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Barrón-Rodríguez RJ, Rojas-Anaya E, Ayala-Sumuano JT, Romero-Espinosa JÁI, Vázquez-Pérez JA, Cortés-Cruz M, García-Espinosa G, Loza-Rubio E. Swine virome on rural backyard farms in Mexico: communities with different abundances of animal viruses and phages. Arch Virol 2021; 166:475-489. [PMID: 33394173 DOI: 10.1007/s00705-020-04894-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 10/06/2020] [Indexed: 11/24/2022]
Abstract
Domestic swine have been introduced by humans into a wide diversity of environments and have been bred in different production systems. This has resulted in an increased risk for the occurrence and spread of diseases. Although viromes of swine in intensive farms have been described, little is known about the virus communities in backyard production systems around the world. The aim of this study was to describe the viral diversity of 23 healthy domestic swine maintained in rural backyards in Morelos, Mexico, through collection and analysis of nasal and rectal samples. Next-generation sequencing was used to identify viruses that are present in swine. Through homology search and bioinformatic analysis of reads and their assemblies, we found that rural backyard swine have a high degree of viral diversity, different from those reported in intensive production systems or under experimental conditions. There was a higher frequency of bacteriophages and lower diversity of animal viruses than reported previously. In addition, sapoviruses, bocaparvoviruses, and mamastroviruses that had not been reported previously in our country were identified. These findings were correlated with the health status of animals, their social interactions, and the breeding/rearing environment (which differed from intensive systems), providing baseline information about viral communities in backyard swine.
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Affiliation(s)
- Rodrigo Jesús Barrón-Rodríguez
- Laboratorio de Biotecnología en Salud Animal, Centro Nacional de Investigación Disciplinaria en Microbiología Animal (CENID-Microbiología), Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias (INIFAP), carretera federal México-Toluca km 15.5, colonia palo Alto, Cuajimalpa, P.C. 05110, Mexico City, Mexico.,Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México (UNAM), Avenida Universidad 3000, colonia Ciudad universitaria, Coyoacán, P.C. 04510, Mexico City, Mexico
| | - Edith Rojas-Anaya
- Laboratorio de Biotecnología en Salud Animal, Centro Nacional de Investigación Disciplinaria en Microbiología Animal (CENID-Microbiología), Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias (INIFAP), carretera federal México-Toluca km 15.5, colonia palo Alto, Cuajimalpa, P.C. 05110, Mexico City, Mexico
| | - Jorge Tonatiuh Ayala-Sumuano
- Idix S.A. de C.V., Sonterra 3035 interior 26, Fraccionamiento Sonterra, P.C. 76230, Santiago de Querétaro, Querétaro, Mexico
| | - José Ángel Iván Romero-Espinosa
- Laboratorio de Virología, Instituto Nacional de Enfermedades Respiratorias (INER), Calzada de Tlalpan 4502, Del. Tlalpan, colonia Sección XVI, Tlalpan, P.C. 14080, Mexico City, Mexico
| | - Joel Armando Vázquez-Pérez
- Laboratorio de Virología, Instituto Nacional de Enfermedades Respiratorias (INER), Calzada de Tlalpan 4502, Del. Tlalpan, colonia Sección XVI, Tlalpan, P.C. 14080, Mexico City, Mexico
| | - Moisés Cortés-Cruz
- Centro Nacional de Recursoso Genéticos (CNRG), Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias (INIFAP), Boulevard de la biodiversidad 400, Rancho las Cruces, P.C. 47600, Tepatitlán de Morelos, Jalisco, Mexico
| | - Gary García-Espinosa
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México (UNAM), Avenida Universidad 3000, colonia Ciudad universitaria, Coyoacán, P.C. 04510, Mexico City, Mexico
| | - Elizabeth Loza-Rubio
- Laboratorio de Biotecnología en Salud Animal, Centro Nacional de Investigación Disciplinaria en Microbiología Animal (CENID-Microbiología), Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias (INIFAP), carretera federal México-Toluca km 15.5, colonia palo Alto, Cuajimalpa, P.C. 05110, Mexico City, Mexico.
