Biology subjects

Haynes, R.

Publications and source records attributed to Haynes, R..

3 recordsLinked to original sources

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↗

bioRxiv2025

Acute temporal, regional, and cell-type specific NKCC1 disruption following severe TBI in the developing gyrencephalic brain.

Traumatic brain injury (TBI) is a leading cause of morbidity and mortality in infants and toddlers, with limited treatment options and persistent neurological sequelae. We developed a multi-pathoanatomic lesion multi-insult (MuLMI) severe TBI model in piglets that replicates age-dependent damage patterns to the cortical ribbon observed in human patients with less injury in postnatal day (PND) 7 "infant" piglets and more extensive tissue damage in PND30 "toddler" piglets. Given that neuronal chloride homeostasis influences excitability, seizure susceptibility, and edema, we examined the developmental and injury-induced regulation of key cation-chloride cotransporters and modulators: NKCC1 (sodium-potassium-2-chloride cotransporter), KCC2 (potassium-chloride cotransporter), and the regulatory kinase SPAK, which are biomarkers of neuronal chloride concentrations. This study is the first to define the spatiotemporal expression and phosphorylation profiles of these proteins in the developing piglet brain. We found a perinatal shift in the ratio of KCC2:NKCC1 across the brain, driven primarily by protein abundance, rather than transcriptional levels. We hypothesized that toddler piglets would exhibit an increase in cortical NKCC1 and SPAK causing hyperexcitability and perhaps explaining their more severe, unilateral cortical damage. Severe TBI induced a transcriptional increase in Slc12a2 and Stk39, and a decrease in Slc12a5 in toddler piglets, but not infant piglets. We further found that infant piglets, not toddler piglets, upregulated SPAK and Tyrosine Receptor Kinase B (TRKB) protein in cortex after TBI, with minimal changes in NKCC1 and KCC2. However, phosphorylated NKCC1 (pNKCC1) was significantly upregulated in surviving cortical neurons after TBI in infant piglets and was unchanged in toddlers, despite more severe injury. These findings suggest that cortical neuronal NKCC1 activation may play a role in post-traumatic excitability or resilience in the immature brain and identify NKCC1 and/or SPAK as a potential therapeutic target. In human tissue, the KCC2:NKCC1 ratio also increased postnatally, and TBI caused region and cell-type specific dysregulation of pNKCC1. Our results establish piglets as a valuable model for investigating age-specific mechanisms of pediatric TBI and for testing targeted interventions, particularly for infant populations where seizure control remains a major clinical challenge.

neuroscience↗