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Zell R, Groth M, Selinka L, Selinka HC. Diversity of Picorna-Like Viruses in the Teltow Canal, Berlin, Germany. Viruses 2024; 16:1020. [PMID: 39066183 PMCID: PMC11281612 DOI: 10.3390/v16071020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 06/23/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
The viromes of freshwater bodies are underexplored. The Picornavirales order, with 371 acknowledged species, is one of the most expansive and diverse groups of eukaryotic RNA viruses. In this study, we add 513 picorna-like viruses to the assemblage of more than 2000 unassigned picorna-like viruses. Our set of the aquatic Picornavirales virome of the Teltow Canal in Berlin, Germany, consists of 239 complete and 274 partial genomes. This urban freshwater body is characterized by the predominance of marna-like viruses (30.8%) and dicistro-like viruses (19.1%), whereas picornaviruses, iflaviruses, solinvi-like viruses, polycipi-like viruses, and nora-like viruses are considerably less prevalent. Caliciviruses and secoviruses were absent in our sample. Although presenting characteristic domains of Picornavirales, more than 100 viruses (20.8%) could not be assigned to any of the 9 Picornavirales families. Thirty-three viruses of the Marnaviridae-mostly locarna-like viruses-exhibit a monocistronic genome layout. Besides a wealth of novel virus sequences, viruses with peculiar features are reported. Among these is a clade of untypeable marna-like viruses with dicistronic genomes, but with the capsid protein-encoding open reading frame located at the 5' part of their RNA. A virus with a similar genome layout but clustering with dicistroviruses was also observed. We further detected monocistronic viruses with a polymerase gene related to aparaviruses. The detection of Aichi virus and five novel posa-like viruses indicates a slight burden in municipal wastewater.
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Affiliation(s)
- Roland Zell
- Section of Experimental Virology, Institute for Medical Microbiology, Jena University Hospital, Friedrich Schiller University, 07743 Jena, Germany
| | - Marco Groth
- CF Next Generation Sequencing, Leibniz Institute on Aging-Fritz Lipmann Institute, 07745 Jena, Germany
| | - Lukas Selinka
- Section of Experimental Virology, Institute for Medical Microbiology, Jena University Hospital, Friedrich Schiller University, 07743 Jena, Germany
| | - Hans-Christoph Selinka
- Section II 1.4 Microbiological Risks, Department of Environmental Hygiene, German Environment Agency, 14195 Berlin, Germany
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Han Z, Xiao J, Song Y, Zhao X, Sun Q, Lu H, Zhang K, Li J, Li J, Si F, Zhang G, Zhao H, Jia S, Zhou J, Wang D, Zhu S, Yan D, Xu W, Fu X, Zhang Y. Highly diverse ribonucleic acid viruses in the viromes of eukaryotic host species in Yunnan province, China. Front Microbiol 2022; 13:1019444. [PMID: 36312977 PMCID: PMC9606678 DOI: 10.3389/fmicb.2022.1019444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
Background The diversity in currently documented viruses and their morphological characteristics indicates the need for understanding the evolutionary characteristics of viruses. Notably, further studies are needed to obtain a comprehensive landscape of virome, the virome of host species in Yunnan province, China. Materials and methods We implemented the metagenomic next-generation sequencing strategy to investigate the viral diversity, which involved in 465 specimens collected from bats, pangolins, monkeys, and other species. The diverse RNA viruses were analyzed, especially focusing on the genome organization, genetic divergence and phylogenetic relationships. Results In this study, we investigated the viral composition of eight libraries from bats, pangolins, monkeys, and other species, and found several diverse RNA viruses, including the Alphacoronavirus from bat specimens. By characterizing the genome organization, genetic divergence, and phylogenetic relationships, we identified five Alphacoronavirus strains, which shared phylogenetic association with Bat-CoV-HKU8-related strains. The pestivirus-like virus related to recently identified Dongyang pangolin virus (DYPV) strains from dead pangolin specimens, suggesting that these viruses are evolving. Some genomes showed higher divergence from known species (e.g., calicivirus CS9-Cali-YN-CHN-2020), and many showed evidence of recombination events with unknown or known strains (e.g., mamastroviruses BF2-astro-YN-CHN-2020 and EV-A122 AKM5-YN-CHN-2020). The newly identified viruses showed extensive changes and could be assigned as new species, or even genus (e.g., calicivirus CS9-Cali-YN-CHN-2020 and iflavirus Ifla-YN-CHN-2020). Moreover, we identified several highly divergent RNA viruses and estimated their evolutionary characteristics among different hosts, providing data for further examination of their evolutionary dynamics. Conclusion Overall, our study emphasizes the close association between emerging viruses and infectious diseases, and the need for more comprehensive surveys.
