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 for humans. During the human COIVD pandemic there was also the possibility of rodents acquiring SARS-CoV-2 from people, so-called reverse zoonoses. To investigate this we have 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 neutralisation ability, that are consistent with rats being exposed to SARS-CoV-2 and / or exposed to other viruses that result in cross-reactive antibodies.

SARS-CoV-2 and other coronaviruses in rats, Berlin, Germany, 2023

“…Virus typing based on the partial RdRp sequences revealed that the viruses found in Berlin rats belong to the genus Alphacoronavirus and are closely related to each other (99.4-100.0% identity on nucleotide level) and to the Lucheng Rn rat coronavirus (Figure 1B). Hence, in contrast to SARS-CoV-2, rodent-associated alphacoronaviruses appear to circulate in the investigated rat population, which is in line with previous studies investigating coronaviruses in rats (2,5).…”

“…Since the pandemic unfolded, it was speculated about the role of animals as amplifying or reservoir hosts. Because of the long-term association between rodents and coronaviruses (1) , the wide range of coronaviruses occurring in wild rodents (2) and the ubiquitous distribution of commensal rodents, it was obvious to also include rodents in susceptibility studies, among them rats. Under experimental conditions using high infection doses, rats were reported as receptive particularly to the SARS-CoV-2 delta variant of concern (VOC), but also experimental infection with other variants like alpha, beta or omicron were described (3,4) , posing the theoretical risk for establishing effective infection chains in nature.…”

“…Accordingly, field studies were initiated early into the pandemic to investigate the situation in wild rats. Indeed, serological and molecular evidences of SARS-CoV-2 infection of a few animals could be found in some studies (2,3,5), while others reported consistently negative results (6,7). However, these studies were conducted before the emergence and worldwide large-scale spread of the omicron VOC and its diverse subvariants.…”

Lack of detection of SARS-CoV-2 in British wildlife 2020–21 and first description of a stoat (Mustela erminea) Minacovirus

“…SARS-CoV-2 infection in Muridae such as house mice (Mus musculus) and brown rats (Rattus norvegicus) may depend on the virus strain: initial studies with the original (Wuhan) strains of the virus failed to infect them [20,21] and field studies failed to demonstrate evidence of infection in wild populations (27 Mus musculus and 97 R. norvegicus). Later variants did however cause infection in laboratory studies [21][22][23][24] and there have been several subsequent field reports of sporadic infection of rats [25][26][27].…”

Lack of detection of SARS-CoV-2 in British wildlife 2020-21 and first description of a stoat (Mustela erminea) Minacovirus

“…SARS-CoV-2 infection in Muridae such as house mice (Mus musculus) and brown rats (Rattus norvegicus) may depend on the virus strain: initial studies with the original (Wuhan) strains of the virus failed to infect them (Dinnon, Leist et al 2020, Shuai, Chan et al 2021 and field studies failed to demonstrate evidence of infection in wild populations (27 M.musculus and 97 R.Norvegicus). Later variants did however cause infection in laboratory studies (Gu, Chen et al 2020, Shuai, Chan et al 2021, Halfmann, Iida et al 2022, Zhang, Cui et al 2022 and there have been several subsequent t field reports of sporadic infection of rats (Fisher, Airey et al 2023, Robinson, Kotwa et al 2023, Wang, Lenoch et al 2023).…”