Location: Arthropod-borne Animal Diseases Research
Project Number: 3020-10400-001-011-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: May 1, 2025
End Date: Apr 30, 2028
Objective:
Perform bioinformatic analysis of metagenome data from field collected flies, with focus on existing and emerging bacterial and viral pathogens including bacteria, zoonotic viruses and particular focus on H5N1 HPAI.
Approach:
Filth flies will be collected from US sites (urban, rural) and sites abroad where military personnel operate (TBD), pooled by site and date (n=15 to 20 flies), and processed by USDA ARS. Total nucleic acid will be extracted and the metagenome (DNA, cDNA) will be prepared and sequenced using long and short read approaches (e.g. Oxford nanopore, Illumina). Cooperator will then analyze metagenome for pathogen presence and prevalence including specific focus on pathogenic bacteria and viruses, particular those causing pandemics, epidemics and/or for for epizootics. There is a particular focus on surveillance of emerging high-priority viruses like H5N1 HPAI.