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Affiliation(s)
- Zhenzhi Han
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, China
| | - Jinbo Xiao
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yang Song
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaonan Zhao
- Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Qiang Sun
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Huanhuan Lu
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Keyi Zhang
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jichen Li
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Junhan Li
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Fenfen Si
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Guoyan Zhang
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hehe Zhao
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Senquan Jia
- Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Jienan Zhou
- Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Dongyan Wang
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shuangli Zhu
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dongmei Yan
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wenbo Xu
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Xiaoqing Fu
- Yunnan Center for Disease Control and Prevention, Kunming, China
- Xiaoqing Fu,
| | - Yong Zhang
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- *Correspondence: Yong Zhang,
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Metagenomic Analysis of RNA Fraction Reveals the Diversity of Swine Oral Virome on South African Backyard Swine Farms in the uMgungundlovu District of KwaZulu-Natal Province. Pathogens 2022; 11:pathogens11080927. [PMID: 36015047 PMCID: PMC9416320 DOI: 10.3390/pathogens11080927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/31/2022] [Accepted: 08/05/2022] [Indexed: 11/16/2022] Open
Abstract
Numerous RNA viruses have been reported in backyard swine populations in various countries. In the absence of active disease surveillance, a persistent knowledge gap exists on the diversity of RNA viruses in South African backyard swine populations. This is the first study investigating the diversity of oral RNA virome of the backyard swine in South Africa. We used three samples of backyard swine oral secretion (saliva) collected from three distantly located backyard swine farms (BSFs) in the uMgungundlovu District, KwaZulu-Natal, South Africa. Total viral RNA was extracted and used for the library preparation for deep sequencing using the Illumina HiSeq X instrument. The FASTQ files containing paired-end reads were analyzed using Genome Detective v 1.135. The assembled nucleotide sequences were analyzed using the PhyML phylogenetic tree. The genome sequence analysis identified a high diversity of swine enteric viruses in the saliva samples obtained from BSF2 and BSF3, while only a few viruses were identified in the saliva obtained from BSF1. The swine enteric viruses belonged to various animal virus families; however, two fungal viruses, four plant viruses, and five unclassified RNA viruses were also identified. Specifically, viruses of the family Astroviridae, according to the number of reads, were the most prevalent. Of note, the genome sequences of Rotavirus A (RVA) and Rotavirus C (RVC) at BSF2 and RVC and Hepatitis E virus (HEV) at BSF3 were also obtained. The occurrence of various swine enteric viruses in swine saliva suggests a high risk of diarrhoeic diseases in the backyard swine. Of note, zoonotic viruses in swine saliva, such as RVA, RVC, and HEV, indicate a risk of zoonotic spillover to the exposed human populations. We recommend the implementation of biosecurity to ensure sustainable backyard swine farming while safeguarding public health.
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Schuele L, Lizarazo-Forero E, Strutzberg-Minder K, Schütze S, Löbert S, Lambrecht C, Harlizius J, Friedrich AW, Peter S, Rossen JWA, Couto N. Application of shotgun metagenomics sequencing and targeted sequence capture to detect circulating porcine viruses in the Dutch-German border region. Transbound Emerg Dis 2021; 69:2306-2319. [PMID: 34347385 PMCID: PMC9540031 DOI: 10.1111/tbed.14249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/16/2021] [Indexed: 12/22/2022]
Abstract
Porcine viruses have been emerging in recent decades, threatening animal and human health, as well as economic stability for pig farmers worldwide. Next‐generation sequencing (NGS) can detect and characterize known and unknown viruses but has limited sensitivity when an unbiased approach, such as shotgun metagenomics sequencing, is used. To increase the sensitivity of NGS for the detection of viruses, we applied and evaluated a broad viral targeted sequence capture (TSC) panel and compared it to an unbiased shotgun metagenomic approach. A cohort of 36 pooled porcine nasal swab and blood serum samples collected from both sides of the Dutch–German border region were evaluated. Overall, we detected 46 different viral species using TSC, compared to 40 viral species with a shotgun metagenomics approach. Furthermore, we performed phylogenetic analysis on recovered influenza A virus (FLUAV) genomes from Germany and revealed a close similarity to a zoonotic influenza strain previously detected in the Netherlands. Although TSC introduced coverage bias within the detected viruses, it improved sensitivity, genome sequence depth and contig length. In‐depth characterization of the swine virome, coupled with developing new enrichment techniques, can play a crucial role in the surveillance of circulating porcine viruses and emerging zoonotic pathogens.
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Affiliation(s)
- Leonard Schuele
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Erley Lizarazo-Forero
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Sabine Schütze
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, Bad Sassendorf, Germany
| | - Sandra Löbert
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, Bad Sassendorf, Germany
| | - Claudia Lambrecht
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, Bad Sassendorf, Germany
| | - Jürgen Harlizius
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, Bad Sassendorf, Germany
| | - Alex W Friedrich
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Natacha Couto
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
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Han Z, Song Y, Xiao J, Zhao X, Lu H, Zhang K, Jia S, Zhou J, Li J, Si F, Sun Q, Zhu S, Wang D, Yan D, Xu W, Fu X, Zhang Y. Monsavirus in monkey rectal swab and throat swab specimens in China: Proposal for Posaliviridae as a new family in Picornavirales. Virus Res 2021; 303:198501. [PMID: 34252491 DOI: 10.1016/j.virusres.2021.198501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 11/16/2022]
Abstract
Posa-like viruses have been detected in the fecal samples of several host species and are considered unclassified members of Picornavirales. Here, we identified genomic fragments of novel posa-like viruses (monsaviruses) in monkey specimens through next generation sequencing and obtained 11 full-length genomes. This monsavirus shared 88.5-89.2% nucleotide similarity with the Tottori-HG1 strain (GenBank accession LC123275). In total, 713 nucleotide polymorphism sites were identified, indicating their persistent evolution during circulation. The genomic organization and phylogenetic relationship of monsavirus were determined. Subsequent phylogenetic analysis of the conserved replication block of Hel-Pro-RdRp and core RNA-dependent RNA polymerase domain-based analysis of posa-like viruses showed significant separation compared with other known families. Further, posa-like virus genomes possessed the classical replication block of picornavirus in the 5' part of genome and picorna-like capsid domains at the structural coding region of 3' part of genome. Based on these results, we proposed the new family Posaliviridae, within Picornavirales. Four genera, which showed 68.6-75.5% amino acid distances but similar genomic organization including the conserved replication block of Hel-Pro-RdRp, the same order of the genomic coding region, and picorna-like capsid domains, were identified. The flexible genomic organization strategy and a large evolutionary scale of Posaliviridae was explicit. This study provides novel information on monsaviruses and important taxonomic data for the family Posaliviridae.
