Vector identity structures mosquito and biting midge viromes in matched peridomestic habitats

Background Mosquitoes and Culicoides biting midges are major blood-feeding Diptera involved in the ecology of vector-borne viruses. Although both vector groups frequently co-occur in peridomestic environments, their viromes have rarely been compared under matched ecological conditions. Methods We performed metatranscriptomic sequencing of 26 pools of mosquitoes and biting midges collected from Jiangxi and Hainan provinces, China, between 2017 and 2019. These pools were organised into 13 habitat-matched mosquito–midge pairs from chicken pens, cattle pens, dog kennels, pig pens, sheep pens and human dwellings. Results From these data, we identified 659 viral species, including 623 RNA viruses and 36 DNA viruses, spanning 15 RNA virus supergroups and four DNA virus families. Most were putative novel species, including 522 RNA viruses and 34 DNA viruses. After applying an RPM > 100 threshold, 285 viral species were retained, including 230 biting midge-only viruses, 49 mosquito-only viruses and only 6 shared viruses. Although total viral load did not differ significantly between vector groups overall, virome composition showed strong vector-associated separation, whereas vertebrate host-associated setting had no significant effect. Arbovirus-related sequences also displayed vector-associated patterns: Japanese encephalitis virus (JEV) and Getah virus (GETV) were detected in mosquitoes, whereas Mangshi virus (MSV), Oya virus (OYAV) and Tibet orbivirus (TIBOV) were detected in biting midges. Viral sharing increased as vector phylogenetic distance decreased, suggesting that vector relatedness contributes to virome overlap. Conclusions In conclusion, matched sampling across peridomestic settings showed that vector taxon, rather than vertebrate host-associated setting, is the primary correlate of total and vector-borne virome composition in co-occurring mosquitoes and biting midges. These findings support further surveillance of biting midges as a separate and under-sampled group in vector virome studies.