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Zhang M, Fan S, Liang M, Wu R, Tian J, Xian J, Zhou X, Chen Q. A panoramic view of the molecular epidemiology, evolution, and cross-species transmission of rosaviruses. Vet Res 2024; 55:145. [PMID: 39516900 PMCID: PMC11545274 DOI: 10.1186/s13567-024-01399-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 09/07/2024] [Indexed: 11/16/2024] Open
Abstract
Rosavirus is a newly discovered member of the family Picornaviridae that was initially detected in wild rodents and subsequently in children with diarrhoea. Nevertheless, there is a significant gap in our understanding of the geographical distribution, phylogenetic relationships, evolutionary patterns, and transmission of rosaviruses. To address these issues, we analysed 434 rodents and shrews from five different species that were collected in southern China. Using PCR screening of faecal samples, we detected rosaviruses in Norway rats (Rattus norvegicus) and identified two previously undocumented host species: tanezumi rats (Rattus tanezumi) and Asian house shrews (Suncus murinus). Rosaviruses were particularly common in these animals, with an overall prevalence rate of 32.49% (141/434). For genetic and evolutionary analyses, we selected six representative positive samples to amplify the complete genomes of rosaviruses. Bayesian phylogenetic analysis suggested that our sequences clustered within the genus Rosavirus, where genotype B sequences are the closest relatives. The elevated nonsynonymous-to-synonymous ratios observed in rosavirus B may be attributed to relaxed selection pressures driven by virus spillover events. On the basis of the available data, it is hypothesized that the genus Rosavirus may have originated from Norway rats around the year 1339. In summary, these findings provide valuable insights into the complex evolutionary history of rosaviruses and underscore the urgent need for ongoing surveillance of this virus.
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Affiliation(s)
- Minyi Zhang
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Shunchang Fan
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Minyi Liang
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Ruojun Wu
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Jingli Tian
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Juxian Xian
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Xiaofeng Zhou
- Department of Epidemiology and Infectious Disease Control, Longhua Centre for Disease Control and Prevention, Shenzhen, 518109, China
| | - Qing Chen
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China.
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2
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Boros Á, Orlovácz K, Pankovics P, Szekeres S, Földvári G, Fahsbender E, Delwart E, Reuter G. Diverse picornaviruses are prevalent among free-living and laboratory rats (Rattus norvegicus) in Hungary and can cause disseminated infections. INFECTION GENETICS AND EVOLUTION 2019; 75:103988. [PMID: 31377399 DOI: 10.1016/j.meegid.2019.103988] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/24/2019] [Accepted: 07/31/2019] [Indexed: 12/28/2022]
Abstract
In this study, the full length genomes of three phylogenetically distant picornaviruses (family Picornaviridae) belonging to the genus Rosavirus (rat08/rRoB/HUN, MN116648), Kobuvirus (rat08/rAiA/HUN, MN116647), and Cardiovirus (rat08/rCaB/HUN, MN116646) were obtained from a single faecal sample of a free-living Norway rat (Rattus norvegicus) in Hungary using viral metagenomics and RT-PCR/Sanger sequencing. The acquired complete genomes were in silico analyzed in detail revealing the presence of a second minor open reading frame encoding an alternative Leader peptide (L*) in rat08/rCaB/HUN and a ca. 222 nt-long sequence repeat with compact secondary RNA structure in the 3' UTR of rat08/rRoB/HUN. The studied rat picornaviruses were frequently detectable by RT-PCR with relatively high viral loads ranged between 8.99E+02 and 1.29E+06 copies/ml in rat faecal samples collected from five geographically distant locations throughout Hungary. The VP1 sequence-based phylogenetic analyses show the presence of multiple, mostly location-specific lineages for all three picornaviruses. Rat rosavirus and rat cardiovirus were identified in spleen while rat cardiovirus was also detected in liver, muscle and kidney samples with variable copy numbers (6.42E+01-1.90E+05 copies/μg total RNA) suggesting extra-intestinal dissemination. Both viruses were also prevalent (70.0% and 18.2%) among two populations of laboratory rats ("Wistar-type" and "hooded-type") held in different, isolated laboratory animal units.
