COSMOS: integrated vector-pathogen metagenomics for mosquito-borne disease

COSMOS reconstructed near-complete arbovirus genomes from mixed field samples, achieving >90% coverage for 101 of 137 viral detections with a median 95x depth across 219 traps in Australia.

• Why it matters: Mosquito-borne disease response needs simultaneous monitoring of pathogen transmission and vector abundance, but standard surveillance uses separate assays that limit taxonomic breadth and ecological context.
• What they did: COSMOS is a targeted metagenomics workflow applied to >120,000 mosquitoes from 219 traps over three annual rounds of a major Australian surveillance program, with computational analysis quantifying mosquito community composition.
• The result: COSMOS matched surveillance data with 98.7% agreement across seven arboviruses, detected Sindbis virus and the state’s first encephalitic Little Sussex virus, and linked virus detections to structured mosquito communities during the 2023 Murray Valley encephalitis virus outbreak.

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