Biology subjects

Koka, H.

Publications and source records attributed to Koka, H..

7 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↗

bioRxiv2025

Detection and Characterization of West Nile Virus with evidence of Transovarial Transmission in the Coastal region, Kenya

BackgroundWest Nile virus (WNV) is a mosquito-borne flavivirus of global public health significance, maintained in an enzootic cycle between birds and mosquitoes, with humans and other mammals as incidental hosts. Understanding WNV circulation in diverse mosquito populations is critical for predicting and mitigating outbreaks. This study investigated mosquito populations from coastal Kenya, where WNV was detected, genetically characterized, and evidence of transovarial transmission in Aedes aegypti was observed. MethodsMosquitoes were collected from Kwale, Kilifi, Mombasa, and Isiolo counties (n=14,105) and pooled by species and location (1,596 pools). Pools were inoculated on Vero E6 cells, followed by RNA extraction, Illumina MiSeq sequencing, and preliminary analysis on CZ-ID. Reads were quality-controlled (PrinseqLite v0.20.4), assembled de novo (MEGAHIT v1.2.9), and analyzed via BLAST. Phylogenetic reconstruction used Maximum Likelihood, and codon-level selection pressure was evaluated using FEL, MEME, and FUBAR on Datamonkey. ResultsWNV was detected in ten pools: eight Lineage 1a and two Lineage 2. Virus isolates came from Culex pipiens, Culex univittatus, Anopheles funestus, Aedes aegypti, and Eretmapodites chrysogaster. Notably, one Lineage 1a isolate from a male Aedes aegypti confirmed transovarial transmission. Six codons were under diversifying selection, NS2B gene was found to carry the V103A mutation. ConclusionWNV in coastal Kenyan mosquitoes revealed transovarial transmission in Aedes aegypti. Lineage-specific evolution, codons under positive selection, and the NS2B:V103A mutation demonstrate ongoing viral adaptation. These findings highlight the need for continued genomic surveillance and targeted vector studies to guide WNV control strategies in Kenya and the wider region. ImportanceWest Nile virus (WNV) remains a globally important arbovirus, yet genomic and experimental data from under-sampled regions such as coastal East Africa are limited. This study provides the first integrated molecular and genotypic characterization of WNV circulating along the Kenyan coast, revealing the co-detection of Lineage 1a and the first identification of Lineage 2 in this region. By combining field surveillance, whole-genome sequencing, evolutionary analyses, and lineage-specific replication assays across multiple vertebrate and mosquito cell lines, we demonstrate clear genetic and biological differences with implications for transmission and adaptation. Importantly, the detection of WNV in a male Aedes aegypti mosquito and recovery of full genomes offers compelling evidence of transovarial transmission, a mechanism that may support viral maintenance independent of vertebrate hosts. These findings expand current knowledge of WNV ecology in Africa and underscore the need for continued genomic surveillance to detect emerging variants and inform public health strategies.

genomics↗

bioRxiv2024

Genomic sequence analysis of the first mpox virus detected in Kenya

Mpox is a zoonotic disease caused by the Monkeypox virus (MPXV) in the family: Poxviridae, genus: Orthopoxvirus. Historically, the disease was restricted mostly to Africa with cases being reported in Central Africa (mostly caused by clade I) and in West Africa (caused by clade II). However, there has been a recent shift in the virus range with outbreaks being reported in Europe and America, and in countries where the virus was initially not endemic. This multi-country outbreak was driven mostly by clade IIb lineage of MPXV. Since December 2023, there has been an ongoing mpox outbreak in the Democratic Republic of Congo (DRC), driven by a new clade I lineage of the virus, designated clade Ib. The DRC outbreak has persisted, with an increase in cases being reported over the past few months. Spillover of these outbreak-related cases to the neighbouring countries have also been reported in multiple countries including Uganda and Rwanda. Here, we report the rapid application of unbiased metagenomic next generation sequencing (mNGS) to reconstruct the genome sequence of the first reported case of MPXV in Kenya. Our findings show that the Kenyan case clusters together with clade Ib MPXV strains, associated with the sustained outbreak in the DRC. Clade Ib lineage has been associated with continuing geographical expansion of the virus to previously unaffected areas, high incidence of the disease as well as high case fatality (CFR 4.9-6.7%). Similar to other clade Ib strains, the Kenyan strain carries predominant APOBEC3-type mutations which is characteristic feature of human-to-human transmission, highlighting the need for surveillance to curtail any potential expansion of this MPXV strain. The lack of information on genomes associated with cases reported in different East African countries, is a gap that urgently needs to be addressed to aid in the monitoring of this MPXV strain. This case investigation, therefore, underscores the need for sequencing efforts to be enhanced across the continent to help improve our understanding of the geographical range and diversity of the MPXV strains, especially those belonging to clade I which is currently under-represented.

