Insect-Specific Flaviviruses in the Viromes of Aedes aegypti (Linnaeus) Population from Liloan, Cebu, the Philippines

Flaviviruses are transmitted by Aedes aegypti and can cause dengue, yellow fever, and Zika infections, which are a significant public health concern in the tropics and subtropics. This study aimed to detect and identify flaviviruses in the viromes of Ae. aegypti population in Liloan, Cebu, the Philippines. RNA was extracted from pooled adult male and female mosquitoes reared from field-collected eggs. The RNA was reverse-transcribed to produce complementary single-stranded DNA and was amplified by PCR using primers targeting a portion of the NS5 gene, and amplicons were sequenced using next-generation sequencing (Illumina). Flavivirus- like sequences were identified from the sequence data of pooled male and female mosquitoes by similarity search using BLAST and phylogenetic analysis. Results revealed the absence of human-pathogenic flaviviruses and the presence of three genera of insect-specific flaviviruses: [1] cell fusing agent virus (CFAV), [2] Aedes flavivirus (AeFLAV), and [3] the existence of novel or uncharacterized lineages within Flavivirus (i.e. Flaviviridae sp.). These CFAV sequences showed closer genetic relatedness to the clade of CFAVs from Cairns, Cambodia, USA, and Surabaya, whereas AeFLAV sequences were closer to those from Bangkok, China, and Narita. The Liloan Flavivirus sequences were apparently conspecific with species from Argentina. Results highlighted the importance of local or regional studies to understand viral genetic diversity useful in mitigating the transmission of vector-borne diseases.