Metagenomics of Vector-Borne Diseases

The question

Surveillance that does not need to know what it is looking for.

Using metagenomics and computational pipelines to detect arbovirus activity in field-collected mosquitoes and ticks.

West Nile virus and its relatives circulate in local mosquito and tick populations long before anyone turns up in a clinic. Sequencing everything inside a field-caught insect — rather than testing for one virus at a time — turns routine surveillance into discovery.

We sequence small RNAs and total nucleic acid from mosquitoes and ticks collected in Southern California, then use computational pipelines to separate the insect's own genome from the viruses it carries. The same data show how the vector's RNA interference machinery responds to infection, which is a read on transmission risk as well as on the virus itself.

Triangular correlation matrix of thirty-six viruses with three highlighted co-occurrence regions — Co-occurrence across thirty-six viruses found in field-collected mosquitoes: what metagenomic surveillance produces before any single virus is named.

How we look

Techniques used in this area

Sequencing & assay

RNA-seq
Small RNA sequencing
Shotgun metagenomics

Analysis

Metagenomic assembly
Viral discovery pipelines

Platforms

Illumina
Oxford Nanopore

Scientific Reports

Scientific Reports2023

Small RNA sequencing of field Culex mosquitoes identifies patterns of viral infection and the mosquito immune response

Abel SM, Hong Z, Williams D, Ireri S, Brown MQ, Su T, Hung KY, Henke JA, Barton JP, Le Roch KG

All 1 papers on metagenomics of vector-borne diseases

All research areas