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2
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Webb B, Rakibuzzaman A, Ramamoorthy S. Torque teno viruses in health and disease. Virus Res 2020; 285:198013. [PMID: 32404273 DOI: 10.1016/j.virusres.2020.198013] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/02/2020] [Accepted: 05/04/2020] [Indexed: 12/19/2022]
Abstract
Torque teno viruses (TTVs) are small, ubiquitous, viruses with a highly diverse, single-stranded, negative sense DNA genome and wide host range. They are detected at high rates in both healthy and diseased individuals and are considered a significant part of the mammalian virome. Similar to human TTVs, swine TTVs (TTSuVs) are epidemiologically linked to several coinfections including porcine circovirus types 2 and 3 and the porcine reproductive and respiratory disease syndrome virus. Experimental infection of gnotobiotic pigs with TTSuVs resulted in lesions in multiple organs and exacerbation of coinfections, making TTSuVs the only members of the Anelloviridae family with experimental evidence for pathogenicity. However, due to the lack of reliable cell culture and animal models, mechanistic studies on viral immunity and pathogenesis are limited. The objective of this review is to summarize the current status of knowledge regarding the biology, detection, pathogenesis and public health significance of TTSuVs, while identifying gaps in knowledge which limit the field.
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Affiliation(s)
- Brett Webb
- Veterinary Diagnostic Laboratory, North Dakota State University, Fargo, ND, United States
| | - Agm Rakibuzzaman
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, United States
| | - Sheela Ramamoorthy
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, United States.
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3
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Virus Metagenomics in Farm Animals: A Systematic Review. Viruses 2020; 12:v12010107. [PMID: 31963174 PMCID: PMC7019290 DOI: 10.3390/v12010107] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/12/2020] [Accepted: 01/14/2020] [Indexed: 02/07/2023] Open
Abstract
A majority of emerging infectious diseases are of zoonotic origin. Metagenomic Next-Generation Sequencing (mNGS) has been employed to identify uncommon and novel infectious etiologies and characterize virus diversity in human, animal, and environmental samples. Here, we systematically reviewed studies that performed viral mNGS in common livestock (cattle, small ruminants, poultry, and pigs). We identified 2481 records and 120 records were ultimately included after a first and second screening. Pigs were the most frequently studied livestock and the virus diversity found in samples from poultry was the highest. Known animal viruses, zoonotic viruses, and novel viruses were reported in available literature, demonstrating the capacity of mNGS to identify both known and novel viruses. However, the coverage of metagenomic studies was patchy, with few data on the virome of small ruminants and respiratory virome of studied livestock. Essential metadata such as age of livestock and farm types were rarely mentioned in available literature, and only 10.8% of the datasets were publicly available. Developing a deeper understanding of livestock virome is crucial for detection of potential zoonotic and animal pathogens and One Health preparedness. Metagenomic studies can provide this background but only when combined with essential metadata and following the “FAIR” (Findable, Accessible, Interoperable, and Reusable) data principles.
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4
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Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins ( Manis javanica). Viruses 2019; 11:v11110979. [PMID: 31652964 PMCID: PMC6893680 DOI: 10.3390/v11110979] [Citation(s) in RCA: 230] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/21/2019] [Accepted: 10/21/2019] [Indexed: 12/14/2022] Open
Abstract
Pangolins are endangered animals in urgent need of protection. Identifying and cataloguing the viruses carried by pangolins is a logical approach to evaluate the range of potential pathogens and help with conservation. This study provides insight into viral communities of Malayan Pangolins (Manis javanica) as well as the molecular epidemiology of dominant pathogenic viruses between Malayan Pangolin and other hosts. A total of 62,508 de novo assembled contigs were constructed, and a BLAST search revealed 3600 ones (≥300 nt) were related to viral sequences, of which 68 contigs had a high level of sequence similarity to known viruses, while dominant viruses were the Sendai virus and Coronavirus. This is the first report on the viral diversity of pangolins, expanding our understanding of the virome in endangered species, and providing insight into the overall diversity of viruses that may be capable of directly or indirectly crossing over into other mammals.