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Affiliation(s)
- Ákos Boros
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs Pécs, Hungary
| | - Katalin Orlovácz
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs Pécs, Hungary
| | - Péter Pankovics
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs Pécs, Hungary
| | - Sándor Szekeres
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, Hungary
| | - Gábor Földvári
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, Hungary; Evolutionary Systems Research Group MTA Centre for Ecological Research, Tihany, Hungary
| | | | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA, USA; University of California, San Francisco, CA, USA
| | - Gábor Reuter
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs Pécs, Hungary.
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Lau SKP, Woo PCY, Li KSM, Zhang HJ, Fan RYY, Zhang AJX, Chan BCC, Lam CSF, Yip CCY, Yuen MC, Chan KH, Chen ZW, Yuen KY. Identification of Novel Rosavirus Species That Infects Diverse Rodent Species and Causes Multisystemic Dissemination in Mouse Model. PLoS Pathog 2016; 12:e1005911. [PMID: 27737017 PMCID: PMC5063349 DOI: 10.1371/journal.ppat.1005911] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/02/2016] [Indexed: 01/14/2023] Open
Abstract
While novel picornaviruses are being discovered in rodents, their host range and pathogenicity are largely unknown. We identified two novel picornaviruses, rosavirus B from the street rat, Norway rat, and rosavirus C from five different wild rat species (chestnut spiny rat, greater bandicoot rat, Indochinese forest rat, roof rat and Coxing's white-bellied rat) in China. Analysis of 13 complete genome sequences showed that “Rosavirus B” and “Rosavirus C” represent two potentially novel picornavirus species infecting different rodents. Though being most closely related to rosavirus A, rosavirus B and C possessed distinct protease cleavage sites and variations in Yn-Xm-AUG sequence in 5’UTR and myristylation site in VP4. Anti-rosavirus B VP1 antibodies were detected in Norway rats, whereas anti-rosavirus C VP1 and neutralizing antibodies were detected in Indochinese forest rats and Coxing's white-bellied rats. While the highest prevalence was observed in Coxing's white-bellied rats by RT-PCR, the detection of rosavirus C from different rat species suggests potential interspecies transmission. Rosavirus C isolated from 3T3 cells causes multisystemic diseases in a mouse model, with high viral loads and positive viral antigen expression in organs of infected mice after oral or intracerebral inoculation. Histological examination revealed alveolar fluid exudation, interstitial infiltration, alveolar fluid exudate and wall thickening in lungs, and hepatocyte degeneration and lymphocytic/monocytic inflammatory infiltrates with giant cell formation in liver sections of sacrificed mice. Since rosavirus A2 has been detected in fecal samples of children, further studies should elucidate the pathogenicity and emergence potential of different rosaviruses. We identified two novel picornaviruses, rosavirus B and C, infecting street and wild rats respectively in China. While rosavirus B was detected from Norway rats, rosavirus C was detected from five different wild rat species (chestnut spiny rat, greater bandicoot rat, Indochinese forest rat, roof rat and Coxing's white-bellied rat) by RT-PCR. Anti-rosavirus B antibodies were detected in Norway rats, whereas anti-rosavirus C antibodies were detected in Indochinese forest rats and Coxing's white-bellied rats, supporting potential interspecies transmission of rosavirus C. Genome analysis supported the classification of rosavirus B and C as two novel picornavirus species, with genome features distinct from rosavirus A. Rosavirus C isolated from 3T3 cells causes multisystemic diseases in a mouse model, with viruses and pathologies detected in various organs of infected mice after oral or intracerebral inoculation. Our results extend our knowledge on the host range and pathogenicity of rodent picornaviruses.