genomics↗

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

Genetic variability and vector competence of Aedes aegypti populations from Kisumu and Busia Counties, Western Kenya, for Chikungunya and Zika viruses

Aedes aegypti is the primary vector of several arboviruses, including dengue virus (DENV), chikungunya virus (CHIKV), yellow fever virus (YFV), and Zika virus (ZIKV). This vector is widespread globally in tropical and subtropical areas, but also found in temperate areas. Kenya experienced its first chikungunya outbreaks in Lamu County in 2004 and later in Mandera: 2016, and Mombasa: 2017. While there is yet to be a report of Zika outbreaks in Kenya, sero-surveillance studies indicate low-level transmission of this virus in coastal and northern parts of the country. Despite the presence of Ae. aegypti in Kisumu and Busia counties in sufficient densities, and free movement of people between the coast and the two western Kenya counties, no outbreaks of either disease have been reported in these regions. To investigate this phenomenon, we collected Ae. aegypti mosquitoes from county headquarter towns near railway stations connecting the coast and western Kenya and reared them under controlled laboratory conditions. The mosquitoes were then assessed for genetic variability using CO1 genes as well as their efficiency to transmit viruses using Laboratory colonies (F1) of the field mosquitoes challenged with an infectious blood meal containing CHIKV and ZIKV. Genetic analysis revealed the presence of both Ae. aegypti subspecies, (Ae. aegypti aegypti [Aaa] and Ae. aegypti formosus [Aaf]) in the two western Kenya counties, with Aaf being dominant (19:8 for Kisumu samples and 25:6 for Busia samples). Additionally, pairwise comparison revealed minimal genetic differentiation (0.62%) between the study populations, with a high genetic variation (99.38%) observed within each population, indicating significant diversity within individual populations. Ae. aegypti populations from Kisumu and Busia counties exhibited competence for CHIKV, with infection, dissemination, and transmission rates of 55.2%, 85.5%, and 27.1% for Kisumu; and 57.8%, 71.8%, and 25% for Busia populations, respectively. There was no significant difference in vector competence between these two populations. Interestingly, neither population was competent for ZIKV. In conclusion, the data shows that the Ae. aegypti populations in the two cities were homogeneous. This could explain the observed similarity in vector competence for CHIKV and ZIKV. Author SummaryOur study investigated the genetic variability and vector competence of Ae. aegypti mosquito populations in Kisumu and Busia Counties to CHIKV and ZIKV; revealing the presence and even distribution of both Aaa and Aaf subspecies. We also found that the Ae. aegypti populations from the two counties were not genetically differentiated. Furthermore, our study revealed that the Ae. aegypti mosquitoes from Kisumu and Busia counties were competent for CHIKV but may be refractory to ZIKV infection. These findings highlight the importance of continued monitoring of Ae. aegypti populations and their potential for arboviral disease transmission in the region.

microbiology↗

bioRxiv2019

Immune gene expression profiling reveals heterogeneity in luminal breast tumors

Disease heterogeneity of immune gene expression patterns of luminal breast cancer (BC) has not been well studied. We performed immune gene expression profiling of tumor and adjacent normal tissue in 92 Asian luminal BC patients and identified three distinct immune subtypes. Tumors in one subtype exhibited signs of T-cell activation, lower ESR1/ESR2 expression ratio and higher expression of immune checkpoint genes, nonsynonymous mutation burden, APOBEC-signature mutations, and increasing body mass index compared to other luminal tumors. Tumors in a second subtype were characterized by increased expression of interferon-stimulated genes and enrichment for TP53 somatic mutations. The presence of three immune subtypes within luminal BC was replicated in cases drawn from The Cancer Genome Atlas and a Korean breast cancer study. Our findings suggest that immune gene expression and associated genomic features could be useful to further stratify luminal BC beyond the current luminal A/B classification.

genomics↗

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↗