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5
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Chen Q, Wang L, Zheng Y, Zhang J, Guo B, Yoon KJ, Gauger PC, Harmon KM, Main RG, Li G. Metagenomic analysis of the RNA fraction of the fecal virome indicates high diversity in pigs infected by porcine endemic diarrhea virus in the United States. Virol J 2018; 15:95. [PMID: 29801460 PMCID: PMC5970503 DOI: 10.1186/s12985-018-1001-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 05/13/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Emergence and re-emergence of porcine epidemic diarrhea virus (PEDV) in North America, Asia and Europe has caused severe economic loss to the global swine industry. However, the virome of PEDV infected pigs and its effect on disease severity remains unknown. The advancements of sequencing technology have made it possible to characterize the entire microbiome of different body sites for any host. METHODS The objective of this study was to characterize the RNA virome in PEDV-positive pigs using the hypothesis-free metagenomics approach based on next-generation sequencing. Specifically, 217 PEDV-positive swine fecal swab samples collected from diarrheic piglets over 17 US states during 2015-2016 were analyzed. RESULTS A Kraken algorithm-based bioinformatics analysis revealed the presence of up to 9 different RNA genera besides PEDV (Alphacoronavirus genus), including Mamastrovirus (52%, 113/217), Enterovirus (39%, 85/217), Sapelovirus (31%, 67/217), Posavirus (30%, 66/217), Kobuvirus (23%, 49/217), Sapovirus (13%, 28/217), Teschovirus (10%, 22/217), Pasivirus (9%, 20/217), and Deltacoronavirus (3%, 6/217). There were 58 out of 217 piglets (27%) have PEDV infection alone whereas the remaining 159 (73%) shed 2 up to 9 different viruses. CONCLUSION These findings demonstrated that PEDV infected diarrheic pigs had an extensive RNA viral flora consisting of four different families: Astroviridae, Picornaviridae, Caliciviridae, and Coronaviridae.
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Affiliation(s)
- Qi Chen
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1907 ISU C-Drive, VMRI#1, Ames, IA, 50011, USA
| | - Leyi Wang
- Department of Veterinary Clinical Medicine and the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, 61802, USA
| | - Ying Zheng
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1907 ISU C-Drive, VMRI#1, Ames, IA, 50011, USA
| | - Jianqiang Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1907 ISU C-Drive, VMRI#1, Ames, IA, 50011, USA
| | - Baoqing Guo
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1907 ISU C-Drive, VMRI#1, Ames, IA, 50011, USA
| | - Kyoung-Jin Yoon
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1907 ISU C-Drive, VMRI#1, Ames, IA, 50011, USA
| | - Phillip C Gauger
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1907 ISU C-Drive, VMRI#1, Ames, IA, 50011, USA
| | - Karen M Harmon
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1907 ISU C-Drive, VMRI#1, Ames, IA, 50011, USA
| | - Rodger G Main
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1907 ISU C-Drive, VMRI#1, Ames, IA, 50011, USA
| | - Ganwu Li
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1907 ISU C-Drive, VMRI#1, Ames, IA, 50011, USA.
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6
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Denner J. The porcine virome and xenotransplantation. Virol J 2017; 14:171. [PMID: 28874166 PMCID: PMC5585927 DOI: 10.1186/s12985-017-0836-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/27/2017] [Indexed: 12/29/2022] Open
Abstract
The composition of the porcine virome includes viruses that infect pig cells, ancient virus-derived elements including endogenous retroviruses inserted in the pig chromosomes, and bacteriophages that infect a broad array of bacteria that inhabit pigs. Viruses infecting pigs, among them viruses also infecting human cells, as well as porcine endogenous retroviruses (PERVs) are of importance when evaluating the virus safety of xenotransplantation. Bacteriophages associated with bacteria mainly in the gut are not relevant in this context. Xenotransplantation using pig cells, tissues or organs is under development in order to alleviate the shortage of human transplants. Here for the first time published data describing the viromes in different pigs and their relevance for the virus safety of xenotransplantation is analysed. In conclusion, the analysis of the porcine virome has resulted in numerous new viruses being described, although their impact on xenotransplantation is unclear. Most importantly, viruses with known or suspected zoonotic potential were often not detected by next generation sequencing, but were revealed by more sensitive methods.
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Affiliation(s)
- Joachim Denner
- Robert Koch Fellow, Robert Koch Institute, Nordufer, 20, Berlin, Germany.
