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

References

• Gibb R, Redding DW, Chin KQ, et al. Zoonotic host diversity increases in human-dominated ecosystems. Nature. 2020;584:398–402. doi:10.1038/s41586-020-2562-8.
   PubMed Web of Science ®Google Scholar
• Albery GF, Carlson CJ, Cohen LE, et al. Urban-adapted mammal species have more known pathogens. Nat Ecol Evol. 2022;6:794–801. doi:10.1038/s41559-022-01723-0.
   PubMed Web of Science ®Google Scholar
• Capizzi D, Bertolino S, Mortelliti A. Rating the rat: global patterns and research priorities in impacts and management of rodent pests. Mammal Rev. 2014;44:148–162. doi:10.1111/mam.12019.
   Web of Science ®Google Scholar
• Hassell JM, Begon M, Ward MJ, et al. Urbanization and disease emergence: dynamics at the wildlife–livestock–human interface. Trends Ecol Evol. 2017;32:55–67. doi:10.1016/j.tree.2017.08.008.
   PubMed Web of Science ®Google Scholar
• Su S, Shen J, Zhu L, et al. Involvement of digestive system in COVID-19: manifestation, pathology, management and challenges. Therap Adv Gastroenterol. 2020;13:1–12.
   Web of Science ®Google Scholar
• Wu Y, Guo C, Tang L, et al. Prolonged presence of SARS-CoV-2 viral RNA in faecal samples. Lancet Gastroenterol Hepatol. 2020;5:P434–P435. doi:10.1016/S2468-1253(20)30083-2.
   PubMed Web of Science ®Google Scholar
• Brown MR, Wade MJ, McIntrye-Nolan S, et al. (2020). Wastewater monitoring of SARS-CoV-2 variants in England: Demonstration case study for Bristol (Dec 2020 – March 2021). Summary for SAGE 8th April 2021. https://www.gov.uk/government/publications/jbc-and-defra-wastewater-monitoring-of-sars-cov-2-variants-in-england-demonstration-case-study-for-bristol-december-2020-to-march-2021-8-april-20.
   Google Scholar
• Karthikeyan S, Levy JI, De Hoff P, et al. Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission. Nature. 2022;609:101–108. doi:10.1038/s41586-022-05049-6.
   PubMed Web of Science ®Google Scholar
• Lau SK, Woo PC, Li KS, et al. Discovery of a novel coronavirus, China Rattus coronavirus HKU24, from Norway rats supports the murine origin of betacoronavirus 1 and has implications for the ancestor of betacoronavirus lineage A. J Virol. 2015;89:3076–3092. doi:10.1128/JVI.02420-14.
   PubMed Web of Science ®Google Scholar
• Ge XY, Yang WH, Zhou JH, et al. Detection of alpha- and betacoronaviruses in rodents from Yunnan, China. Virol J. 2017;14:98. doi:10.1186/s12985-017-0766-9.
   PubMed Web of Science ®Google Scholar
• Monchatre-Leroy E, Boué F, Boucher JM, et al. Identification of alpha and beta coronavirus in wildlife species in France: bats, rodents, rabbits, and hedgehogs. Viruses. 2017;9:364. doi:10.3390/v9120364.
   PubMed Web of Science ®Google Scholar
• Han BA, Schmidt JP, Bowden SE, et al. Rodent reservoirs of future zoonotic diseases. Proc Natl Acad Sci USA. 2015;112:7039–7044. doi:10.1073/pnas.1501598112.
   PubMed Web of Science ®Google Scholar
• Wardeh M, Baylis M, Blagrove MS. Predicting mammalian hosts in which novel coronaviruses can be generated. Nat Commun. 2021;12:1–12. doi:10.1038/s41467-020-20314-w.
   PubMed Web of Science ®Google Scholar
• Chan JF, Zhang AJ, Yuan S, et al. Simulation of the clinical and pathological manifestations of coronavirus disease 2019 (COVID-19) in a golden Syrian hamster model: implications for disease pathogenesis and transmissibility. Clin Infect Dis. 2020;71:2428–2446.
   PubMed Web of Science ®Google Scholar
• Fagre A, Lewis J, Eckley M, et al. SARS-CoV-2 infection, neuropathogenesis and transmission among deer mice: implications for spillback to New world rodents. PLoS Pathog. 2021;17:e1009585. doi:10.1371/journal.ppat.1009585.
   PubMed Web of Science ®Google Scholar
• Janik E, Niemcewicz M, Podogrocki M, et al. The emerging concern and interest SARS-CoV-2 variants. Pathogens. 2021;10:633. doi:10.3390/pathogens10060633.