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Affiliation(s)
- Zhenzhi Han
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Medical Virology, NHC Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yang Song
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Medical Virology, NHC Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jinbo Xiao
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Medical Virology, NHC Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xiaonan Zhao
- Yunnan Center for Disease Control and Prevention, Kunming 650022, PR China
| | - Huanhuan Lu
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Medical Virology, NHC Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Keyi Zhang
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Medical Virology, NHC Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Senquan Jia
- Yunnan Center for Disease Control and Prevention, Kunming 650022, PR China
| | - Jienan Zhou
- Yunnan Center for Disease Control and Prevention, Kunming 650022, PR China
| | - Junhan Li
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Medical Virology, NHC Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Fenfen Si
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Medical Virology, NHC Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Qiang Sun
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Medical Virology, NHC Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Shuangli Zhu
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Medical Virology, NHC Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Dongyan Wang
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Medical Virology, NHC Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Dongmei Yan
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Medical Virology, NHC Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Wenbo Xu
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Medical Virology, NHC Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China; Center for Biosafety Mega-Science, Chinese Academy of Sciences. Wuhan 430071, PR China
| | - Xiaoqing Fu
- Yunnan Center for Disease Control and Prevention, Kunming 650022, PR China.
| | - Yong Zhang
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Medical Virology, NHC Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China; Center for Biosafety Mega-Science, Chinese Academy of Sciences. Wuhan 430071, PR China.
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Multiple clades of Husavirus in South America revealed by next generation sequencing. PLoS One 2021; 16:e0248486. [PMID: 33755700 PMCID: PMC7987173 DOI: 10.1371/journal.pone.0248486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 02/28/2021] [Indexed: 11/19/2022] Open
Abstract
Husavirus (HuV) is an unclassified virus of the order Picornavirales that has already been identified worldwide in various locations. The genetic, epidemiological, and pathogenic characteristics are, however, little understood. In children with acute gastroenteritis, this study used next-generation sequencing to recognize unknown sources of viruses. In particular, 251 fecal samples obtained from individuals were sequenced in southern, northeastern, and northern Brazil. all samples were also analyzed using culture methods and parasitological tests to classify other enteric pathogens such as bacteria, parasites, and viruses. 1.9% of the samples tested positive for HuV, for a total of 5 positive children, with a mean age of 2 year, with three males and two females. Detailed molecular characterization of full genomes showed that Brazilian HuVs’ nucleotide divergence is less than 11%. The genetic gap between Brazilian sequences and the closest HuV reported previously, on the other hand, is 18%. The study showed that Brazilian sequences are closely related to the HuV defined in Viet Nam in 2013, further characterization based on phylogenetics. At least two divergent clades of HuV in South America were also seen in the phylogenetic study.
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Han Z, Xiao J, Song Y, Hong M, Dai G, Lu H, Zhang M, Liang Y, Yan D, Zhu S, Xu W, Zhang Y. The Husavirus Posa-Like Viruses in China, and a New Group of Picornavirales. Viruses 2020; 12:v12090995. [PMID: 32906743 PMCID: PMC7551994 DOI: 10.3390/v12090995] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/30/2020] [Accepted: 09/04/2020] [Indexed: 01/09/2023] Open
Abstract
Novel posa-like viral genomes were first identified in swine fecal samples using metagenomics and were designated as unclassified viruses in the order Picornavirales. In the present study, nine husavirus strains were identified in China. Their genomes share 94.1–99.9% similarity, and alignment of these nine husavirus strains identified 697 nucleotide polymorphism sites across their full-length genomes. These nine strains were directly clustered with the Husavirus 1 lineage, and their genomic arrangement showed similar characteristics. These posa-like viruses have undergone a complex evolutionary process, and have a wide geographic distribution, complex host spectrum, deep phylogenetic divergence, and diverse genomic organizations. The clade of posa-like viruses forms a single group, which is evolutionarily distinct from other known families and could represent a distinct family within the Picornavirales. The genomic arrangement of Picornavirales and the new posa-like viruses are different, whereas the posa-like viruses have genomic modules similar to the families Dicistroviridae and Marnaviridae. The present study provides valuable genetic evidence of husaviruses in China, and clarifies the phylogenetic dynamics and the evolutionary characteristics of Picornavirales.
