The ecology of viruses in urban rodents with a focus on SARS-CoV-2

ABSTRACT

Wild animals are naturally infected with a range of viruses, some of which may be zoonotic. During the human COVID pandemic there was also the possibility of rodents acquiring SARS-CoV-2 from people, so-called reverse zoonoses. To investigate this, we sampled rats (Rattus norvegicus) and mice (Apodemus sylvaticus) from urban environments in 2020 during the human COVID-19 pandemic. We metagenomically sequenced lung and gut tissue and faeces for viruses, PCR screened for SARS-CoV-2, and serologically surveyed for anti-SARS-CoV-2 Spike antibodies. We describe the range of viruses that we found in these two rodent species. We found no molecular evidence of SARS-CoV-2 infection, though in rats we found lung antibody responses and evidence of neutralization ability that are consistent with rats being exposed to SARS-CoV-2 and/or exposed to other viruses that result in cross-reactive antibodies.

KEYWORDS:

• Urban
• rodents
• virus
• virome
• COVID
• zoonosis
• SARS-CoV-2

Acknowledgments

We would like to thank Mark Garth, Adam Johnson and colleagues for assistance with trapping; Alex Wade for help in obtaining rodent samples; David Hall, Simon King and Andy Brigham from the pest control industry for help and advice; Sam Haldenby for bioinformatics advice; Eleanor Riley for advice and discussions; James Stewart for help with the control immunizations. This work was funded by a grant from NERC (NE/V009028/1) and funds from the University of Liverpool. EGB is supported by the University of Liverpool; YL is supported by the University of Liverpool and the China Scholarship Council.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This work was supported by Natural Environment Research Council.