   PubMed Web of Science ®Google Scholar
• Montagutelli X, Prot M, Levillayer L, et al. The B1.351 and P.1 variants extend SARS-CoV-2 host range to mice. bioRxiv 2021.03.18.436013. 2021. doi:10.1101/2021.03.18.436013.
   Google Scholar
• Gu H, Chen Q, Yang G, et al. Adaptation of SARS-CoV-2 in BALB/c mice for testing vaccine efficacy. Science. 2020;369:1603–1607. doi:10.1126/science.abc4730.
   PubMed Web of Science ®Google Scholar
• Huang K, Zhang Y, Hui X, et al. Q493k and Q498H substitutions in spike promote adaptation of SARS-CoV-2 in mice. EbioMed. 2021;67:103381. doi:10.1016/j.ebiom.2021.103381.
   PubMed Web of Science ®Google Scholar
• Huang H, Zhu Y, Niu Z, et al. SARS-CoV-2 N501Y variants of concern and their potential transmission by mouse. Cell Death Differ. 2021;28:2840–2842. doi:10.1038/s41418-021-00846-4.
   PubMed Web of Science ®Google Scholar
• Otto SP, Day T, Arnio J, et al. The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic. Curr Biol. 2021;31:R918–R929. doi:10.1016/j.cub.2021.06.049.
   PubMed Web of Science ®Google Scholar
• DEFRA. (2021). https://www.gov.uk/government/publications/jbc-and-defra-a-qualitative-risk-assessment-to-estimate-the-likelihood-of-sars-cov-2-infection-of-rodents-from-contact-with-the-environment-and-onwar.
   Google Scholar
• Colombo VC, Sluydts V, Mariën J, et al. SARS-CoV-2 surveillance in Norway rats (Rattus norvegicus) from Antwerp sewer system, Belgium. Transbound Emerg Dis. 2021;2021:1–6. doi:10.1111/tbed.14219
   Google Scholar
• Miot EF, Worthington BM, Ng KH, et al. Surveillance of rodent pests for SARS-CoV-2 and other coronaviruses, Hong Kong. Emerg Infect Dis. 2022;28:467–470. doi:10.3201/eid2802.211586.
   PubMed Web of Science ®Google Scholar
• Wang Y, Lenoch J, Kohler D, et al. SARS-CoV-2 exposure in Norway rats (Rattus norvegicus) from New York city. mBio. 2023;mBio 14:e03621–22. doi:10.1128/mbio.03621-22
   Web of Science ®Google Scholar
• Hadfield J, Megill C, Bell SM, et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics. 2018;34:4121–4123. nextstrain.org/ncov. doi:10.1093/bioinformatics/bty407
   PubMed Web of Science ®Google Scholar
• Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biol. 2019;20:257. doi:10.1186/s13059-019-1891-0.
   PubMed Web of Science ®Google Scholar
• Bankevich A, Nurk S, Antipov D, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comp Biol. 2012;19:455–477. doi:10.1089/cmb.2012.0021.
   PubMed Web of Science ®Google Scholar
• Artic. (2020). https://github.com/artic-network/primer-schemes/blob/master/nCoV-2019/V3/nCoV-2019.tsv.
   Google Scholar
• Yang J, Wang W, Chen Z, et al. A vaccine targeting the RBD of the S protein of SARS-CoV-2 induces protective immunity. Nature. 2020;586:572–577. doi:10.1038/s41586-020-2599-8.
   PubMed Web of Science ®Google Scholar
• Adaken C, Scott JT, Sharma R, et al. Ebola virus antibody decay–stimulation in a high proportion of survivors. Nature. 2021;590:468–472. doi:10.1038/s41586-020-03146-y.
   PubMed Web of Science ®Google Scholar
• Abolins S, King E, Lazarou L, et al. The comparative immunology of wild and laboratory mice Mus musculus domesticus. Nat Commun. 2017;8:14811. doi:10.1038/ncomms14811
   PubMed Web of Science ®Google Scholar
• Naderi S, Chen PE, Murall CL, et al. Zooanthroponotic transmission of SARS-CoV-2 and host-specific viral mutations revealed by genome-wide phylogenetic analysis. eLife. 2023;12:e83685. doi:10.7554/eLife.83685.
   PubMed Web of Science ®Google Scholar
• Phan TG, Kapusinszky B, Wang C, et al. The fecal viral flora of wild rodents. PLoS Pathog. 2011;7:e1002218. doi:10.1371/journal.ppat.1002218.