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Affiliation(s)
- Susanna K. P. Lau
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Patrick C. Y. Woo
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Kenneth S. M. Li
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Hao-Ji Zhang
- Department of Veterinary Medicine, Foshan University, Foshan, China
| | - Rachel Y. Y. Fan
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Anna J. X. Zhang
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Brandon C. C. Chan
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Carol S. F. Lam
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Cyril C. Y. Yip
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Ming-Chi Yuen
- Food and Environmental Hygiene Department, Hong Kong, China
| | - Kwok-Hung Chan
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Zhi-Wei Chen
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
- * E-mail:
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Asnani M, Pestova TV, Hellen CUT. Initiation on the divergent Type I cadicivirus IRES: factor requirements and interactions with the translation apparatus. Nucleic Acids Res 2016; 44:3390-407. [PMID: 26873921 PMCID: PMC4838371 DOI: 10.1093/nar/gkw074] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 01/29/2016] [Indexed: 01/03/2023] Open
Abstract
Cadicivirus (CDV) is unique amongst picornaviruses in having a dicistronic genome with internal ribosomal entry sites (IRESs) preceding both open reading frames. Here, we investigated initiation on the 5'-terminal IRES. We report that the 982-nt long 5'UTR comprises 12 domains (d1-d12), five of which (d8-d12, nts 341-950) constitute a divergent Type I IRES. It comprises central elements (the apex of d10, d11 and the following polypyrimidine tract) that are homologous to corresponding elements in canonical Type 1 IRESs, and non-canonical flanking domains (d8, d9 and d12). In vitro reconstitution revealed that as with canonical Type I IRESs, 48S complex formation requires eukaryotic initiation factors (eIFs) 1, 1A, 2, 3, 4A, 4B and 4G, and the poly(C) binding protein 2 (PCBP2), and starts with specific binding of eIF4G/eIF4A to d11. However, in contrast to canonical Type I IRESs, subsequent recruitment of 43S ribosomal complexes does not require direct interaction of their eIF3 constituent with the IRES-bound eIF4G. On the other hand, the CDV IRES forms a 40S/eIF3/IRES ternary complex, with multiple points of contact. These additional interactions with translational components could potentially stimulate recruitment of the 43S complex and alleviate the necessity for direct eIF4G/eIF3 interaction.
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Affiliation(s)
- Mukta Asnani
- Department of Cell Biology, SUNY Downstate Medical Center, 450 Clarkson Avenue, MSC44, Brooklyn, NY 11203, USA
| | - Tatyana V Pestova
- Department of Cell Biology, SUNY Downstate Medical Center, 450 Clarkson Avenue, MSC44, Brooklyn, NY 11203, USA
| | - Christopher U T Hellen
- Department of Cell Biology, SUNY Downstate Medical Center, 450 Clarkson Avenue, MSC44, Brooklyn, NY 11203, USA
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Genome analysis of a novel, highly divergent picornavirus from common kestrel (Falco tinnunculus): the first non-enteroviral picornavirus with type-I-like IRES. INFECTION GENETICS AND EVOLUTION 2015; 32:425-31. [PMID: 25864424 DOI: 10.1016/j.meegid.2015.04.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 04/02/2015] [Accepted: 04/03/2015] [Indexed: 12/23/2022]
Abstract
Although the number of identified avian-borne picornaviruses (family Picornaviridae) is continuously increasing there remains several species-rich avian host groups, such as the order Falconiformes (with 290 bird species) from which picornaviruses have not been identified. This study reports the first complete genome of a novel, highly divergent picornavirus, named as Falcovirus A1 (KP230449), from the carnivorous bird, the common kestrel (Falco tinnunculus, order Falconiformes). Falcovirus A1 has the longest 3D(RdRp) genome region and distant phylogenetic relationship to the Hepatitis A virus 1 (Hepatovirus) and Avian encephalomyelitis virus 1 (Tremovirus). It has a type-I (enterovirus-like) IRES in the 5'UTR - identified for the first time among avian-borne picornaviruses suggesting that type-I IRES is not restricted only to enteroviruses and providing further evidence of mosaicism of this region among different picornavirus genera.
