Metagenomic analysis of coastal Kenya female Aedes aegypti mosquito RNA metaviromes reveal presence of diverse insect specific viruses
Open Access
- 23 March 2023
- journal article
- Published by F1000 Research Ltd in Wellcome Open Research
Abstract
Background: Coastal Kenya has experienced repeated outbreaks of Chikungunya (CHIKV) and Dengue (DENV) viruses mediated by competent Aedes aegypti mosquito populations. These mosquitoes harbor insect specific viruses (ISVs), some of which can prevent arboviral transmission. However, there has been no systematic molecular entomological surveillance in coastal Kenya and the diversity of viruses in local Aedes aegypti populations remains largely unknown. Methods: To obtain a snapshot of the Aedes aegypti viromes from coastal Kenya, we took advantage of a cross-sectional survey of mosquitoes to determine the prevalence of Zika virus. We collected adult mosquitoes using lured Biogent’s sentinel traps at 16 different localities along the Kenyan coast between May to September 2017. Pools of 20 female Aedes aegypti mosquitoes were generated following grouping by morphological characteristics. Presence of arboviruses in the mosquito pools was determined using virus-specific and genera-specific primers with real-time PCR. Metagenomic next generation sequencing (mNGS) on Illumina Miseq and analysis was used to characterize the virome. Results: A total of 16,520 female Aedes aegypti grouped into 826 pools were analysed. Flaviviruses were detected in 69/826 (8.4%) pools by real time PCR. Sequencing generated 8,459/971,754 (0.87%) clean reads that were taxonomically assigned to 16 and 28 viral families and species, respectively. The family Phenuiviridae represented by Phasi Charoen-like phasivirus (PCLV) species was the most prevalent, detected in 64/73 (87%) mosquito pools. No pathogenic viruses were identified by mNGS. Phylogenetic analysis revealed local PCLV and Cell fusing agent virus (CFAV) were distinct from global sequences. Conclusions: Our data provides information about virus diversity and composition of the Aedes aegypti mosquitoes from coastal Kenya and contributes to the body of knowledge of the Aedes aegypti virome. To the best of our knowledge, this is the first study to provide this information from this region.Funding Information
- Wellcome Trust (203077_Z_16_Z)
- Medical Research Council, Wellcome Trust, and Newton Fund (MC_PC_15092)
This publication has 66 references indexed in Scilit:
- A New Insect-Specific Flavivirus from Northern Australia Suppresses Replication of West Nile Virus and Murray Valley Encephalitis Virus in Co-infected Mosquito CellsPLOS ONE, 2013
- Development of one-step quantitative reverse transcription PCR for the rapid detection of flavivirusesVirology Journal, 2013
- MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and UsabilityMolecular Biology and Evolution, 2013
- House-to-house human movement drives dengue virus transmissionProceedings of the National Academy of Sciences of the United States of America, 2012
- Transmission dynamics of an insect-specific flavivirus in a naturally infected Culex pipiens laboratory colony and effects of co-infection on vector competence for West Nile virusVirology, 2012
- SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell SequencingJournal of Computational Biology, 2012
- Transmission of West Nile Virus by Culex quinquefasciatus Say Infected with Culex Flavivirus IzabalPLoS Neglected Tropical Diseases, 2010
- BLAST+: architecture and applicationsBMC Bioinformatics, 2009
- The Sequence Alignment/Map format and SAMtoolsBioinformatics, 2009
- Fast and accurate short read alignment with Burrows–Wheeler transformBioinformatics, 2009