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Li Y, Khalafalla AI, Paden CR, Yusof MF, Eltahir YM, Al Hammadi ZM, Tao Y, Queen K, Hosani FA, Gerber SI, Hall AJ, Al Muhairi S, Tong S. Identification of diverse viruses in upper respiratory samples in dromedary camels from United Arab Emirates. PLoS One 2017; 12:e0184718. [PMID: 28902913 PMCID: PMC5597213 DOI: 10.1371/journal.pone.0184718] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/29/2017] [Indexed: 02/05/2023] Open
Abstract
Camels are known carriers for many viral pathogens, including Middle East respiratory syndrome coronavirus (MERS-CoV). It is likely that there are additional, as yet unidentified viruses in camels with the potential to cause disease in humans. In this study, we performed metagenomic sequencing analysis on nasopharyngeal swab samples from 108 MERS-CoV-positive dromedary camels from a live animal market in Abu Dhabi, United Arab Emirates. We obtained a total of 846.72 million high-quality reads from these nasopharyngeal swab samples, of which 2.88 million (0.34%) were related to viral sequences while 512.63 million (60.5%) and 50.87 million (6%) matched bacterial and eukaryotic sequences, respectively. Among the viral reads, sequences related to mammalian viruses from 13 genera in 10 viral families were identified, including Coronaviridae, Nairoviridae, Paramyxoviridae, Parvoviridae, Polyomaviridae, Papillomaviridae, Astroviridae, Picornaviridae, Poxviridae, and Genomoviridae. Some viral sequences belong to known camel or human viruses and others are from potentially novel camel viruses with only limited sequence similarity to virus sequences in GenBank. A total of five potentially novel virus species or strains were identified. Co-infection of at least two recently identified camel coronaviruses was detected in 92.6% of the camels in the study. This study provides a comprehensive survey of viruses in the virome of upper respiratory samples in camels that have extensive contact with the human population.
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Affiliation(s)
- Yan Li
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | | | - Clinton R. Paden
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, United States of America
| | - Mohammed F. Yusof
- Animal Wealth Sector, Abu Dhabi Food Control Authority, Abu Dhabi, United Arab Emirates
| | - Yassir M. Eltahir
- Animal Wealth Sector, Abu Dhabi Food Control Authority, Abu Dhabi, United Arab Emirates
| | | | - Ying Tao
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Krista Queen
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, United States of America
| | | | - Susan I. Gerber
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Aron J. Hall
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Salama Al Muhairi
- Animal Wealth Sector, Abu Dhabi Food Control Authority, Abu Dhabi, United Arab Emirates
- * E-mail: (ST); (SAM)
| | - Suxiang Tong
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail: (ST); (SAM)
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8
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Sano K, Naoi Y, Kishimoto M, Masuda T, Tanabe H, Ito M, Niira K, Haga K, Asano K, Tsuchiaka S, Omatsu T, Furuya T, Katayama Y, Oba M, Ouchi Y, Yamasato H, Ishida M, Shirai J, Katayama K, Mizutani T, Nagai M. Identification of further diversity among posaviruses. Arch Virol 2016; 161:3541-3548. [PMID: 27619795 DOI: 10.1007/s00705-016-3048-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 09/01/2016] [Indexed: 02/06/2023]
Abstract
Recently, there have been reports of new members of posavirus-like viruses in the order Picornavirales. In this study, using a metagenomics approach, 11 posavirus-like sequences (>7,000 nucleotides) were detected in 155 porcine fecal samples. Phylogenetic analysis revealed that the newly identified virus sequences, together with other posavirus-like viruses, form distinct clusters within the order Picornavirales, composed of eight genogroups and unassigned sequences based on amino acid sequences of the helicase and RNA-dependent RNA polymerase regions, with <40 % and <50 % sequence identity, respectively. We propose further classifications of highly diverse posavirus populations based on newly identified sequences from Japanese pig feces.
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Affiliation(s)
- Kaori Sano
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Yuki Naoi
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Mai Kishimoto
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Tsuneyuki Masuda
- Kurayoshi Livestock Hygiene Service Center, Kurayoshi, Tottori, 683-0017, Japan
| | - Hitomi Tanabe
- Rokko Livestock Hygiene Service Center, Hokota, Ibaraki, 311-1593, Japan
| | - Mika Ito
- Ishikawa Nanbu Livestock Hygiene Service Center, Kanazawa, Ishikawa, 920-3101, Japan
| | - Kazutaka Niira
- Tochigi Prefectural South District Animal Hygiene Service Center, Tochigi, Tochigi, 328-0002, Japan
| | - Kei Haga
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo, 208-0011, Japan
| | - Keigo Asano
- Department of Bioproduction Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836, Japan
| | - Shinobu Tsuchiaka
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Tsutomu Omatsu
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Tetsuya Furuya
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Yukie Katayama
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Mami Oba
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Yoshinao Ouchi
- Kenhoku Livestock Hygiene Service Center, Mito, Ibaraki, 310-0002, Japan
| | - Hiroshi Yamasato
- Kurayoshi Livestock Hygiene Service Center, Kurayoshi, Tottori, 683-0017, Japan
| | - Motohiko Ishida
- Department of Bioproduction Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836, Japan
| | - Junsuke Shirai
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Kazuhiko Katayama
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo, 208-0011, Japan
| | - Tetsuya Mizutani
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Makoto Nagai
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan. .,Department of Bioproduction Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836, Japan.
