Detection of zoonotic pathogens and characterization of novel viruses carried by commensal Rattus norvegicus in New York City

Abstract

Norway rats (Rattus norvegicus) are globally distributed and concentrate in urban environments, where they live and feed in closer proximity to human populations than most other mammals. Despite the potential role of rats as reservoirs of zoonotic diseases, the microbial diversity present in urban rat populations remains unexplored. In this study, we used targeted molecular assays to detect known bacterial, viral, and protozoan human pathogens and unbiased high-throughput sequencing to identify novel viruses related to agents of human disease in commensal Norway rats in New York City. We found that these rats are infected with bacterial pathogens known to cause acute or mild gastroenteritis in people, including atypical enteropathogenic Escherichia coli, Clostridium difficile, and Salmonella enterica, as well as infectious agents that have been associated with undifferentiated febrile illnesses, including Bartonella spp., Streptobacillus moniliformis, Leptospira interrogans, and Seoul hantavirus. We also identified a wide range of known and novel viruses from groups that contain important human pathogens, including sapoviruses, cardioviruses, kobuviruses, parechoviruses, rotaviruses, and hepaciviruses. The two novel hepaciviruses discovered in this study replicate in the liver of Norway rats and may have utility in establishing a small animal model of human hepatitis C virus infection. The results of this study demonstrate the diversity of microbes carried by commensal rodent species and highlight the need for improved pathogen surveillance and disease monitoring in urban environments. Importance: The observation that most emerging infectious diseases of humans originate in animal reservoirs has led to wide-scale microbial surveillance and discovery programs in wildlife, particularly in the developing world. Strikingly, less attention has been focused on commensal animals like rats, despite their abundance in urban centers and close proximity to human populations. To begin to explore the zoonotic disease risk posed by urban rat populations, we trapped and surveyed Norway rats collected in New York City over a 1-year period. This analysis revealed a striking diversity of known pathogens and novel viruses in our study population, including multiple agents associated with acute gastroenteritis or febrile illnesses in people. Our findings indicate that urban rats are reservoirs for a vast diversity of microbes that may affect human health and indicate a need for increased surveillance and awareness of the disease risks associated with urban rodent infestation.

FIG 1

Viral RNA quantification and phylogenetic relationships of SEOV Baxter. (A) Quantification of SEOV Baxter RNA in tissue, oral swab, and serum samples from infected animals collected in this study. Viral RNA copy numbers were calculated per copy of GAPDH for tissue samples or per 1 ml for serum and oral swab samples. (B) MCC tree showing close phylogenetic relationships between SEOV Baxter and viruses from the United Kingdom and China. Estimated times to most recent common ancestor are shown in years above the nodes leading to SEOV Baxter, with the associated 95% highest probability density values in parentheses. Branch colors correspond to countries for which N gene sequences of SEOV were available for analysis, and BPP values of ≥0.7 are shown beneath the associated nodes.

FIG 2

Phylogenetic relationships and strand-specific RNA quantification of the flaviviruses. (A) Unrooted ML tree of a highly conserved region of the NS5B protein (340-aa) of representative members of the Flaviviridae family. Grey circles indicate genera, and the four viruses characterized in this study are indicated by red branches. Nodal support is shown beneath associated nodes when both BSP and BPP values are ≥70% in the format BSP/BPP. TABV, Tamana bat virus. The scale bar is in units of substitutions per site. (B) ML tree of the complete NS5B gene of all members of the Pegivirus and Hepacivirus genera, showing the relative positions of NrPgV, NrHV-1, and NrHV-2 (red branches). For clarity, nodal support values are indicated by an asterisk when both BSP and BPP values were ≥70%. The scale bar is in units of substitutions per site. Viruses previously identified in rodents are indicated by the relevant species name (e.g., Neotoma sp., Myodes sp., Rhabdomys sp., Peromyscus sp.). BPgV, bat pegivirus; GBV-A to -D, GB viruses A to D or GB virus C troglodytes; EqPgV, equine pegivirus; BHV, bat hepacivirus; Guereza, guereza hepacivirus; NPHV, nonprimate hepacivirus. (C) ML tree of the complete NS5B gene of all members of the Pestivirus genus, indicating the basal position of NrPV (red branch). For clarity, nodal support values are indicated by an asterisk when both BSP and BPP values were ≥70%. Bungo, Bungowannah virus; BVDV, bovine viral diarrhea virus; Giraffe-1, Giraffe-1 pestivirus; Th/04, TH/04_KhonKaen atypical pestivirus; CSFV, classical swine fever virus; BDV, border disease virus. The scale bar is in units of substitutions per site. (D) ssqPCR quantification of NrHV-1 and NrHV-2 positive- and negative-sense RNA, indicated by + or −, respectively. Viral RNA copy numbers were calculated per 250 ng of tissue or 1 ml of serum.

FIG 3

Phylogenetic relationships of the picornaviruses. (A) Unrooted ML tree of a highly conserved, 385-aa region of the RdRp of the eight picornaviruses identified here (red branches) and select representatives of all picornavirus genera (gray circles). For clarity, when BSP and BPP values were both ≥70%, the nodal support is indicated by an asterisk. EMCV, encephalomyocarditis virus; PeV, parechovirus; Sebokele 1, Sebokele virus 1; Ljungan, Ljungan virus. (B) ML tree of the complete VP1 protein of NrKoV-1 and NrKoV-2 (red branches), as well as representatives of the Kobuvirus genus. When the BSP and BPP values are both ≥70%, nodal support is shown beneath the associated node in the format BSP/BPP. Scale bar is in substitutions/site.

FIG 4

ML tree based on complete VP1 gene sequences of Ro-SaV1 and Ro-SaV2 (red branches) and representatives of the Sapovirus genus. Human sapovirus (Hu-SaV) and porcine sapovirus (Po-SaV) genogroups are indicated. When the BSP and BPP values are both ≥70%, nodal support is shown beneath the associated node in the format BSP/BPP. Scale bar is in substitutions/site.