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

Abstract

By 2050, almost half of the global population will be at risk of mosquito-borne disease. Effective response requires monitoring both pathogen transmission and vector abundance, yet these are typically assessed using separate assays with limited taxonomic breadth. Here we present COSMOS (COmprehensive Sequencing for MOSquito-borne disease), a targeted metagenomics workflow designed to reconstruct pathogen genomes and mosquito community composition directly from mixed field-collected samples. Over three annual rounds of a major Australian surveillance program, we evaluated >120,000 mosquitoes in 219 traps, with 98.7% agreement with surveillance data across seven monitored arboviruses, and additional detections of Sindbis virus and the state's first detection of encephalitic Little Sussex virus. Of 137 viral detections, 101 yielded near-complete genomes (>90% coverage) at median 95x depth. Using an accompanying computational workflow, COSMOS quantified mosquito composition, matching entomological estimates of reported vector species (CCC 0.78-0.89). Joint analysis of virus and vector composition identified structured mosquito communities associated with spatial and temporal environmental variation, allowing the ecological context of arbovirus detections to be characterised. Detections during the Murray Valley encephalitis virus outbreak in 2023 were concentrated within a narrowly defined mosquito-community space corresponding to rural communities dominated by the inland S-AUS sub-lineage of Culex annulirostris. Integrated vector-pathogen metagenomics provides ecological and evolutionary context for arbovirus activity within a single scalable workflow for surveillance and outbreak response.

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BibTeX RIS

BibTeX

@misc{forster2026cosmos,
  title = {{COSMOS: integrated vector-pathogen metagenomics for mosquito-borne disease}},
  author = {A. J. Forster and A. A. Khan and E. Garrett and C. Toi and C. J. Suster and J. Haniotis and K. Dang and J. Watson and S. Doggett and S. C.-A. Chen and M. R. Watts and J. Kok and V. Sintchenko and M. Payne and C. Webb and R. J. Rockett and T. Golubchik},
  howpublished = {bioRxiv},
  year = {2026},
  month = nov,
  doi = {10.64898/2026.11.03.763828},
  url = {https://www.biorxiv.org/content/10.64898/2026.11.03.763828v1},
  note = {CC BY-NC-ND},
}

RIS

TY  - UNPB
TI  - COSMOS: integrated vector-pathogen metagenomics for mosquito-borne disease
AU  - A. J. Forster
AU  - A. A. Khan
AU  - E. Garrett
AU  - C. Toi
AU  - C. J. Suster
AU  - J. Haniotis
AU  - K. Dang
AU  - J. Watson
AU  - S. Doggett
AU  - S. C.-A. Chen
AU  - M. R. Watts
AU  - J. Kok
AU  - V. Sintchenko
AU  - M. Payne
AU  - C. Webb
AU  - R. J. Rockett
AU  - T. Golubchik
PY  - 2026
DA  - 2026/11/03
PB  - bioRxiv
DO  - 10.64898/2026.11.03.763828
UR  - https://www.biorxiv.org/content/10.64898/2026.11.03.763828v1
AB  - By 2050, almost half of the global population will be at risk of mosquito-borne disease. Effective response requires monitoring both pathogen transmission and vector abundance, yet these are typically assessed using separate assays with limited taxonomic breadth. Here we present COSMOS (COmprehensive Sequencing for MOSquito-borne disease), a targeted metagenomics workflow designed to reconstruct pathogen genomes and mosquito community composition directly from mixed field-collected samples. Over three annual rounds of a major Australian surveillance program, we evaluated >120,000 mosquitoes in 219 traps, with 98.7% agreement with surveillance data across seven monitored arboviruses, and additional detections of Sindbis virus and the state's first detection of encephalitic Little Sussex virus. Of 137 viral detections, 101 yielded near-complete genomes (>90% coverage) at median 95x depth. Using an accompanying computational workflow, COSMOS quantified mosquito composition, matching entomological estimates of reported vector species (CCC 0.78-0.89). Joint analysis of virus and vector composition identified structured mosquito communities associated with spatial and temporal environmental variation, allowing the ecological context of arbovirus detections to be characterised. Detections during the Murray Valley encephalitis virus outbreak in 2023 were concentrated within a narrowly defined mosquito-community space corresponding to rural communities dominated by the inland S-AUS sub-lineage of Culex annulirostris. Integrated vector-pathogen metagenomics provides ecological and evolutionary context for arbovirus activity within a single scalable workflow for surveillance and outbreak response.
ER  -

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