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9
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Naoi Y, Kishimoto M, Masuda T, Ito M, Tsuchiaka S, Sano K, Yamasato H, Omatsu T, Aoki H, Furuya T, Katayama Y, Oba M, Okada T, Shirai J, Mizutani T, Nagai M. Characterization and phylogenetic analysis of a novel picornavirus from swine feces in Japan. Arch Virol 2016; 161:1685-90. [DOI: 10.1007/s00705-016-2834-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/16/2016] [Indexed: 01/10/2023]
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10
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Karlsson OE, Larsson J, Hayer J, Berg M, Jacobson M. The Intestinal Eukaryotic Virome in Healthy and Diarrhoeic Neonatal Piglets. PLoS One 2016; 11:e0151481. [PMID: 26982708 PMCID: PMC4794121 DOI: 10.1371/journal.pone.0151481] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 02/29/2016] [Indexed: 12/29/2022] Open
Abstract
Neonatal porcine diarrhoea of uncertain aetiology has been reported from a number of European countries. The aim of the present study was to use viral metagenomics to examine a potential viral involvement in this diarrhoea and to describe the intestinal virome with focus on eukaryotic viruses. Samples from the distal jejunum of 50 diarrhoeic and 19 healthy piglets from 10 affected herds were analysed. The viral fraction of the samples was isolated and nucleic acids (RNA and DNA fractions) were subjected to sequence independent amplification. Samples from diarrhoeic piglets from the same herds were pooled whereas samples from healthy piglets were analysed individually. In total, 29 clinical samples, plus two negative controls and one positive control consisting of a mock metagenome were sequenced using the Ion Torrent platform. The resulting sequence data was subjected to taxonomic classification using Kraken, Diamond and HMMER. In the healthy specimens, eight different mammalian virus families were detected (Adenoviridae, Anelloviridae, Astroviridae, Caliciviridae, Circoviridae, Parvoviridae, Picornaviridae, and Reoviridae) compared to four in the pooled diarrhoeic samples (Anelloviridae, Circoviridae, Picornaviridae, and Reoviridae). It was not possible to associate a particular virus family with the investigated diarrhoea. In conclusion, this study does not support the hypothesis that the investigated diarrhoea was caused by known mammalian viruses. The results do, however, indicate that known mammalian viruses were present in the intestine as early as 24–48 hours after birth, indicating immediate infection post-partum or possibly transplacental infection.
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Affiliation(s)
- Oskar E. Karlsson
- Department of Biomedical Sciences and Veterinary Public Health (BVF), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics (HGEN), SLU, Uppsala, Sweden
- The OIE Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Uppsala, Sweden
- * E-mail:
| | - Jenny Larsson
- Department of Clinical Sciences (KV), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Juliette Hayer
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics (HGEN), SLU, Uppsala, Sweden
| | - Mikael Berg
- Department of Biomedical Sciences and Veterinary Public Health (BVF), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
- The OIE Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Uppsala, Sweden
| | - Magdalena Jacobson
- Department of Clinical Sciences (KV), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
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11
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The dilemma of rare events: Porcine epidemic diarrhea virus in North America. Prev Vet Med 2015; 122:235-41. [PMID: 26318527 PMCID: PMC7132378 DOI: 10.1016/j.prevetmed.2015.08.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 07/27/2015] [Accepted: 08/08/2015] [Indexed: 11/21/2022]
Abstract
Porcine epidemic diarrhea virus (PEDV) has been recognized as a swine pathogen for 40 years, but until 2013 had not been detected in the Western Hemisphere. From originally causing a relatively mild and sporadic disease, PEDV has been more recently associated with severe outbreaks of diarrheal disease in Asia, and subsequently North America. PEDV shares some important characteristics with two major pandemic viruses (porcine reproductive and respiratory virus; porcine circovirus type 2) of pigs that have high rates of mutation and high host specificity, and appear to have been present in the swine virome for decades prior to emerging to cause severe clinical disease. A unique feature of the PEDV in North America has been the implication of feed as a vehicle for transmission, with particular concerns related to ingredients of porcine origin. The importance of relatively rare events in contributing to both the emergence and transmission of PEDV is discussed in relation to approaches for managing the associated risks.