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Asnani M, Kumar P, Hellen CUT. Widespread distribution and structural diversity of Type IV IRESs in members of Picornaviridae. Virology 2015; 478:61-74. [PMID: 25726971 DOI: 10.1016/j.virol.2015.02.016] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 02/05/2015] [Accepted: 02/09/2015] [Indexed: 01/13/2023]
Abstract
Picornavirus genomes contain internal ribosomal entry sites (IRESs) that promote end-independent translation initiation. Five structural classes of picornavirus IRES have been identified, but numerous IRESs remain unclassified. Here, previously unrecognized Type IV IRESs were identified in members of three proposed picornavirus genera (Limnipivirus, Pasivirus, Rafivirus) and four recognized genera (Kobuvirus, Megrivirus, Sapelovirus, Parechovirus). These IRESs are ~230-420 nucleotides long, reflecting heterogeneity outside a common structural core. Closer analysis yielded insights into evolutionary processes that have shaped contemporary IRESs. The presence of related IRESs in diverse genera supports the hypothesis that they are heritable genetic elements that spread by horizontal gene transfer. Recombination likely also accounts for the exchange of some peripheral subdomains, suggesting that IRES evolution involves incremental addition of elements to a pre-existing core. Nucleotide conservation is concentrated in ribosome-binding sites, and at the junction of helical domains, likely to ensure orientation of subdomains in an active conformation.
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Affiliation(s)
- Mukta Asnani
- Department of Cell Biology, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA
| | - Parimal Kumar
- Department of Cell Biology, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA
| | - Christopher U T Hellen
- Department of Cell Biology, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA.
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7
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Sasaki M, Orba Y, Ueno K, Ishii A, Moonga L, Hang'ombe BM, Mweene AS, Ito K, Sawa H. Metagenomic analysis of the shrew enteric virome reveals novel viruses related to human stool-associated viruses. J Gen Virol 2014; 96:440-452. [PMID: 25381053 DOI: 10.1099/vir.0.071209-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Shrews are small insectivorous mammals that are distributed worldwide. Similar to rodents, shrews live on the ground and are commonly found near human residences. In this study, we investigated the enteric virome of wild shrews in the genus Crocidura using a sequence-independent viral metagenomics approach. A large portion of the shrew enteric virome was composed of insect viruses, whilst novel viruses including cyclovirus, picornavirus and picorna-like virus were also identified. Several cycloviruses, including variants of human cycloviruses detected in cerebrospinal fluid and stools, were detected in wild shrews at a high prevalence rate. The identified picornavirus was distantly related to human parechovirus, inferring the presence of a new genus in this family. The identified picorna-like viruses were characterized as different species of calhevirus 1, which was discovered previously in human stools. Complete or nearly complete genome sequences of these novel viruses were determined in this study and then were subjected to further genetic characterization. Our study provides an initial view of the diversity and distinctiveness of the shrew enteric virome and highlights unique novel viruses related to human stool-associated viruses.
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Affiliation(s)
- Michihito Sasaki
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Keisuke Ueno
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Akihiro Ishii
- Hokudai Center for Zoonosis Control in Zambia, PO Box 32379, Lusaka, Zambia
| | - Ladslav Moonga
- Department of Paraclinical Studies, School of Veterinary and Medicine, University of Zambia, PO Box 32379, Lusaka, Zambia
| | - Bernard M Hang'ombe
- Department of Paraclinical Studies, School of Veterinary and Medicine, University of Zambia, PO Box 32379, Lusaka, Zambia
| | - Aaron S Mweene
- Department of Disease Control, School of Veterinary and Medicine, University of Zambia, PO Box 32379, Lusaka, Zambia
| | - Kimihito Ito
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Hirofumi Sawa
- Global Institution for Collaborative Research and Education, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan.,Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
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8
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Detection of zoonotic pathogens and characterization of novel viruses carried by commensal Rattus norvegicus in New York City. mBio 2014; 5:e01933-14. [PMID: 25316698 PMCID: PMC4205793 DOI: 10.1128/mbio.01933-14] [Citation(s) in RCA: 294] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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. 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.
