Biology subjects

Eyase, F.

Publications and source records attributed to Eyase, F..

8 recordsLinked to original sources

bioRxiv2026

Isolation and characterisation of novel fruit bat alphaherpesvirus from Rousettus aegyptiacus bats in Coastal Kenya

BackgroundHerpesviruses are a group of double-stranded DNA viruses known to infect a wide range of vertebrates and establish life-long latent infections. While bats serve as natural reservoir hosts for numerous viral families, relatively few bat herpesviruses have been successfully isolated. In this study, we report the isolation and characterization of two novel alphaherpesvirus strains obtained from Rousettus aegyptiacus bats in Coastal Kenya. MethodsThe samples of oral and rectal swabs were collected from three different species of bats from coastal Kenya between October 2024 and April 2025; the bat species collected include Hipposideros spp., Coleura afra, and Rousettus aegyptiacus. Virus isolation was performed by inoculation of samples in Vero E6 cells and subsequent monitoring for cytopathic effects (CPE). Total nucleic acids were extracted from CPE positive cultures and subjected to library preparation to enable unbiased detection of both RNA and DNA viruses. The libraries were sequenced using next-generation sequencing with Illumina MiSeq platform. Subsequently, bioinformatic analysis was carried out to identify the virus, generate consensus genomes as well as phylogenetic analysis to determine the placement of identified viruses. ResultsTwo samples from R. aegyptiacus (KIK_460_O and KIK_465_O) induced typical CPE within five days. Sequencing and assembly yielded partial consensus sequences of approximately 60 kb (KIK_460_O) and 70 kb (KIK_465_O), representing extended genomic data for a bat-associated alphaherpesvirus. This virus has a genome of about 140kb, indicating that our partial assemblies account for about 43-50% of the total genome. Both isolates were found to be closely related to Dzifa herpesvirus, an alphaherpesvirus previously identified in Kilifi, Kenya. Alphaherpesvirus was identified based on partial sequencing of UL19 (3,787bp) and UL30 (2,846bp) genes. The two isolates were found to be identical at the UL19 gene, showing that they belonged to the same virus strain. Phylogenetic analysis showed that the novel alphaherpesvirus belongs to primate alphaherpesviruses under the subfamily Alphaherpesvirinae. ConclusionThis study reports the isolation and genomic characterization of a novel fruit bat alphaherpesvirus from Kenyan Rousettus aegyptiacus bats. The partial genome assembly (60-70 kb) represent the first extended genomic data for this virus, covering approximately 43-50% of the estimated 140 kb complete genome. The phylogenetic placement of this alphaherpesvirus near primate viruses, especially Pteropodid alphaherpesvirus 1, suggests bat-association and needs further investigation into its zoonotic potential.

microbiology↗

bioRxiv2026

Pyrethroid Resistance Status and Multiple kdr Mutations (F1534C/L) in Aedes aegypti Populations from Zika-prone Areas in Lamu County, Kenya

Aedes aegypti mosquitoes are the primary vectors for dengue, yellow fever, chikungunya and zika virus transmission, posing significant public health risks. In Kenya, these viruses drive disease outbreaks especially, dengue and chikungunya with coastal Kenya being the most affected. Low-level circulation of the Zika virus has been reported in parts of the Kenyan coast, with confirmed cases reported in Lamu County between August to September 2024. Except for yellow fever, there are no approved vaccines or therapeutics, hence vector control remains the most effective means of protection. However, prolonged exposure to insecticides can lead to resistance, threatening these interventions. Therefore, monitoring resistance in mosquito populations is critical to allow for appropriate interventions using effective chemical classes to prevent disease outbreaks. This study aimed to establish the levels of resistance to pyrethroids, and associated markers, among Ae. aegypti populations in sections of Lamu County where there had been a recent localized outbreak of Zika. Mosquito eggs were collected from Mkomani, Kashmir, and Kandahar villages in Lamu County, reared and tested for susceptibility to three pyrethroid insecticides (0.75% permethrin, 0.05% Alpha-cypermethrin and 0.05% deltamethrin) using WHO tube assays. Genotyping of knockdown resistance (kdr) mutations L982W, S989P, A1007G, V1016G/I, and F1534C was done using Sanger sequencing. Association between resistant phenotypes and genotypes were inferred. The results varied between the three pyrethroids with high resistance to permethrin observed (6-15% mortality), for deltamethrin mortality ranged between 53-57%, while for alphacypermethrin 88%-99% mortality was observed. Two mutation types and six genotypes were identified at F1534. No other kdr mutations were detected. The CC genotype was significantly associated with 0.75% permethrin resistance in Ae. aegypti populations (OR = 2.87, 95% CI: 1.34-6.17, P = 0.0036). The current data show that Ae. aegypti from Kandahar, Kashmir and Mkomani villages in Lamu County have developed very high resistance to permethrin, and varying resistance to other pyrethroids, thus threatening pyrethroid-based control strategies in this region, highlighting the need for alternative strategies to control the vector for arboviruses.

