018, the Ministry of Agriculture, Livestock, Fisheries and Irrigation in collaboration with the International Livestock Research Institute commenced a programme to build the resilience of pastoral holdings using their animal assets rather than depending on humanitarian emergency responses. Interventions necessitated changes in management practices related to sheep and goat production. Core innovation groups (CIG) each comprising 30 pastoral households in select communities were established to model new practices for wider adoption using participatory processes in Isiolo, Marsabit and Turkana Counties. CIG members went through a 3-year phased training programme on animal management practices for more efficient, resilient and productive animals. The adoption of new practices in CIG focks was monitored by extension personnel. Data were analysed using logistic regression techniques to assess household-level adoption of livestock breed improvement, feeding and disease control interventions. The 3 years of the programme (2018–2021) were relatively satisfactory in terms of pasture availability; hence, communities pursued strategies to enhance their focks. All CIG adopted more than one of the introduced technologies concurrently. Prevention of diseases was the most readily adopted, followed by crossbreeding using indigenous breeds of sheep and goats from other arid areas of Kenya. Turkana County had the lowest probability of adopting any of the technologies as previous devastating droughts have resulted in an increased emphasis on animals for survival rather than productivity. The study shows that pastoral communities are open to technological interventions for animal productivity. Adoption of the technologies was enhanced by the experiential capacity development activities adapted to the education level of the different communitie

Substantial molecular variation and low genetic structure in Kenya’s black rhinoceros: implications for conservation

Kenya’s black rhinoceros population declined by more than 98% from 20,000 individuals in the 1970s to around 400 individuals in 1990 due to the effects of poaching, at which time the surviving individuals were isolated in a series of demographically inviable subpopulations. An initial management exercise translocated the survivors into four high security sanctuaries to control poaching and enhance breeding, and this measure successfully arrested the decline. Subsequently, new sanctuaries were established and the metapopulation size reached 650 animals by 2008. However, translocations and the current management strategy that partitions the metapopulation into ‘montane’ and ‘lowland’ rhinoceros may have substantial consequences at the population level and their impact on population genetic diversity has not been investigated. In this study, 12 of the 16 extant subpopulations were analysed using 408 bp of mitochondrial control region sequence (n = 170) and nine microsatellite loci (n = 145). Both markers detected moderate to high genetic diversity (h = 0.78 ± 0.027, n = 170; HO = 0.70 ± 0.087, n = 145) consistent with previous studies on Diceros bicornis michaeli. However, mtDNA and nDNA diversity varied substantially between subpopulations. The results suggest that the Masai Mara is more differentiated, inbred and isolated than other subpopulations. It also suggests that there are neither distinct montane and lowland groups nor other detectable historical barriers to gene flow. Instead the large majority of genetic diversity was partitioned at the level of individuals; highlighting the need to conserve as many individuals as possible. Future translocations should consider the genetic profile of individuals and the demographic history of both the donor and recipient subpopulations

Comparative analysis of SLA-1, SLA-2, and DQB1 genetic diversity in locally-adapted Kenyan pigs and their wild relatives, warthogs

Swine leukocyte antigen (SLA) plays a central role in controlling the immune response by discriminating self and foreign antigens and initiating an immune response. Studies on SLA polymorphism have demonstrated associations between SLA allelic variants, immune response, and disease resistance. The SLA polymorphism is due to host-pathogen co-evolution resulting in improved adaptation to diverse environments making SLA a crucial genomic region for comparative diversity studies. Although locally-adapted African pigs have small body sizes, they possess increased resilience under harsh environmental conditions and robust immune systems with reported tolerance to some diseases, including African swine fever. However, data on the SLA diversity in these pigs are not available. We characterized the SLA of unrelated locally-adapted domestic pigs from Homa Bay, Kenya, alongside exotic pigs and warthogs. We undertook SLA comparative diversity of the functionally expressed SLA class I (SLA-1, SLA-2) and II (DQB1) repertoires in these three suids using the reverse transcription polymerase chain reaction (RT-PCR) sequence-based typing (SBT) method. Our data revealed higher genetic diversity in the locally-adapted pigs and warthogs compared to the exotic pigs. The nucleotide substitution rates were higher in the peptide-binding regions of the SLA-1, SLA-2, and DQB1 loci, indicative of adaptive evolution. We obtained high allele frequencies in the three SLA loci, including some breed-specific private alleles, which could guide breeders to increase their frequency through selection if confirmed to be associated with enhanced resilience. Our study contributes to the growing body of knowledge on genetic diversity in free-ranging animal populations in their natural environment, availing the first DQB1 gene data from locally-adapted Kenyan pigs