   PubMed Web of Science ®Google Scholar
• Sachsenröder J, Braun A, Machnowska P, et al. Metagenomic identification of novel enteric viruses in urban wild rats and genome characterization of a group A rotavirus. J Gen Virol. 2014;95:2734–2747. doi:10.1099/vir.0.070029-0.
   PubMed Web of Science ®Google Scholar
• Tsoleridis T, Onianwa O, Horncastle E, et al. Discovery of novel alphacoronaviruses in European rodents and shrews. Viruses. 2016;8:84.
   PubMed Web of Science ®Google Scholar
• Tsoleridis T, Chappell JG, Onianwa O, et al. Shared common ancestry of rodent alphacoronaviruses sampled globally. Viruses. 2019;11:125. doi:10.3390/v11020125.
   PubMed Web of Science ®Google Scholar
• Kumakamba C, Niama FR, Muyembe F, et al. Coronavirus surveillance in wildlife from two Congo basin countries detects RNA of multiple species circulating in bats and rodents. PLoS One. 2021;16m:e0236971.
   Google Scholar
• Wang W, Lin XD, Guo WP, et al. Discovery, diversity and evolution of novel coronaviruses sampled from rodents in China. Virology. 2015;474:19–27. doi:10.1016/j.virol.2014.10.017.
   PubMed Web of Science ®Google Scholar
• Wang W, Lin XD, Zhang HL, et al. Extensive genetic diversity and host range of rodent-borne coronaviruses. Virus Evol. 2020;6:veaa078.
   PubMed Web of Science ®Google Scholar
• Monastiri A, Martín-Carrillo N, Foronda P, et al. First coronavirus active survey in rodents from the canary islands. Front Vet Sci. 2021;8:708079. doi:10.3389/fvets.2021.708079.
   PubMed Web of Science ®Google Scholar
• Easterbrook JD, Kaplan JB, Glass GE, et al. A survey of rodent-borne pathogens carried by wild-caught Norway rats: A potential threat to laboratory rodent colonies. Lab Anim (NY). 2008;42:92–98. doi:10.1258/la.2007.06015e.
   Web of Science ®Google Scholar
• Corman VM, Kallies R, Philipps H, et al. Characterization of a novel betacoronavirus related to Middle East respiratory syndrome coronavirus in European hedgehogs. J Virol. 2014;88:717–724. doi:10.1128/JVI.01600-13.
   PubMed Web of Science ®Google Scholar
• Saldanha Lawson IF, Goharriz B, Rodriguez-Ramos H, et al. Extension of the known distribution of a novel clade C betacoronavirus in a wildlife host. Epidemiol Infect. 2019;147:e169. doi:10.1017/S0950268819000207.
   PubMed Web of Science ®Google Scholar
• Widagdo W, Sooksawasdi Na Ayudhya S, Hundie GB, et al. Host determinants of MERS-CoV transmission and pathogenesis. Viruses. 2019;11:280. doi:10.3390/v11030280.
   PubMed Web of Science ®Google Scholar
• Vaheri A, Strandin T, Hepojoki J, et al. Uncovering the mysteries of hantavirus infections. Nat Rev Microbiol. 2013;11:539–550. doi:10.1038/nrmicro3066.
   PubMed Web of Science ®Google Scholar
• Dupinay T, Pounder KC, Ayral F, et al. Detection and genetic characterization of Seoul virus from commensal brown rats in France. Virol J. 2014;11:32. doi:10.1186/1743-422X-11-32.
   PubMed Web of Science ®Google Scholar
• McElhinney LM, Marston DA, Pounder KC, et al. High prevalence of Seoul hantavirus in a breeding colony of pet rats. Epidemiol Infect. 2017;145:3115–3124. doi:10.1017/S0950268817001819.
   PubMed Web of Science ®Google Scholar
• Ling J, Verner-Carlsson J, Eriksson P, et al. Genetic analyses of Seoul hantavirus genome recovered from rats (Rattus norvegicus) in The Netherlands unveils diverse routes of spread into Europe. J Med Virol. 2019;91:724–730. doi:10.1002/jmv.25390.
   PubMed Web of Science ®Google Scholar
• Murphy EG, Williams NJ, Bennett M, et al. Detection of Seoul virus in wild brown rats (Rattus norvegicus) from pig farms in Northern England. Vet Record. 2019;184:525–525. doi:10.1136/vr.105249.
   PubMed Web of Science ®Google Scholar
• Chen L, Liu B, Wu Z, et al. DRodvir: A resource for exploring the virome diversity in rodents. J Genet Genomics. 2017;44:259–264. doi:10.1016/j.jgg.2017.04.004.
   PubMed Web of Science ®Google Scholar