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Affiliation(s)
- Zhenzhi Han
- WHO WPRO Regional Polio Reference Laboratory and NHC Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Z.H.); (J.X.); (Y.S.); (H.L.); (M.Z.); (Y.L.); (D.Y.); (S.Z.); (W.X.)
| | - Jinbo Xiao
- WHO WPRO Regional Polio Reference Laboratory and NHC Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Z.H.); (J.X.); (Y.S.); (H.L.); (M.Z.); (Y.L.); (D.Y.); (S.Z.); (W.X.)
| | - Yang Song
- WHO WPRO Regional Polio Reference Laboratory and NHC Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Z.H.); (J.X.); (Y.S.); (H.L.); (M.Z.); (Y.L.); (D.Y.); (S.Z.); (W.X.)
| | - Mei Hong
- Tibet Center for Disease Control and Prevention, Tibet Autonomous Region, Lhasa 850000, China; (M.H.); (G.D.)
| | - Guolong Dai
- Tibet Center for Disease Control and Prevention, Tibet Autonomous Region, Lhasa 850000, China; (M.H.); (G.D.)
| | - Huanhuan Lu
- WHO WPRO Regional Polio Reference Laboratory and NHC Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Z.H.); (J.X.); (Y.S.); (H.L.); (M.Z.); (Y.L.); (D.Y.); (S.Z.); (W.X.)
| | - Man Zhang
- WHO WPRO Regional Polio Reference Laboratory and NHC Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Z.H.); (J.X.); (Y.S.); (H.L.); (M.Z.); (Y.L.); (D.Y.); (S.Z.); (W.X.)
| | - Yueling Liang
- WHO WPRO Regional Polio Reference Laboratory and NHC Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Z.H.); (J.X.); (Y.S.); (H.L.); (M.Z.); (Y.L.); (D.Y.); (S.Z.); (W.X.)
| | - Dongmei Yan
- WHO WPRO Regional Polio Reference Laboratory and NHC Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Z.H.); (J.X.); (Y.S.); (H.L.); (M.Z.); (Y.L.); (D.Y.); (S.Z.); (W.X.)
| | - Shuangli Zhu
- WHO WPRO Regional Polio Reference Laboratory and NHC Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Z.H.); (J.X.); (Y.S.); (H.L.); (M.Z.); (Y.L.); (D.Y.); (S.Z.); (W.X.)
| | - Wenbo Xu
- WHO WPRO Regional Polio Reference Laboratory and NHC Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Z.H.); (J.X.); (Y.S.); (H.L.); (M.Z.); (Y.L.); (D.Y.); (S.Z.); (W.X.)
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yong Zhang
- WHO WPRO Regional Polio Reference Laboratory and NHC Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Z.H.); (J.X.); (Y.S.); (H.L.); (M.Z.); (Y.L.); (D.Y.); (S.Z.); (W.X.)
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
- Correspondence: ; Tel.: +86-10-58900183; Fax: +86-10-58900184
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8
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Van Borm S, Vanneste K, Fu Q, Maes D, Schoos A, Vallaey E, Vandenbussche F. Increased viral read counts and metagenomic full genome characterization of porcine astrovirus 4 and Posavirus 1 in sows in a swine farm with unexplained neonatal piglet diarrhea. Virus Genes 2020; 56:696-704. [PMID: 32880793 DOI: 10.1007/s11262-020-01791-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/21/2020] [Indexed: 12/18/2022]
Abstract
Neonatal diarrhea in piglets may cause major losses in affected pig herds. The present study used random high-throughput RNA sequencing (metagenomic next generation sequencing, mNGS) to investigate the virome of sows from a farm with persistent neonatal piglet diarrhea in comparison to two control farms without diarrhea problems. A variety of known swine gastrointestinal viruses was detected in the control farms as well as in the problem farm (Mamastrovirus, Enterovirus, Picobirnavirus, Posavirus 1, Kobuvirus, Proprismacovirus). A substantial increase in normalized viral read counts was observed in the affected farm compared to the control farms. The increase was attributable to a single viral species in each of the sampled sows (porcine astrovirus 4 and Posavirus 1). The complete genomes of a porcine astrovirus 4 and two co-infecting Posavirus 1 were de novo assembled and characterized. The 6734 nt single-stranded RNA genome of porcine astrovirus 4 (PoAstV-4) strain Belgium/2019 contains three overlapping open reading frames (nonstructural protein 1ab, nonstructural protein 1a, capsid protein). Posavirus 1 strains Belgium/01/2019 and Belgium/02/2019 have a 9814 nt single-stranded positive-sense RNA genome encoding a single open reading frame (polyprotein precursor) containing the five expected Picornavirales-conserved protein domains. The study highlights the potential of mNGS workflows to study unexplained neonatal diarrhea in piglets and contributes to the scarce availability of both PoAstV-4 and Posavirus-1 whole genome sequences from Western Europe.
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Affiliation(s)
- Steven Van Borm
- Department of Animal Infectious Diseases, Sciensano, Brussels, Belgium.