evolutionary biology↗

bioRxiv2026

Mitochondrial DNA Variation in the D-LOOP and ND Loci identified in the Kenyan Population: Potential Implications for precision Oncology

BackgroundPrecision oncology is dominated by studies focused on nuclear genomic alterations, leaving mitochondrial DNA (mtDNA) variation excluded from routine clinical genomic testing. However, mitochondria regulate oxidative phosphorylation (OXPHOS), reactive oxygen species (ROS) production, apoptosis, and metabolic reprogramming pathways that are central to chemotherapy response. Methods468 Complete mitochondrial genomes from Kenyan individuals representing diverse ethnic groups were analyzed. Seven variants associated with effect on cancer treatment were identified. These include; m.310T>C(D-loop), m.10398A>G (MT-ND3), m.13708G>A (MT-ND5), m.16189T>C, m.13928G>C, m9055G>A and m.16519T>C (D-loop). Allele frequencies and distribution were assessed. ResultsThe coding-region variants (m.10398A>G and m.13708G>A) occur in Complex I subunits and are associated with altered oxidative phosphorylation efficiency and ROS production. The control-region variants (m.16189T>C and m.16519T>C) influence mtDNA replication and copy number. These variants have been implicated in differential response to chemotherapeutic agents including platinum-based therapies and anthracyclines. m.13928G>C sits in the MT-CYB gene and could possibly affect mitochondrial respiratory function; this variant could influence how tumors respond to therapies that rely on apoptosis or ROS generation.m.9055G>A is a MT-ATP6 variant classified as benign in mitochondrial disease but may represent a marker of haplogroup background rather than a direct cancer driver. While m.310T>C itself does not encode a protein, its location in the regulatory D-loop influences mitochondrial function, which can affect how tumor cells respond to chemotherapies that rely on mitochondrial-mediated apoptosis or oxidative stress. ConclusionPharmacogenomic relevant mitochondrial variants are present in the Kenyan population. With the rise of cancer burden in Kenya there is a need carry out more studies to understand the impact of these variations on cancer treatment. This can inform the integration of mtDNA analysis into precision oncology strategies in African populations.

genomics↗

bioRxiv2026

Metagenomic Characterization of Aedes aegypti Virome in Kwale County, Kenya

BackgroundAedes aegypti is a primary vector of arboviruses, including dengue, chikungunya, yellow fever, and Zika, and is widespread along the Kenyan coast, a region with recurrent outbreaks. In addition to human-pathogenic arboviruses, Ae. aegypti harbors insect-specific viruses (ISVs) that replicate exclusively in arthropods and may influence mosquito physiology, immunity, and vector competence. However, data on ISVs in Kenyan Ae. aegypti populations are limited. MethodsTwenty-nine mosquito pools containing 20 individual mosquitoes from Kwale County were homogenized, combined into a superpool, and subjected to total RNA extraction. Libraries were sequenced on an Illumina MiSeq platform. Initial analysis was done on CZ-ID platform. Reads were quality-filtered using PrinseqLite and assembled de novo with MEGAHIT. Phylogenetic analyses was performed with IQ-TREE using the Maximum Likelihood method. ResultsMetagenomic analysis revealed diverse ISVs in Ae. aegypti. Complete genomes of Fako virus and Tesano Aedes virus, and partial genomes of Aedes partiti-like virus, Cell fusing agent virus, and Formosus virus, were recovered. Genome lengths ranged from 1,149 to 10,146 nucleotides, with 91-99.5% identity to reference strains. Phylogenetic analysis placed the viruses within established ISV lineages, showing close evolutionary relationships with strains previously reported from Africa and other regions. ConclusionsThis study provides comprehensive characterization of ISVs in Ae. aegypti from Kwale County. The recovery of complete and near-complete genomes demonstrates the diversity and active circulation of ISVs, establishing a baseline for future studies on mosquito viromes, virus-mosquito interactions, and potential impacts on vector competence. ImportanceInsect-specific viruses (ISVs) are widespread in mosquitoes and replicate exclusively in arthropods, influencing mosquito physiology, immunity, and potentially vector competence for human-pathogenic arboviruses. Despite recurrent arboviral outbreaks along the Kenyan coast, the diversity and ecological roles of ISVs in Aedes aegypti remain poorly understood. This study provides a comprehensive metagenomic characterization of ISVs in Ae. aegypti from Kwale County, revealing complete genomes of Fako virus and Tesano Aedes virus, along with near-complete genomes of Aedes partiti-like virus, Cell fusing agent virus, and Formosus virus. These findings establish a baseline for mosquito virome composition in this region and underscore the active circulation of diverse ISVs in natural populations. Understanding these virus-mosquito interactions is critical for interpreting arbovirus ecology, assessing the potential impacts of ISVs on vector competence, and informing future vector surveillance and biological control strategies.

