Rats are Another Animal Link in the COVID-19 Chain

A new study shows there are currently 8 million wild animals in New York City with the potential to incite secondary zoonotic transmission of SARS-CoV-2 to humans, including new variants the human population has not encountered yet.

“Rats likely play an important role in the evolution of Alpha, Delta, Omicron variants, which has the potential to result in the emergence of new variants in rats that are naive to the human population and may contain properties harmful to humans,” a multi-institutional research team writes in their newest study on SARS-CoV-2 in wild rats in NYC.

It is estimated that New York City has approximately 8 million wild rats inhabiting the sewer systems, mass transit routes and elsewhere. With that being the case, were the rats susceptible to reverse zoonosis of SARS-CoV-2 during the height of the pandemic in NYC?

To answer that question, a team of researchers from the USDA's Wildlife Services National Wildlife Disease Program, University of Missouri, Walter Reed Army Institute of Research, Rice University and Yale University captured 79 rats in September and November 2021. Most of the rats were trapped in city parks within Brooklyn, although some were captured near buildings outside of park boundaries.

According to the study results, published in mBio, 13 of the 79 rats—or 16.5%—tested IgG- or IgM-positive. In addition, 4 samples were qRT-PCR-positive for SARS-CoV-2, and the team was able to recover partial genomes from all four samples. Subsequent genomic analyses showed that the detected viruses were associated with genetic lineage B, which was predominant in NYC in the spring of 2020 during the early pandemic period.

“We speculate that these B-lineage viruses are enzootic in rat populations after being introduced to the NYC rat populations during the early stages of the pandemic, or that rats could have been exposed to the B-lineage viruses present in unknown sources,” explain the researchers.

To gather more information on rat susceptibility to SARS-CoV-2 variants, the scientists conducted a virus challenge study. The tests confirmed the Alpha, Delta and Omicron variants not only cause infections in wild-type rats, but also replicate to high levels in both the upper and lower respiratory tracts of the rats.

Of the three variants, Delta replicated the most efficiently, while Omicron replicated the least efficiently compared with both Alpha and Delta. This finding is consistent with earlier literature—and real-world observations—that showed Omicron was less harmful to mouse models and humans compared with its predecessor variants.

“Our findings highlight the need for further monitoring of SARS-CoV-2 in rat populations to determine if the virus is circulating in the animals and evolving into new strains that could pose a risk to humans,” said study principal investigator Henry Wan, director of the Center for Influenza and Emerging Infectious Diseases at the University of Missouri. “SARS-CoV-2 virus presents a typical one-health challenge which requires collaborative, multisectoral and transdisciplinary approaches to fully understand such challenges.”