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Qiang Fu
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Dominiek Maes
- Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Alexandra Schoos
- Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
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9
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Chung HC, Nguyen VG, Huynh TML, Do HQ, Vo DC, Park YH, Park BK. Molecular-based investigation and genetic characterization of porcine stool-associated RNA virus (posavirus) lineages 1 to 3 in pigs in South Korea from 2017 to 2019. Res Vet Sci 2019; 128:286-292. [PMID: 31869594 DOI: 10.1016/j.rvsc.2019.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 11/07/2019] [Accepted: 11/19/2019] [Indexed: 12/25/2022]
Abstract
Recent results on the detection and genetic characterization of stool-associated RNA viruses from different species have increased the knowledge about the extreme genetic diversity of picornaviruses. This study aimed to investigate the presence of unclassified porcine stool-associated RNA viruses (posaviruses) in South Korea and to elucidate the molecular evolution of the viruses. By RT-PCR, posaviruses 1 and 3 were exclusively found in fecal samples and consistently detected in three consecutive years in six of eight provinces, with 148/697 (21.2%) and 33/84 (39.3%) positive samples and farms, respectively. Every age group but the older age groups (finisher, sow) had significantly higher positive rates of posavirus 1 than posavirus 3. An analysis of the RNA-dependent RNA polymerase sequences by likelihood mapping and maximum-likelihood-based phylogenetic analysis revealed that stool-associated RNA viruses formed four supergroups that were well separated from all recognized families of the order Picornavirales. Five genomes of Korean posaviruses generated in this study were phylogenetically grouped with posavirus 1 and posavirus 3 and were predicted to have the typical genome organization of picornaviruses.
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Affiliation(s)
- Hee-Chun Chung
- Department of Veterinary Medicine Virology Laboratory, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 151-742, Republic of Korea
| | - Van-Giap Nguyen
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Viet Nam
| | - Thi-My-Le Huynh
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Viet Nam
| | - Hai-Quynh Do
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Viet Nam
| | - Dinh-Chuong Vo
- Devision of Veterinary Epidemiology, Department of Animal Health, Ministry of Agriculture and Rural Development, Hanoi, Viet Nam
| | - Yong-Ho Park
- Department of Veterinary Microbiology, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 151-742, Republic of Korea.
| | - Bong-Kyun Park
- Department of Veterinary Medicine Virology Laboratory, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 151-742, Republic of Korea.
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10
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Phylogenetic analysis of novel posaviruses detected in feces of Japanese pigs with posaviruses and posa-like viruses of vertebrates and invertebrates. Arch Virol 2019; 164:2147-2151. [PMID: 31111261 DOI: 10.1007/s00705-019-04289-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 04/24/2019] [Indexed: 01/20/2023]
Abstract
Posaviruses and posa-like viruses are unclassified viruses with sequence similarity to viruses of the order Picornavirales. They have been reported in various vertebrates and invertebrates. We identified 11 posavirus-like sequences in porcine feces and performed phylogenic analysis. Previously reported Japanese posaviruses and those identified in this study clustered with posavirus 1, 4, and 7 and husavirus 1, while five viruses branched into three independent lineages, tentatively named posavirus 10, 11, and 12. Interestingly, posaviruses, except for posavirus 8 and 9, husaviruses, and rasaviruses, formed a cluster consisting of viruses only from pigs, humans, and rats, while posavirus 8 and 9, fisavirus, and basaviruses clustered with posa-like viruses from invertebrates.
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11
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Richard CA, Hervet C, Ménard D, Gutsche I, Normand V, Renois F, Meurens F, Eléouët JF. First demonstration of the circulation of a pneumovirus in French pigs by detection of anti-swine orthopneumovirus nucleoprotein antibodies. Vet Res 2018; 49:118. [PMID: 30518406 PMCID: PMC6280484 DOI: 10.1186/s13567-018-0615-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/29/2018] [Indexed: 12/22/2022] Open
Abstract
The presence of pneumoviruses in pigs is poorly documented. In this study, we used the published sequence of the nucleoprotein (N) of the recently identified Swine Orthopneumovirus (SOV) to express and purify SOV N as a recombinant protein in Escherichia coli. This protein was purified as nanorings and used to set up an enzyme-linked immunosorbent assay, which was used to analyse the presence of anti-pneumovirus N antibodies in swine sera. Sera collected from different pig farms in the West of France and from specific pathogen free piglets before colostrum uptake showed indirectly that a pneumovirus is circulating in pig populations with some variations between animals. Piglets before colostrum uptake were sero-negative for anti-pneumovirus antibodies while most of the other pigs showed positivity. Interestingly, in two farms presenting respiratory clinical signs and negative or under control for some common respiratory pathogens, pigs were detected positive for anti-pneumovirus antibodies. Globally, anti-pneumovirus N antibody concentrations were variable between and within farms. Further studies will aim to isolate the circulating virus and determine its potential pathogenicity. SOV could potentially become a new member of the porcine respiratory complex, important on its own or in association with other viral and bacterial micro-organisms.
