Address gaps in surveillance and investigation activities for sars-COV-2 in animals, including farmed animals, captive wildlife, free-ranging wildlife, and companion animals

The Pennsylvania State University (Penn State) received a $4,453,973 cooperative agreement award from the United States Department of Agriculture Animal and Plant Health Inspection Service (USDA APHIS) under the Plant and Animal Disease, Pest Control, and Animal Care federal grant program (CFDA 10.025).

The award funds surveillance and research activities to address gaps in understanding SARS-CoV-2 transmission between animals and humans. Penn State will conduct surveillance to distinguish viral hosts and identify transmission hotspots. Longitudinal sampling at white-tailed deer pens will demonstrate interspecies transmission and transmission heterogeneities. Genome sequencing and analysis will determine transmission directionality between animal and human viral populations.

Two subawards were also issued. Ginkgo Bioworks will receive $996k to perform all genome sequencing given their expertise sequencing over 40k SARS-CoV-2 genomes. Xavier Didelot at the University of Warwick will receive $15.6k to conduct transphylo genomic analysis to reconstruct virus transmission.

The research aims to safeguard human, wildlife, and agricultural health by developing diagnostics, therapeutics, and vaccines and providing training opportunities for students. The two-year cooperative agreement was awarded on August 1, 2023 to address gaps within USDA APHIS' mission to protect U.S. agriculture from disease and pests.

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 sequ ences deposited in gsaid will foster 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.)