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Sachsenröder J, Braun A, Machnowska P, Ng TFF, Deng X, Guenther S, Bernstein S, Ulrich RG, Delwart E, Johne R. 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. [PMID: 25121550 DOI: 10.1099/vir.0.070029-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Rats are known as reservoirs and vectors for several zoonotic pathogens. However, information on the viruses shed by urban wild rats that could pose a zoonotic risk to human health is scare. Here, intestinal contents from 20 wild Norway rats (Rattus norvegicus) collected in the city of Berlin, Germany, were subjected to metagenomic analysis of viral nucleic acids. The determined faecal viromes of rats consisted of a variety of known and unknown viruses, and were highly variable among the individuals. Members of the families Parvoviridae and Picobirnaviridae represented the most abundant species. Novel picornaviruses, bocaviruses, sapoviruses and stool-associated circular ssDNA viruses were identified, which showed only low sequence identity to known representatives of the corresponding taxa. In addition, noroviruses and rotaviruses were detected as potential zoonotic gastroenteritis viruses. However, partial-genome sequence analyses indicated that the norovirus was closely related to the recently identified rat norovirus and the rotavirus B was closely related to the rat rotavirus strain IDIR; both viruses clustered separately from respective human virus strains in phylogenetic trees. In contrast, the rotavirus A sequences showed high identity to human and animal strains. Analysis of the nearly complete genome of this virus revealed the known genotypes G3, P[3] and N2 for three of the genome segments, whereas the remaining eight genome segments represented the novel genotypes I20-R11-C11-M10-A22-T14-E18-H13. Our results indicated a high heterogeneity of enteric viruses present in urban wild rats; their ability to be transmitted to humans remains to be assessed in the future.
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Affiliation(s)
- Jana Sachsenröder
- Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Anne Braun
- Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Patrycja Machnowska
- Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Terry Fei Fan Ng
- Blood Systems Research Institute, 270 Masonic Avenue, San Francisco, CA 94118, USA
| | - Xutao Deng
- Blood Systems Research Institute, 270 Masonic Avenue, San Francisco, CA 94118, USA
| | - Sebastian Guenther
- Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Strasse 7-13, 14163 Berlin, Germany
| | - Samuel Bernstein
- Friedrich-Loeffler-Institut, Institute for Novel and Emerging Infectious Diseases, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Rainer G Ulrich
- Friedrich-Loeffler-Institut, Institute for Novel and Emerging Infectious Diseases, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Eric Delwart
- Blood Systems Research Institute, 270 Masonic Avenue, San Francisco, CA 94118, USA
| | - Reimar Johne
- Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
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10
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Lim ES, Cao S, Holtz LR, Antonio M, Stine OC, Wang D. Discovery of rosavirus 2, a novel variant of a rodent-associated picornavirus, in children from The Gambia. Virology 2014; 454-455:25-33. [PMID: 24725928 DOI: 10.1016/j.virol.2014.01.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 01/16/2014] [Accepted: 01/22/2014] [Indexed: 12/18/2022]
Abstract
We describe the identification of a novel picornavirus recovered from the fecal specimen of a child in The Gambia, provisionally named rosavirus 2. Comparison of the rosavirus 2 complete genome demonstrated 71.9% nucleotide identity to its closest relative rosavirus M-7, an unclassified picornavirus identified from rodent fecal material. A unique RNA structure was predicted in the 3' UTR of rosavirus 2 that was conserved with rosavirus M-7 and cadiciviruses. We detected rosavirus 2 in four pediatric fecal specimens (0.55% prevalence) in a Gambian diarrheal case-control cohort, but we did not detect it in a panel of 634 pediatric diarrheal stool specimens from the USA. There was no statistical evidence that rosavirus 2 was associated with diarrheal cases. This study broadens our understanding of unknown viruses present in children in developing country settings.
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Affiliation(s)
- Efrem S Lim
- Departments of Molecular Microbiology and Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Song Cao
- Departments of Molecular Microbiology and Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Lori R Holtz
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | | | - O Colin Stine
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - David Wang
- Departments of Molecular Microbiology and Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA.
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