AP23OA000000C025

The purpose of this award is to address gaps in surveillance and investigation activities for SARS-CoV-2 in animals, including farmed animals, captive wildlife, free-ranging wildlife, and companion animals.

First, we will fill gaps in surveillance using a model-informed process that allows us to distinguish between dead-end hosts and hosts responsible for viral amplification and onward transmission both within and between species. These key hosts are likely involved in sylvatic transmission chains, which would promote viral persistence.

Second, we will demonstrate interspecies transmission and identify transmission heterogeneities that increase the value of the basic reproduction number (R0) via targeted longitudinal sampling at white-tailed deer pens, which we expect to be transmission hotspots.

Third, we will determine transmission directionality and the degree to which viruses circulating in non-human animals are mixing with the viral populations of humans and vice versa.

The recipient must meet the objectives and deliverables stated in their work plan and must complete quarterly financial and performance reports and a final accomplishment report. Whole-genome sequences deposited in GSAID will foster the development of more comprehensive diagnostics and pharmaceuticals, therapeutics, and vaccines.

Further end-user benefit comes in the form of many undergraduate researchers and minority female post-doctoral scholars gaining valuable field ecology experience as well as epidemiological skills in the lab. The overall goal is to safeguard the health of the human population, wildlife, and agricultural systems.

Subcontracts include Ginkgo Bioworks for $996,585 (Ginkgo will accomplish the sequencing for all objectives because it is their specialty and they have sequenced >40,000 SARS-CoV-2 whole genomes for state and federal public health stakeholders, including the Centers for Disease Control and Prevention (CDC)) and Xavier Didelot at Warwick University for $15,596 (Xavier will accomplish the transphylo analysis of the sequence data from all three objectives because he developed the program and is the leader in this new and blossoming field of transmission reconstruction).

The Pennsylvania State University

10.025 - Plant and Animal Disease, Pest Control, and Animal Care

Animal and Plant Health Inspection Service (APHIS) [USDA]

Pennsylvania United States

State-Wide

USDA APHIS American Rescue Plan: SARS-CoV-2 in Animals (USDA-APHIS-10025-OA000000-23-0001)

COVID-19 $4,453,973 (100%) percent of this Cooperative Agreement was funded by COVID-19 emergency acts including the American Rescue Plan Act of 2021.