Mosquitoes harbor a wide diversity of microorganisms, including viruses that are human pathogens, or that are insect specific. We used metatranscriptomics, an unbiased high-throughput molecular approach, to describe the composition of viral and other microbial communities in six medically important mosquito species from across Western Australia: Aedes vigilax, Culex annulirostris, Cx. australicus, Cx. globocoxitus, Cx. pipiens biotype molestus, and Cx. quinquefasciatus. We identified 42 viral species, including 13 novel viruses, from 19 families. Culex mosquitoes exhibited a significantly higher diversity of viruses than Aedes mosquitoes, and no virus was shared between the two genera. Comparison of mosquito populations revealed a heterogenous distribution of viruses between geographical regions and between closely related species, suggesting that geography and host species may play a role in shaping virome composition. We also detected bacterial and parasitic microorganisms, among which Wolbachia bacteria were detected in three members of the Cx. pipiens complex, Cx. australicus, Cx. pipiens biotype molestus, and Cx. quinquefasciatus. In summary, our unbiased metatranscriptomics approach provides important insights into viral and other microbial diversity in Western Australian mosquitoes that vector medically important viruses.

Japanese encephalitis virus (JEV) emerged across mainland Australia in 2022, causing substantial impacts on public health and the pig industry. Its emergence raised concerns regarding potential spread into Western Australia (WA). This study aimed to determine JEV activity in WA with a focus on the Kimberley region between 2022 and 2024. It also examined potential pathways of JEV introduction into the state and the challenges associated with flavivirus serology. An integrated surveillance program comprising targeted feral pig surveillance and sentinel chicken monitoring was implemented across northern WA. Sera were screened using flavivirus ELISAs and confirmatory plaque reduction neutralisation tests (PRNT), while feral pig tonsils were tested by RT-qPCR. Evidence of JEV activity was detected in WA between 2022 and 2024. Serological findings from two feral pigs sampled in October 2022 provided the earliest indication of JEV transmission in the Kimberley region. Sentinel chicken surveillance subsequently identified JEV activity in Kununurra, Wyndham, Halls Creek and Newman during 2023 and Derby in 2024. These results provide the first published evidence of JEV activity in WA and highlight the importance of ongoing surveillance, vaccination, mosquito control and preparedness activities in northern Australia.