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12
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Conceição-Neto N, Zeller M, Heylen E, Lefrère H, Mesquita JR, Matthijnssens J. Fecal virome analysis of three carnivores reveals a novel nodavirus and multiple gemycircularviruses. Virol J 2015; 12:79. [PMID: 25986582 PMCID: PMC4459443 DOI: 10.1186/s12985-015-0305-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 04/30/2015] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND More knowledge about viral populations in wild animals is needed in order to better understand and assess the risk of zoonotic diseases. In this study we performed viral metagenomic analysis of fecal samples from three healthy carnivores: a badger (Meles meles), a mongoose (Herpestes ichneumon) and an otter (Lutra lutra) from Portugal. RESULTS We detected the presence of novel highly divergent viruses in the fecal material of the carnivores analyzed, such as five gemycircularviruses. Four of these gemycircularviruses were found in the mongoose and one in the badger. In addition we also identified an RNA-dependent RNA polymerase gene from a putative novel member of the Nodaviridae family in the fecal material of the otter. CONCLUSIONS Together these results underline that many novel viruses are yet to be discovered and that fecal associated viruses are not always related to disease. Our study expands the knowledge of viral species present in the gut, although the interpretation of the true host species of such novel viruses needs to be reviewed with great caution.
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Affiliation(s)
- Nádia Conceição-Neto
- Laboratory of viral metagenomics, Rega Institute for Medical Research Leuven, Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, B-3000, Belgium.
| | - Mark Zeller
- Laboratory of viral metagenomics, Rega Institute for Medical Research Leuven, Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, B-3000, Belgium.
| | - Elisabeth Heylen
- Laboratory of viral metagenomics, Rega Institute for Medical Research Leuven, Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, B-3000, Belgium.
| | - Hanne Lefrère
- Laboratory of viral metagenomics, Rega Institute for Medical Research Leuven, Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, B-3000, Belgium.
| | - João Rodrigo Mesquita
- Polytechnic Institute of Viseu, Department of Animal Science, Rural Engineering and Veterinary, Viseu, Portugal.
| | - Jelle Matthijnssens
- Laboratory of viral metagenomics, Rega Institute for Medical Research Leuven, Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, B-3000, Belgium.
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13
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A metagenomics and case-control study to identify viruses associated with bovine respiratory disease. J Virol 2015; 89:5340-9. [PMID: 25740998 DOI: 10.1128/jvi.00064-15] [Citation(s) in RCA: 161] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 02/21/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Bovine respiratory disease (BRD) is a common health problem for both dairy and beef cattle, resulting in significant economic loses. In order to identify viruses associated with BRD, we used a metagenomics approach to enrich and sequence viral nucleic acids in the nasal swabs of 50 young dairy cattle with symptoms of BRD. Following deep sequencing, de novo assembly, and translated protein sequence similarity searches, numerous known and previously uncharacterized viruses were identified. Bovine adenovirus 3, bovine adeno-associated virus, bovine influenza D virus, bovine parvovirus 2, bovine herpesvirus 6, bovine rhinitis A virus, and multiple genotypes of bovine rhinitis B virus were identified. The genomes of a previously uncharacterized astrovirus and picobirnaviruses were also partially or fully sequenced. Using real-time PCR, the rates of detection of the eight viruses that generated the most reads were compared for the nasal secretions of 50 animals with BRD versus 50 location-matched healthy control animals. Viruses were detected in 68% of BRD-affected animals versus 16% of healthy control animals. Thirty-eight percent of sick animals versus 8% of controls were infected with multiple respiratory viruses. Significantly associated with BRD were bovine adenovirus 3 (P < 0.0001), bovine rhinitis A virus (P = 0.005), and the recently described bovine influenza D virus (P = 0.006), which were detected either alone or in combination in 62% of animals with BRD. A metagenomics and real-time PCR detection approach in carefully matched cases and controls can provide a rapid means to identify viruses associated with a complex disease, paving the way for further confirmatory tests and ultimately to effective intervention strategies. IMPORTANCE Bovine respiratory disease is the most economically important disease affecting the cattle industry, whose complex root causes include environmental, genetics, and infectious factors. Using an unbiased metagenomics approach, we characterized the viruses in respiratory secretions from BRD cases and identified known and previously uncharacterized viruses belonging to seven viral families. Using a case-control format with location-matched animals, we compared the rates of viral detection and identified 3 viruses associated with severe BRD signs. Combining a metagenomics and case-control format can provide candidate pathogens associated with complex infectious diseases and inform further studies aimed at reducing their impact.
