Zika virus genome sequencing directly from field collected mosquitoes

Zika virus (ZIKV) is a negative sense RNA virus from the Flaviviridae family. ZIKV was a relatively unknown virus until the first epidemic in Micronesia in 2007 and further spread to French Polynesia and the Americas being responsible for millions of human infections and associated with neurological disorders in infants and adults. Although ZIKV transmission can be associated with sexual intercourse and blood transfusion, the main mode of transmission is similar to other arboviruses (such as Dengue and Chikungunya viruses) through the mosquito bite. Evidences suggest that both Aedes aegypti and Culex quinquefasciatus are able to replicate and transmit the virus, but so far the large majority of the studies were restricted to laboratory experiments. Here we employed an extensive mosquito field sampling in the Recife metropolitan area (the epicenter of the 2015-2016 ZIKV epidemics) associated with molecular detection with quantitative RT-PCR and viral whole genome sequencing in order to investigate if arboviruses surveillance can be performed at epidemic situations and whether information can be obtained from the natural viral variability. We were able to sequence 10 draft ZIKV genomes, 5 pools from each Ae. aegypti Culex quinquefasciatus species. Genome coverage breadth ranged from 16 to 100% and average depth from 45 to 1000x. Overall, our data shows that both Ae. aegypti and Cx. quinquefasciatus can act as ZIKV vectors and that no mutations that could lead to adaptation in different vector species occurred. Lastly, we are able to recover partial and full ZIKV genomes from those samples corroborating that arboviruses surveillance can be performed using mosquitoes sampling and viral genotyping by qRT-PCR associated with viral whole genome sequencing in order to obtain more in depth information about natural viral genomic variability.<br>