Speaker
Description
Warming climate and extreme weather events are changing the range of virus-competent mosquito species and their animal hosts, bringing viruses in contact with immunologically naive human populations. In Australia, this has resulted in unusual epidemics, including the 2022 emergence of Japanese Encephalitis Virus (JEV), and a spike in cases of Murray Valley Encephalitis Virus in 2023. Australia has a strong mosquito surveillance program, which includes mosquito species identification and detection of several viruses, but this relies on prior context and can miss pathogen emergence, as happened with JEV.
We present COSMOS (COmprehensive Sequencing of MOSquito-borne pathogens), a custom multi-pathogen sequencing assay, designed to reconstruct the genomes of mosquito-borne viruses in parallel with quantification of vector species abundance, which we benchmarked against expert morphological species identification and gold-standard PCR.
Using COSMOS, we simultaneously sequenced arboviral genomes and identified vector species composition of field-collected mosquitos from the NSW Mosquito Surveillance program. Targeted genomes included all >100 known arboviruses. All viruses detected by PCR were detected by COSMOS, and 78% of these produced complete genomes. COSMOS also detected multiple cases of arboviruses for which no screening is available, including Sindbis virus, and previously unseen Little Sussex Virus.
Phylogenetic reconstruction revealed diverse evolutionary histories of co-circulating pathogens, including evidence for co-circulating variants of Ross River Virus potentially associated with distinct subpopulations of the mosquito vector species. Mosquito biodiversity differed markedly along a geographic cline from coastal to inland locations, in agreement with expert entomological assessment.
Broad multi-pathogen sequencing techniques offer a robust and cost-effective approach with clearly defined limits of detection for a very wide range of pathogens, which is crucial for the analysis of geographically and temporally structured surveillance data. We highlight the need for multidisciplinary efforts that combine entomological and epidemiological information with both viral and vector genomics.