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14
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Dumarest M, Muth E, Cheval J, Gratigny M, Hébert C, Gagnieur L, Eloit M. Viral diversity in swine intestinal mucus used for the manufacture of heparin as analyzed by high-throughput sequencing. Biologicals 2014; 43:31-6. [PMID: 25466699 PMCID: PMC7172073 DOI: 10.1016/j.biologicals.2014.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 09/18/2014] [Accepted: 10/23/2014] [Indexed: 12/17/2022] Open
Abstract
Heparin is one of the main pharmaceutical products manufactured from raw animal material. In order to describe the viral burden associated with this raw material, we performed high-throughput sequencing (HTS) on mucus samples destined for heparin manufacturing, which were collected from European pigs. We identified Circoviridae and Parvoviridae members as the most prevalent contaminating viruses, together with viruses from the Picornaviridae, Astroviridae, Reoviridae, Caliciviridae, Adenoviridae, Birnaviridae, and Anelloviridae families. Putative new viral species were also identified. The load of several known or novel small non-enveloped viruses, which are particularly difficult to inactivate or eliminate during heparin processing, was quantified by qPCR. Analysis of the combined HTS and specific qPCR results will influence the refining and validation of inactivation procedures, as well as aiding in risk analysis of viral heparin contamination.
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Affiliation(s)
- Marine Dumarest
- Institut Pasteur, Laboratory of Pathogen Discovery, Department of Virology, 28 rue du Docteur Roux, F-75724 Paris, France
| | - Erika Muth
- PathoQuest, Bâtiment François Jacob, 25 rue du Dr Roux, 75015 Paris, France
| | - Justine Cheval
- PathoQuest, Bâtiment François Jacob, 25 rue du Dr Roux, 75015 Paris, France
| | - Marlène Gratigny
- PathoQuest, Bâtiment François Jacob, 25 rue du Dr Roux, 75015 Paris, France
| | - Charles Hébert
- PathoQuest, Bâtiment François Jacob, 25 rue du Dr Roux, 75015 Paris, France
| | - Léa Gagnieur
- Institut Pasteur, Laboratory of Pathogen Discovery, Department of Virology, 28 rue du Docteur Roux, F-75724 Paris, France
| | - Marc Eloit
- Institut Pasteur, Laboratory of Pathogen Discovery, Department of Virology, 28 rue du Docteur Roux, F-75724 Paris, France; PathoQuest, Bâtiment François Jacob, 25 rue du Dr Roux, 75015 Paris, France; Ecole Nationale Vétérinaire d'Alfort, UMR 1161 Virologie ENVA, INRA, ANSES, 7 Avenue Général de Gaulle, F-94704 Maisons Alfort, France.
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15
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Woo PCY, Lau SKP, Teng JLL, Tsang AKL, Joseph M, Wong EYM, Tang Y, Sivakumar S, Bai R, Wernery R, Wernery U, Yuen KY. Metagenomic analysis of viromes of dromedary camel fecal samples reveals large number and high diversity of circoviruses and picobirnaviruses. Virology 2014; 471-473:117-25. [PMID: 25461537 PMCID: PMC7112128 DOI: 10.1016/j.virol.2014.09.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 08/15/2014] [Accepted: 09/23/2014] [Indexed: 12/20/2022]
Abstract
The recent discovery of Middle East Respiratory Coronavirus and another novel dromedary camel coronavirus UAE-HKU23 in dromedaries has boosted interest in search of novel viruses in dromedaries. In this study, fecal samples of 203 dromedaries in Dubai were pooled and deep sequenced. Among the 7330 assembled viral contigs, 1970 were assigned to mammalian viruses. The largest groups of these contigs matched to Picobirnaviridae, Circoviridae, Picornaviridae, Parvoviridae, Astroviridae and Hepeviridae. Many of these viral families were previously unknown to dromedaries. In addition to the high abundance of contigs from Circoviridae (n=598 with 14 complete genomes) and Picobirnaviridae (n=1236), a high diversity of contigs from these two families was found, with the 14 Circoviridae complete genomes forming at least five clusters and contigs from both genogroup I and genogroup II potentially novel picobirnaviruses. Further studies comparing the incidence of these viral families in healthy and sick dromedaries will reveal their pathogenic potential. The viromes of fecal samples from dromedaries in the Middle East were analyzed. Circoviridae and Picobirnaviridae are most abundant among the mammalian viruses. A high diversity of contigs from Circoviridae and Picobirnaviridae was observed.