genomics↗

bioRxiv2025

Identification and genetic characterization of Jingmen tick virus from ticks sampled in select regions of Kenya; 2022-2024

Jingmen tick virus (JMTV), an emerging segmented RNA virus classified as an ungrouped flavivirus, poses a growing public health concern globally. Known for its association with febrile illnesses and wide host range, JMTV has been detected in Rhipicephalus, Hyalomma, and Amblyomma ticks collected from cattle, goats, sheep, camels, and chickens in pastoral regions of Kenya, including Baringo, Mandera, Malindi, Lamu, Mombasa, Wajir, Isiolo, and West Pokot. Using viral metagenomics next-generation sequencing, this study analysed adult ticks (n=1547, 72 pools). A total of 53% (38/72) pools were positive for at least one viral pathogen, with JMTV detected in 87% (33/38) of these pools across all study sites. Phylogenetic analyses revealed evidence of distinct Kenyan JMTV strains, with sequence segments from Malindi and Wajir clustering uniquely in their own clade; suggesting potential localised evolutionary pressures. Time calibrated phylogeny for the segment 1(RdRp) suggested varied ancestral origins and evolutionary relationships for the JMTV strains. MEME, BUSTED and FUBAR methods implemented in the Data-Monkey, unanimously identified codon 290 in segment 1 and 30 in segment 4 to be undergoing episodic positive selection. Recombination analysis performed using the RDP4 recombination detection tool indicated a recombination event in segment 2 of the Lamu JMTV strain that was confirmed by seven detection methods and visualised in BootScan. These findings suggest that Kenyan JMTV strains are undergoing positive selection, potentially driven by unique ecological and host factors. Segmented genome evidence of recombination highlights the increasing viruss potential for antigenic diversity. Host diversity and virus phylogenetic patterns underscore the zoonotic potential and its capacity for regional spread, emphasizing the critical need for enhanced vector surveillance. Temporal and ecological drivers like seasonal tick activity and livestock movement warrant investigation to elucidate JMTV transmission dynamics. Prioritizing tick-borne virus surveillance in Kenya will strengthen public health strategies and mitigates emerging viral risks.

evolutionary biology↗

bioRxiv2024

Characterization of West Nile virus Koutango lineage from Phlebotomine Sandflies in Kenya 2021

The West Nile virus (WNV), primarily transmitted by mosquitoes, is one of the most widespread flaviviruses globally, with past outbreaks occurring in the USA and Europe. Recent studies in parts of Africa, including Kenya, have identified the West Nile virus Koutango lineage (WN-KOUTV) among phlebotomine sandfly populations, however, our understanding of this virus remains limited. Hence, this study aimed to characterize WN-KOUTV from phlebotomine sandflies. Sandflies were sampled between 12-16th March 2021 from six villages in Baringo South, Kenya, using CDC light traps. Female sandflies were taxonomically identified and pooled based on genus. Virus isolation was performed in Vero cells. Viral genome was determined using next-generation sequencing. Phylogenetic and molecular clock analyses were done to decipher the viruss evolutionary relationships. Comparative analyses of amino acid sequences were performed to determine variations. Protein modeling in Pymol was conducted to elucidate variations in key protein regions. Evolutionary pressure analysis investigated the selection pressures on the virus. In vitro experiments were done to investigate the virus growth kinetics in mammalian (Vero-E6) and mosquito (C636) cells. We report the isolation of WN-KOUTV from Salabani Baringo South, Kenya. The isolated WN-KOUTV clustered with previously identified WN-KOUTV strains. Comparative analysis revealed unique amino acid at NS5 653. Diversifying pressure was acting NS3 267 of the WN-KOUTV lineage. WN-KOUTV replicates efficiently in Vero-E6 and C636 cells comparable to West Nile virus Lineage 1a, isolated from mosquitoes. The isolation of WN-KOUTV in sandflies points to them as potential vectors, however, vector competence studies would confirm this. The efficient replication in mammalian and mosquito cell lines elucidated its adaptability to host and vector. We speculate the close genetic relationship of WN-KOUTV strains is enabled by the bird migratory route between East and West Africa. If proven, this may point to a potential future pandemic pathway for this virus.

microbiology↗

bioRxiv2023

Detection of pathogenic bacteria in ticks from Isiolo and Kwale counties of Kenya using metagenomics.

