There is an urgent need for coronavirus (CoV) surveillance in both wildlife and livestock.
As seen repeatedly, CoVs have a propensity to jump species from their bat, rodent and
avian reservoirs, often to intermediate species including livestock, before infecting
humans. Our knowledge of North American CoVs in wildlife species is sparse and
routine sequencing of livestock CoVs are limited.
In our first aim, to detect and sequence coronaviruses in wildlife and livestock,
we will utilize a pan-coronavirus RT-PCR to screen a unique sample set consisting of
bats and wildlife rarely surveilled. The sample set is comprised of ~500 animals
submitted to our veterinary diagnostic laboratory for rabies testing over a 12-month
period and consists of pooled lung, spleen and intestine tissue homogenate. In parallel,
we will screen food animal diagnostic submissions from animals with acute enteric and
Our second aim, to further characterize coronavirus genomes and characterize
virus isolates, phylogenetic and recombination analysis will be performed with the
assembled CoV genomes. Specifically, assembled genomes will be annotated and
submitted to Genbank and made publicly available immediately. Phylogenetic analysis
will determine if SARS-CoV-2, CoVs similar to SARS-CoV-2 or novel CoVs have
emerged in non-human species. Recombination analysis will next be performed using
SARS-CoV-2 and the assembled CoV genomes to determine if SARS-CoV-2 or related
CoVs have undergone natural recombination and contributed genetic material to
endemic CoV. Another component of this aim is to isolate and propagate the detected
CoVs in cell culture. This latter aim is critical for further pathogenesis studies in the
natural host and model organisms.
This R21 exploratory project meets an urgent need for CoV surveillance at the
human-animal interface, both in wildlife and livestock. Results from this study will
identify emerging disease threats and develop critical tools, including sequences,
detection methodology and cell culture adapted viruses that will enable further studies
on possible zoonosis and enable preemptive action.