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Affiliation(s)
- Charles-Adrien Richard
- Unité de Virologie et Immunologie Moléculaires, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Caroline Hervet
- BIOEPAR, INRA, Oniris, Université Bretagne Loire, 44307, Nantes, France
| | - Déborah Ménard
- BIOEPAR, INRA, Oniris, Université Bretagne Loire, 44307, Nantes, France
| | - Irina Gutsche
- CNRS, CEA, IBS, University of Grenoble Alpes, 38000, Grenoble, France
| | - Valérie Normand
- Porc.Spective Swine Vet Practice, Chêne Vert Conseil Veterinary Group, ZA de Gohélève, 56920, Noyal-Pontivy, France
| | - Fanny Renois
- BIOEPAR, INRA, Oniris, Université Bretagne Loire, 44307, Nantes, France
| | - François Meurens
- BIOEPAR, INRA, Oniris, Université Bretagne Loire, 44307, Nantes, France
| | - Jean-François Eléouët
- Unité de Virologie et Immunologie Moléculaires, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
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12
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Wolf YI, Kazlauskas D, Iranzo J, Lucía-Sanz A, Kuhn JH, Krupovic M, Dolja VV, Koonin EV. Origins and Evolution of the Global RNA Virome. mBio 2018; 9:e02329-18. [PMID: 30482837 PMCID: PMC6282212 DOI: 10.1128/mbio.02329-18] [Citation(s) in RCA: 310] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 10/31/2018] [Indexed: 01/12/2023] Open
Abstract
Viruses with RNA genomes dominate the eukaryotic virome, reaching enormous diversity in animals and plants. The recent advances of metaviromics prompted us to perform a detailed phylogenomic reconstruction of the evolution of the dramatically expanded global RNA virome. The only universal gene among RNA viruses is the gene encoding the RNA-dependent RNA polymerase (RdRp). We developed an iterative computational procedure that alternates the RdRp phylogenetic tree construction with refinement of the underlying multiple-sequence alignments. The resulting tree encompasses 4,617 RNA virus RdRps and consists of 5 major branches; 2 of the branches include positive-sense RNA viruses, 1 is a mix of positive-sense (+) RNA and double-stranded RNA (dsRNA) viruses, and 2 consist of dsRNA and negative-sense (-) RNA viruses, respectively. This tree topology implies that dsRNA viruses evolved from +RNA viruses on at least two independent occasions, whereas -RNA viruses evolved from dsRNA viruses. Reconstruction of RNA virus evolution using the RdRp tree as the scaffold suggests that the last common ancestors of the major branches of +RNA viruses encoded only the RdRp and a single jelly-roll capsid protein. Subsequent evolution involved independent capture of additional genes, in particular, those encoding distinct RNA helicases, enabling replication of larger RNA genomes and facilitating virus genome expression and virus-host interactions. Phylogenomic analysis reveals extensive gene module exchange among diverse viruses and horizontal virus transfer between distantly related hosts. Although the network of evolutionary relationships within the RNA virome is bound to further expand, the present results call for a thorough reevaluation of the RNA virus taxonomy.IMPORTANCE The majority of the diverse viruses infecting eukaryotes have RNA genomes, including numerous human, animal, and plant pathogens. Recent advances of metagenomics have led to the discovery of many new groups of RNA viruses in a wide range of hosts. These findings enable a far more complete reconstruction of the evolution of RNA viruses than was attainable previously. This reconstruction reveals the relationships between different Baltimore classes of viruses and indicates extensive transfer of viruses between distantly related hosts, such as plants and animals. These results call for a major revision of the existing taxonomy of RNA viruses.
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Affiliation(s)
- Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Darius Kazlauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- Département de Microbiologie, Institut Pasteur, Paris, France
| | - Jaime Iranzo
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Adriana Lucía-Sanz
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
- Centro Nacional de Biotecnología, Madrid, Spain
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
| | - Mart Krupovic
- Département de Microbiologie, Institut Pasteur, Paris, France
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
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13
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Siqueira JD, Dominguez-Bello MG, Contreras M, Lander O, Caballero-Arias H, Xutao D, Noya-Alarcon O, Delwart E. Complex virome in feces from Amerindian children in isolated Amazonian villages. Nat Commun 2018; 9:4270. [PMID: 30323210 PMCID: PMC6189175 DOI: 10.1038/s41467-018-06502-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 09/06/2018] [Indexed: 01/22/2023] Open
Abstract
The number of viruses circulating in small isolated human populations may be reduced by viral extinctions and rare introductions. Here we used viral metagenomics to characterize the eukaryotic virome in feces from healthy children from a large urban center and from three Amerindian villages with minimal outside contact. Numerous human enteric viruses, mainly from the Picornaviridae and Caliciviridae families, were sequenced from each of the sites. Multiple children from the same villages shed closely related viruses reflecting frequent transmission clusters. Feces of isolated villagers also contained multiple viral genomes of unknown cellular origin from the Picornavirales order and CRESS-DNA group and higher levels of nematode and protozoan DNA. Despite cultural and geographic isolation, the diversity of enteric human viruses was therefore not reduced in these Amazonian villages. Frequent viral introductions and/or increased susceptibility to enteric infections may account for the complex fecal virome of Amerindian children in isolated villages.
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Affiliation(s)
- Juliana D Siqueira
- Blood Systems Research Institute, San Francisco, CA, 94118, USA.,Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, 20.231-050, Brazil
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology and of Anthropology, Rutgers University, New Brunswick, NJ, 08901-8554, USA
| | - Monica Contreras
- Center for Biophysics and Biochemistry, Venezuelan Institute of Scientific Research (IVIC), Caracas, 01204, Venezuela
| | - Orlana Lander
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, 1051, Venezuela
| | - Hortensia Caballero-Arias
- Department of Anthropology, Venezuelan Institute of Scientific Research (IVIC), Caracas, 01204, Venezuela
| | - Deng Xutao
- Blood Systems Research Institute, San Francisco, CA, 94118, USA.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94118, USA
| | - Oscar Noya-Alarcon
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, 1051, Venezuela.,Amazonic Center for Research and Control of Tropical Diseases (CAICET), Puerto Ayacucho, 7101, Venezuela
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, 94118, USA. .,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94118, USA.
