Investigation of Rift Valley Fever Virus, Emerging Arboviruses, Mosquito Vectors and Rainfall Patterns in Nyandarua County, Kenya

Abstract

Rift Valley fever (RVF) is a zoonotic viral disease of economic and public health importance in Kenya and other regions of the world. The disease affects ruminants and is transmitted by Aedes spp., Culex spp., and Mansonia mosquito species. Humans are also infected mainly by contact with contaminated tissues and consumption of animal products from infected animals. Rainfall intensities, mosquito densities, and animal movement play a major role in outbreaks and the transmission of the disease. Rift Valley fever-outbreaks have been generally reported in arid and semi-arid areas in Kenya. A few suspected cases have also been reported for the first time in Nyandarua, an area, previously known to be free of the disease. Nevertheless, information on the disease status, mosquito diversities and rainfall patterns in Nyandarua still remains generally unknown. There are also no previous reports of outbreaks of diseases caused by other emerging arboviruses. Therefore, this study investigated RVF virus, other emerging arboviruses, mosquito vectors ,and rainfall patterns in Nyandarua. A cross-sectional study design was done and 301 sera and whole blood were sampled purposively from cattle (164), sheep (118), and goats (19) raised in 57 homesteads in Nyandarua. A total of 791 Mosquito samples were also collected using the CDC Light trap (John W. Hock Company). Questionnaires were administered to selected farmers in the 57 homesteads using Epicollect5 software. The sera were screened for IgG and IgM antibodies against RVF virus using competitive and capture ELISA (IDVet Innovative Diagnostics, Grabels, France) respectively. RVF virus and other emerging arboviruses were detected by metagenomic analysis. The viral-RNAs was extracted from whole blood using TANBead® Nucleic Acid Extractor and cDNA libraries synthesized using RT-PCR and Oxford Nanopore Rapid Barcoding Kit 96. Gene sequencing was done using Oxford Nanopore. The FASTAQ nucleotide reads were analysed using the EPI2ME software. Sequence identities and mapping of the reads were done using the BlASTn tool (https://www.ncbi.nlm.nih.gov/labs/virus/vssi) and Geneious software respectively. Mosquito species and their genetic diversities were identified using a dissection microscope, Polymerase chain reaction and Sanger sequencing. Phylogenetic analysis was done using MEGA......................................................