Biology subjects

Langat, S.

Publications and source records attributed to Langat, S..

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

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

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

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↗

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

Molecular Characterization and Phylogenetic analysis of Wuchereria bancrofti in human blood samples from Malindi and Tana River Delta, endemic regions in Kenya.

IntroductionLymphatic filariasis is a debilitating disease caused by filarial worms; Wuchereria bancrofti, Brugia Malayi and B. Timori. It is earmarked for elimination by the year 2020 through the Global Program for the Elimination of Lymphatic Filariasis (GPELF). In Kenya, mass treatment has been ongoing since the year 2002 though it has not been consistent as recommended by World health organization (WHO). Taking this into account, the emergence of W. bancrofti resistance strains against the current choice of drugs cannot be ruled out. Information on genetic structure and variations is important in assessment of Programs success. Data on genetic characterization of W. bancrofti in Kenya is lacking. This study, therefore reports the first genetic diversity of W. bancrofti in two Kenyan endemic regions.\n\nMethodologyGenomic DNA was extracted from 100 human blood samples obtained from Mpirani district in Malindi and Kipini district in Tana River Delta. They were then amplified by PCR and detected through gel electrophoresis. Seventeen PCR products positive for Wuchereria PCR bancrofti were purified and then DNA quantified for Sanger sequencing. Chromas version 2.6.5 and BioEdit softwares were used for sequence alignment and editing. Fourteen sequences were selected for analysis by MEGA7 and six more related sequences retrieved from the Gene Bank for further analysis with the study sequences. Intrapopulation, interpopulation diversity and pair wise distance were determined and the phylogenetic trees constructed. Tajimas D-test of neutrality was also determined and Statistical evolutionary rate was done using Chi-square (X2) test.\n\nResults and DiscussionThe mean diversity of Malindi and Tana River Delta isolates was 1.42 and the overall mean distance was 0.99. Tajimas (D) test for test of Neutrality was 4.149 and nucleotide diversity({pi}) was 0.603. These results revealed high genetic variations of W. bancrofti in Kenyan endemic regions. This variation could be attributed to prolonged use of the mass drug administration (MDA) and the long period of parasite circulation in these populations.\n\nAuthor SummaryElephantiasis is a disabling disease that causes severe swellings to the affected limbs. It is caused by parasites of Wuchereria bancrofti, Brugia Timori and B. malayi which are transmitted by mosquito vectors. The disease is under the control by the Global Programme to eliminate filariasis and due to the effect of continued treatment through mass drug administration there have been changes in the genetic makeup of the parasite. This may result to resistant strains which may have negative impact on the treatment interventions. We therefore aimed at characterizing the genetic sequences of the Wuchereria bancrofti parasite found in Kenya. Through analyzing parasites obtained in different years after treatment, we were able to track any genetic variations since the start of mass drug administration in Kenya. These variations would be due to the effect of drug pressure, human population movements or mosquito vector movement. This kind of study is important for drug developments and for evaluating the progress of the control programmes.

evolutionary biology↗