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14
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Altan E, Aiemjoy K, Phan TG, Deng X, Aragie S, Tadesse Z, Callahan KE, Keenan J, Delwart E. Enteric virome of Ethiopian children participating in a clean water intervention trial. PLoS One 2018; 13:e0202054. [PMID: 30114205 PMCID: PMC6095524 DOI: 10.1371/journal.pone.0202054] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/26/2018] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The enteric viruses shed by different populations can be influenced by multiple factors including access to clean drinking water. We describe here the eukaryotic viral genomes in the feces of Ethiopian children participating in a clean water intervention trial. METHODOLOGY/PRINCIPAL FINDINGS Fecal samples from 269 children with a mean age of 2.7 years were collected from 14 villages in the Amhara region of Ethiopia, half of which received a new hand-dug water well. Feces from these villages were then analyzed in 29 sample pools using viral metagenomics. A total of 127 different viruses belonging to 3 RNA and 3 DNA viral families were detected. Picornaviridae family sequence reads were the most commonly found, originating from 14 enterovirus and 6 parechovirus genotypes plus multiple members of four other picornavirus genera (cosaviruses, saliviruses, kobuviruses, and hepatoviruses). Picornaviruses with nearly identical capsid VP1 were detected in different pools reflecting recent spread of these viral strains. Next in read frequencies and positive pools were sequences from the Caliciviridae family including noroviruses GI and GII and sapoviruses. DNA viruses from multiple genera of the Parvoviridae family were detected (bocaviruses 1-4, bufavirus 3, and dependoparvoviruses), together with four species of adenoviruses and common anelloviruses shedding. RNA in the order Picornavirales and CRESS-DNA viral genomes, possibly originating from intestinal parasites or dietary sources, were also characterized. No significant difference was observed between the number of mammalian viruses shed from children from villages with and without a new water well. CONCLUSIONS We describe an approach to estimate the efficacy of potentially virus transmission-reducing interventions and the first complete (DNA and RNA viruses) description of the enteric viromes of East African children. A wide diversity of human enteric viruses was found in both intervention and control groups. Mammalian enteric virome diversity was not reduced in children from villages with a new water well. This population-based sampling also provides a baseline of the enteric viruses present in Northern Ethiopia against which to compare future viromes.
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Affiliation(s)
- Eda Altan
- Blood Systems Research Institute, San Francisco, California, United States of America
- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
| | - Kristen Aiemjoy
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, California, United States of America
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | - Tung G. Phan
- Blood Systems Research Institute, San Francisco, California, United States of America
- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, California, United States of America
- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
| | | | | | | | - Jeremy Keenan
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, California, United States of America
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, California, United States of America
- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
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15
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Chen J, Lu M, Ma T, Cao L, Zhu X, Zhang X, Shi D, Shi H, Liu J, Feng L. Detection and complete genome characteristics of Posavirus 1 from pigs in China. Virus Genes 2017; 54:145-148. [PMID: 29181630 DOI: 10.1007/s11262-017-1512-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 10/05/2017] [Indexed: 11/26/2022]
Abstract
Porcine stool-associated RNA virus 1 (Posavirus 1) is a novel member of picornaviruses and first identified from fecal samples of 30-day-old pigs with diarrhea in USA in 2011. To evaluate the existence of Posavirus 1 in swine herds, 118 clinical samples from diarrheal pigs and 31 fecal swabs from healthy pigs were collected and detected by reverse transcription-polymerase chain reaction (RT-PCR) using Posavirus 1-specific primers. Only five fecal samples from diarrheal pigs on two swine farms were positive for Posavirus 1. The complete genome sequences [excluding poly (A) tail] of two representative isolates SDQD-25 and HBTS-11 are determined and consist of 9840 and 9819 nucleotides in length, and encode one putative polyprotein of 3070 and 2952 amino acids, respectively. They share 90.3% homology with each other and 81.3-95.4% homologies with American Posavirus 1 isolates or strains at the nucleotide sequence level. The phylogenetic analysis based on the entire genomes of reference picornavirus strains or isolates showed SDQD-25, HBTS-11 cluster together with American Posavirus 1 isolates or strains, yet are clearly distant from the other picornaviruses. The complete genome sequences of Chinese Posavirus 1 isolates will enrich the information of Posavirus 1 sequence database and further expedite posavirus research on the genetic diversity, epidemiology, and evolution in China.
