'COVID-19' Incorporation of SARS-CoV-2 primers into a targeted NGS panel for surveillance use in cats

Project Summary SARS-CoV-2, the viral cause of COVID-19, has infected at least 94 pet cats in the United States, based on confirmed cases by the USDA. Many infections in cats are asymptomatic, and there are only a few ongoing surveillance studies in companion animals, so the number of cases in cats is likely higher. Cats are infected by SARS-CoV-2 from their human owners but have been shown experimentally to transmit the virus cat-to-cat. Once infected, at least experimentally, the virus quickly adapts in cats through genetic drift and positive selection at important residues within the spike protein, a protein used for cellular attachment. These adapted viruses are then spread to additional cats and maintained within the group. This can lead to accelerated fixation of potentially concerning variants for the human population if the virus is then able to re-infect humans. Additionally, cats may serve as a means for introducing variant viruses into wildlife populations based on their hunting behavior. Therefore, surveillance of cats for SARS-CoV-2 is warranted based on these considerations. Targeted surveillance should involve the interface of humans and animals, as this is most likely where these events will occur (infection of animals from humans with a potential of spillback to humans from animals). Pet cats in positive SARS-CoV-2 households are already known to be at risk for infection and should be included in a targeted active surveillance program involving domestic cats. Additionally, some cats show respiratory signs when infected with SARS-CoV-2, so the inclusion of SARS-CoV-2 testing, along with testing for the more likely pathogens that produce respiratory disease in cats, allows for additional passive surveillance. Cats submitted to diagnostic labs for necropsies can also easily be included in a surveillance program. To address surveillance needs, the Purdue Animal Disease Diagnostic Laboratory proposes to add SARS-CoV-2 primer sets to the targeted next-generation sequencing panel for detection of infectious diseases of dogs and cats. The amended panel will be validated for the detection of SARS-CoV-2 by using a set of sequenced positive samples, which contains all the current SARS-CoV-2 variants of interest and concern, as defined by the CDC. Additionally, nasal and oropharyngeal swabs will be collected from cats for surveillance testing based on the above criteria. These samples will be tested by both an approved RT-PCR for SARS-CoV-2 and the targeted NGS panel to determine the diagnostic sensitivity/specificity of the panel for detection of SARS-CoV-2. Additionally, any positive samples we obtain from the cats will be sequenced to evaluate variants associated with infection. Addition of this virus to commonly used panels for infectious diseases will allow for continued passive surveillance without the need to specifically request and obtain approval for the testing. This should enhance our detection of this virus in cats, potentially preventing the unwanted introduction or spread into new populations.