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Affiliation(s)
- Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China; Department of Microbiology, 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.
| | - Susanna K P Lau
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China; Department of Microbiology, 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
| | - Jade L L Teng
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Alan K L Tsang
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Marina Joseph
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | - Emily Y M Wong
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Ying Tang
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | | | - Ru Bai
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Renate Wernery
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | - Ulrich Wernery
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates.
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China; Department of Microbiology, 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
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16
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Sachsenröder J, Twardziok SO, Scheuch M, Johne R. The general composition of the faecal virome of pigs depends on age, but not on feeding with a probiotic bacterium. PLoS One 2014; 9:e88888. [PMID: 24586429 PMCID: PMC3929612 DOI: 10.1371/journal.pone.0088888] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 01/13/2014] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The pig faecal virome, which comprises the community of viruses present in pig faeces, is complex and consists of pig viruses, bacteriophages, transiently passaged plant viruses and other minor virus species. Only little is known about factors influencing its general composition. Here, the effect of the probiotic bacterium Enterococcus faecium (E. faecium) NCIMB 10415 on the pig faecal virome composition was analysed in a pig feeding trial with sows and their piglets, which received either the probiotic bacterium or not. RESULTS From 8 pooled faecal samples derived from the feeding trial, DNA and RNA virus particles were prepared and subjected to process-controlled Next Generation Sequencing resulting in 390,650 sequence reads. In average, 14% of the reads showed significant sequence identities to known viruses. The percentage of detected mammalian virus sequences was highest (55-77%) in the samples of the youngest piglets and lowest (8-10%) in the samples of the sows. In contrast, the percentage of bacteriophage sequences increased from 22-44% in the youngest piglets to approximately 90% in the sows. The dominating mammalian viruses differed remarkably among 12 day-old piglets (kobuvirus), 54 day-old piglets (boca-, dependo- and pig stool-associated small circular DNA virus [PigSCV]) and the sows (PigSCV, circovirus and "circovirus-like" viruses CB-A and RW-A). In addition, the Shannon index, which reflects the diversity of sequences present in a sample, was generally higher for the sows as compared to the piglets. No consistent differences in the virome composition could be identified between the viromes of the probiotic bacterium-treated group and the control group. CONCLUSION The analysis indicates that the pig faecal virome shows a high variability and that its general composition is mainly dependent on the age of the pigs. Changes caused by feeding with the probiotic bacterium E. faecium could not be demonstrated using the applied metagenomics method.
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Affiliation(s)
| | - Sven O. Twardziok
- Institute for Molecular Biology and Bioinformatic, Charité Berlin, Berlin, Germany
| | | | - Reimar Johne
- Federal Institute for Risk Assessment, Berlin, Germany
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17
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Cheung AK, Ng TF, Lager KM, Bayles DO, Alt DP, Delwart EL, Pogranichniy RM, Kehrli ME. A divergent clade of circular single-stranded DNA viruses from pig feces. Arch Virol 2013; 158:2157-62. [PMID: 23612924 PMCID: PMC4175981 DOI: 10.1007/s00705-013-1701-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 03/19/2013] [Indexed: 02/03/2023]
Abstract
Using metagenomics and molecular cloning methods, we characterized five novel small, circular viral genomes from pig feces that are distantly related to chimpanzee and porcine stool-associated circular viruses, (ChiSCV and PoSCV1). Phylogenetic analysis placed these viruses into a highly divergent clade of this rapidly growing new viral family. This new clade of viruses, provisionally named porcine stool-associated circular virus 2 and 3 (PoSCV2 and PoSCV3), encodes a stem–loop structure (presumably the origin of DNA replication) in the small intergenic region and a replication initiator protein commonly found in other biological systems that replicate their genomes via the rolling–circle mechanism. Furthermore, these viruses also exhibit three additional overlapping open reading frames in the large intergenic region between the capsid and replication initiator protein genes.
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Affiliation(s)
- Andrew K Cheung
- Virus and Prion Diseases, Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, PO Box 70, Ames, IA, 50010, USA,
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