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Affiliation(s)
- Jianfei Chen
- Division of Swine Digestive System Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Manman Lu
- Division of Swine Digestive System Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Tianxin Ma
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Liyan Cao
- Division of Swine Digestive System Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Xiangdong Zhu
- Division of Swine Digestive System Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Xin Zhang
- Division of Swine Digestive System Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Da Shi
- Division of Swine Digestive System Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Hongyan Shi
- Division of Swine Digestive System Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Jianbo Liu
- Division of Swine Digestive System Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Li Feng
- Division of Swine Digestive System Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
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16
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Oude Munnink BB, Phan MVT, Simmonds P, Koopmans MPG, Kellam P, van der Hoek L, Cotten M. Characterization of Posa and Posa-like virus genomes in fecal samples from humans, pigs, rats, and bats collected from a single location in Vietnam. Virus Evol 2017; 3:vex022. [PMID: 28948041 PMCID: PMC5597861 DOI: 10.1093/ve/vex022] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Porcine stool-associated RNA virus (posavirus), and Human stool-associated RNA virus
(husavirus) are viruses in the order Picornavirales recently described in
porcine and human fecal samples. The tentative group (Posa and Posa-like viruses: PPLVs)
also includes fish stool-associated RNA virus (fisavirus) as well as members detected in
insects (Drosophila subobscura and Anopheles sinensis)
and parasites (Ascaris suum). As part of an agnostic deep sequencing
survey of animal and human viruses in Vietnam, we detected three husaviruses in human
fecal samples, two of which share 97–98% amino acid identity to Dutch husavirus strains
and one highly divergent husavirus with only 25% amino acid identity to known husaviruses.
In addition, the current study found forty-seven complete posavirus genomes from pigs, ten
novel rat stool-associated RNA virus genomes (tentatively named rasavirus), and sixteen
novel bat stool-associated RNA virus genomes (tentatively named basavirus). The five
expected Picornavirales protein domains (helicase, 3C-protease,
RNA-dependent RNA polymerase, and two Picornavirus capsid domain) were found to be encoded
by all PPLV genomes. In addition, a nucleotide composition analysis revealed that the
PPLVs shared compositional properties with arthropod viruses and predicted non-mammalian
hosts for all PPLV lineages. The study adds seventy-six genomes to the twenty-nine PPLV
genomes currently available and greatly extends our sequence knowledge of this group of
viruses within the Picornavirales order.
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Affiliation(s)
- Bas B Oude Munnink
- Department of Virus Genomics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.,Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - My V T Phan
- Department of Virus Genomics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.,Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, UK
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Paul Kellam
- Department of Virus Genomics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.,Department of Infectious Diseases and Immunity, Imperial College London, London, UK
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Matthew Cotten
- Department of Virus Genomics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.,Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
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17
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Zhang W, Yang S, Shan T, Hou R, Liu Z, Li W, Guo L, Wang Y, Chen P, Wang X, Feng F, Wang H, Chen C, Shen Q, Zhou C, Hua X, Cui L, Deng X, Zhang Z, Qi D, Delwart E. Virome comparisons in wild-diseased and healthy captive giant pandas. MICROBIOME 2017; 5:90. [PMID: 28780905 PMCID: PMC5545856 DOI: 10.1186/s40168-017-0308-0] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 07/13/2017] [Indexed: 05/12/2023]
Abstract
BACKGROUND The giant panda (Ailuropoda melanoleuca) is a vulnerable mammal herbivore living wild in central China. Viral infections have become a potential threat to the health of these endangered animals, but limited information related to these infections is available. METHODS Using a viral metagenomic approach, we surveyed viruses in the feces, nasopharyngeal secretions, blood, and different tissues from a wild giant panda that died from an unknown disease, a healthy wild giant panda, and 46 healthy captive animals. RESULTS The previously uncharacterized complete or near complete genomes of four viruses from three genera in Papillomaviridae family, six viruses in a proposed new Picornaviridae genus (Aimelvirus), two unclassified viruses related to posaviruses in Picornavirales order, 19 anelloviruses in four different clades of Anelloviridae family, four putative circoviruses, and 15 viruses belonging to the recently described Genomoviridae family were sequenced. Reflecting the diet of giant pandas, numerous insect virus sequences related to the families Iflaviridae, Dicistroviridae, Iridoviridae, Baculoviridae, Polydnaviridae, and subfamily Densovirinae and plant viruses sequences related to the families Tombusviridae, Partitiviridae, Secoviridae, Geminiviridae, Luteoviridae, Virgaviridae, and Rhabdoviridae; genus Umbravirus, Alphaflexiviridae, and Phycodnaviridae were also detected in fecal samples. A small number of insect virus sequences were also detected in the nasopharyngeal secretions of healthy giant pandas and lung tissues from the dead wild giant panda. Although the viral families present in the sick giant panda were also detected in the healthy ones, a higher proportion of papillomaviruses, picornaviruses, and anelloviruses reads were detected in the diseased panda. CONCLUSION This viral survey increases our understanding of eukaryotic viruses in giant pandas and provides a baseline for comparison to viruses detected in future infectious disease outbreaks. The similar viral families detected in sick and healthy giant pandas indicate that these viruses result in commensal infections in most immuno-competent animals.
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Affiliation(s)
- Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Tongling Shan
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241 China
| | - Rong Hou
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Zhijian Liu
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Wang Li
- Department of Laboratory Medicine, Jiangsu Taizhou People’s Hospital, Taizhou, Jiangsu 225300 China
| | - Lianghua Guo
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240 China
| | - Yan Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Peng Chen
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Xiaochun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Feifei Feng
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Hua Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Chao Chen
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Quan Shen
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Chenglin Zhou
- Department of Laboratory Medicine, Jiangsu Taizhou People’s Hospital, Taizhou, Jiangsu 225300 China
| | - Xiuguo Hua
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240 China
| | - Li Cui
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240 China
| | - Xutao Deng
- Blood Systems Research Institute, Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118 USA
| | - Zhihe Zhang
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Dunwu Qi
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610000 China
| | - Eric Delwart
- Blood Systems Research Institute, Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118 USA
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18
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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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