PARTNERSHIP: Rapid Detection of Incursions of SARS-CoV-2 and Novel Coronaviruses on Texas Meat and Dairy Farms

The SARS-CoV-2 pandemic markedly compromised national food security through explosive outbreaks among agriculture workers.1 Two years into the pandemic, sustained transmission of SARS-CoV-2 in humans, again threatens US livestock systems as the viruses are spilling over to new domestic animal and wildlife species. As of August 2022, human-adapted SARS-CoV-2 has infected at least 27 unique animals species in 39 countries.2,3 These spillbacks have occurred in at least 30 U.S. states with the greatest number (n=108) documented in Texas.4 Although evidence has been mixed, research findings suggest that some strains of SARS-CoV-2 may infect livestock including pigs4-10 and cattle.11-13 Adding to these threats, novel coronaviruses continue to circulate among livestock herds in Asia14,15 that may soon cause incursions in the United States. Even so, virtually no active surveillance for novel coronavirus is being conducted in US agriculture systems. Barriers include surveillance cost and the lack of broad diagnostics to detect novel coronavirus incursions on farms. In this proposal we will demonstrate that we can use a low-cost pan-species assay we developed16 and a similar commercial product as new biosecurity tools on livestock farms. We will also characterize novel coronaviruses we detect to understand how they may be spilling over to new species. We are well-positioned to perform this work as our team has detected multiple spillover events, including the 2009 H1N1 pandemic virus among pigs,17 H3N8 equine influenza A virus among camels,18 evidence of influenza D virus among poultry,19 human enteroviruses among pigs,20 novel zoonotic coronaviruses,16 and a vampire-bat-like adenovirus21 among humans. Recently, we cultured and fully sequenced a novel canine-like alpha-coronavirus from hospitalized pneumonia patients in Sarawak, Malaysia.22 As this virus was later found by another research team to be a cause of respiratory disease in Haiti,23 it appears that this virus is the 8th coronavirus recognized to infect humans.24-26 Indeed, this virus could be a pre-pandemic threat itself. Additionally, our veterinary co-investigator Professor Sarah Hamer has considerable coronavirus experience in that she has documented more than 100 of the 108 SARS-CoV-2 infections in animals in Texas.27,28 In this proposal, we seek support to continue conducting One Health-focused surveillance for novel respiratory viruses among livestock farms in Texas.