Ticks are arachnid ectoparasites which rank second only to mosquitoes in the transmission of human diseases including bacteria responsible for anaplasmosis, ehrlichiosis, spotted fevers, and Lyme disease among other febrile illnesses. Due to paucity of data on bacteria transmitted by ticks in Kenya, this study undertook a bacterial metagenomic-based characterization of ticks collected from Isiolo, a semi-arid pastoralist County in Eastern Kenya, and Kwale, a coastal County with monsoon climate on the southern Kenyan border with Tanzania. A total of 2,918 ticks belonging to 3 genera and 10 species were pooled and screened in this study. Tick identification was confirmed through the sequencing of Cytochrome C Oxidase Subunit 1 (COI) gene. Bacterial 16S rRNA gene PCR amplicons obtained from the above samples were sequenced using the MinION (Oxford Nanopore Technologies) platform. The resulting reads were demultiplexed in Porechop, followed by trimming and filtering in Trimmomatic before clustering using Qiime2-VSearch. A SILVA database pretrained naive Bayes classifier was used to taxonomically classify the Operational Taxonomic Units (OTUs). The bacteria of clinical interest detected in pooled tick assays were as follows: Rickettsia spp. 59.43% of pools, Coxiella burnetii 37.88%, Proteus mirabilis 5.08%, Cutibacterium acnes 6.08% and Corynebacterium ulcerans 2.43%. These bacteria are responsible for spotted fevers, query fever (Q-fever), urinary tract infections, skin and soft tissue infections, eye infections and diphtheria-like infections in humans, respectively. P. mirabilis, C. acnes and C. ulcerans were detected only in Isiolo. Additionally, COI sequences allowed for the identification of Rickettsia and Coxiella species to strain level in some of the pools. Diversity analysis revealed that the tick genera had high levels of Alpha diversity but the differences between the microbiomes of the three tick genera studied were not significant. The detection of Cutibacterium acnes, commonly associated with human skin flora suggests that the ticks may have contact with humans potentially exposing them to bacterial infections. The findings in this study highlight the need for further investigation into the viability of these bacteria and the competency of ticks to transmit them. Clinicians in these high-risk areas also need to be appraised for them to include Rickettsial diseases and Q-fever as part of their differential diagnosis.

bioinformatics↗

bioRxiv2018

Recent outbreaks of chikungunya virus (CHIKV) in Africa and Asia are driven by a variant carrying mutations associated with increased fitness for Aedes aegypti

BackgroundIn 2016, a chikungunya virus (CHIKV) outbreak was reported in Mandera, Kenya. This was the first major CHIKV outbreak in the country since the global re-emergence of this virus, which arose as an initial outbreak in Kenya in 2004. Therefore, we collected samples and sequenced viral genomes from the 2016 Mandera outbreak.\n\nMethodology/Principal FindingsAll Kenyan genomes contained two mutations, E1:K211E and E2:V264A, recently reported to have an association with increased infectivity, dissemination and transmission in the Aedes aegypti (Ae. aegypti) vector. Phylogeographic inference of temporal and spatial virus relationships using Bayesian approaches showed that this Ae. aegypti adapted strain emerged within the East, Central, and South African (ECSA) lineage of CHIKV between 2005 and 2008, most probably in India. It was also in India where the first large outbreak caused by this strain appeared, in New Delhi, 2010. More importantly, our results also showed that this strain is no longer contained to India, and that it has more recently caused several major outbreaks of CHIKV, including the 2016 outbreaks in India, Pakistan and Kenya, and the 2017 outbreak in Bangladesh. In addition to its capability to cause large outbreaks in different regions of the world, this CHIKV strain has the capacity to replace less adapted wild type strains in Ae. aegypti-rich regions. Indeed, all the latest full CHIKV genomes of the ECSA Indian Ocean Lineage (IOL), from the regions of high Ae. aegypti prevalence, carry these two mutations, including samples collected in Japan, Australia, and China.\n\nConclusions/SignificanceOur results point to the importance of continued genomic-based surveillance of this strains global spread, and they prompt urgent vector competence studies in Asian and African countries, in order to assess the level of vector receptiveness, virus transmission, and the impact this might have on this strains ability to cause major outbreaks.\n\nAuthor summaryChikungunya virus (CHIKV) causes a debilitating infection with high fever, intense muscle and bone pain, rash, nausea, vomiting and headaches, and persistent and/or recurrent joint pains for months or years after contracting the virus. CHIKV is spread by two mosquito vectors, Aedes albopictus and Aedes aegypti, with increased presence around the globe. In this study, we report global spread of a CHIKV strain that carries two mutations that have been suggested to increase this virus ability to infect the Aedes aegypti mosquito, as well as to increase CHIKVs ability to be transmitted by this vector. We show that this strain appeared sometime between 2005 and 2008, most probably in India, and has now spread to Africa, Asia, and Australia. We show that this strain is capable of driving large outbreaks of CHIKV in the human population, causing recent major outbreaks in Kenya, Pakistan, India and Bangladesh. Thus, our results stress the importance of monitoring this strains global spread, as well as the need of improved vector control strategies in the areas of Aedes aegypti prevalence.

evolutionary biology↗