Location: Zoonotic and Emerging Disease Research
Project Number: 3022-32000-021-024-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Sep 5, 2025
End Date: Sep 4, 2026
Objective:
We aim to detect zoonotic viruses in bats and ectoparasites (ticks) of bats and animals using virome capture sequencing, followed by targeted qPCR to surveil zoonotic agents with spillover potential in USA. Based on viral sequencing, we will develop high-throughput serological assays using short-peptide phage display to detect past exposures of high-risk zoonotic agents with spillover potential in domestic and farm animals in USA. Together, these efforts will enhance surveillance of emerging viruses in the country and inform risks of cross-species transmission through direct interactions through contact or interactions through intermediate hosts (ectoparasite/ticks).
Approach:
Aim 1: Molecular surveillance of zoonotic viruses in bats and ectoparasites (ticks)
Virus detection across in bats and high-risk interactions through ectoparasites (ticks) of bats and domestic and farm animals will be performed using viral high through-put sequencing. We will collect and use archival fecal, and oral samples from the free-ranging bats, ticks from bats, and ticks from farm/domestic animals for Virome Capture Sequencing (VCS) platform for Vertebrate Viruses (VirCapSeq-VERT) to explore the high-risk viruses for domestic animals, poultry, and dairy animals. We will study pooled samples from 300 bats and 500 ticks in a year (summer and winter season). Based on VCS analysis we will run qPCR on up to top 10 highest risk agents on individual samples to discover pandemic potential viruses.
Aim 2: Highthroughput serology (short-peptide phage display) to characterize antibody responses in experimentally infected animals, and develop serological assays to detect past viral exposures in domestic and farm animals in USA
Because viral infections are often self-limiting in a host, molecular tests directed at detecting viral shedding and the potential for active transmission usually reveal lower numbers of positives than serological tests which may identify up to 100% of individuals previously exposed to a virus. Using well characterized samples from experimentally infected laboratory animals and high-throughput serological assays, we will identify panels of linear immunogenic epitopes for the development of serodiagnosis assays. Using these serodiagnosis assays, we will screen for serological evidence of bats and tick-borne viruses in livestock, and peri-domestic animals to get information on circulating pathogenic viruses in USA and potential spillover events.
This dual approach—molecular and serological—provides a more complete picture of pathogen circulation and spillover risk. Together, these efforts will improve USDA’s ability to detect emerging threats early, design responsive diagnostics, and safeguard animal health and agricultural productivity from zoonotic viruses with pandemic potential.