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Han Z, Wang F, Xiao J, Fu H, Song Y, Jiang M, Lu H, Li J, Xu Y, Zhu R, Zhang Y, Zhao L. Synergetic association between coxsackievirus A16 genotype evolution and recombinant form shifts. Virus Evol 2023; 10:vead080. [PMID: 38361814 PMCID: PMC10868544 DOI: 10.1093/ve/vead080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 11/05/2023] [Accepted: 12/17/2023] [Indexed: 02/17/2024] Open
Abstract
Coxsackievirus A16 (CVA16) is a major pathogen that causes hand, foot, and mouth disease (HFMD). The recombination form (RF) shifts and global transmission dynamics of CVA16 remain unknown. In this retrospective study, global sequences of CVA16 were retrieved from the GenBank database and analyzed using comprehensive phylogenetic inference, RF surveys, and population structure. A total of 1,663 sequences were collected, forming a 442-sequences dataset for VP1 coding region analysis and a 345-sequences dataset for RF identification. Based on the VP1 coding region used for serotyping, three genotypes (A, B, and D), two subgenotypes of genotype B (B1 and B2), and three clusters of subgenotype B1 (B1a, B1b, and B1c) were identified. Cluster B1b has dominated the global epidemics, B2 disappeared in 2000, and D is an emerging genotype dating back to August 2002. Globally, four oscillation phases of CVA16 evolution, with a peak in 2013, and three migration pathways were identified. Europe, China, and Japan have served as the seeds for the global transmission of CVA16. Based on the 3D coding region of the RFs, five clusters of RFs (RF-A to -E) were identified. The shift in RFs from RF-B and RF-C to RF-D was accompanied by a change in genotype from B2 to B1a and B1c and then to B1b. In conclusion, the evolution and population dynamics of CVA16, especially the coevolution of 3D and VP1 genes, revealed that genotype evolution and RF replacement were synergistic rather than stochastic.
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Affiliation(s)
| | - Fangming Wang
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing 100020, China
| | - Jinbo Xiao
- WHO WPRO Regional Polio Reference Laboratory, 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, No.155 Changbai Road, Changping District, Beijing 102206, People’s Republic of China
| | - Hanhaoyu Fu
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing 100020, China
| | - Yang Song
- WHO WPRO Regional Polio Reference Laboratory, 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, No.155 Changbai Road, Changping District, Beijing 102206, People’s Republic of China
| | - Mingli Jiang
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing 100020, China
| | - Huanhuan Lu
- WHO WPRO Regional Polio Reference Laboratory, 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, No.155 Changbai Road, Changping District, Beijing 102206, People’s Republic of China
| | - Jichen Li
- WHO WPRO Regional Polio Reference Laboratory, 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, No.155 Changbai Road, Changping District, Beijing 102206, People’s Republic of China
| | - Yanpeng Xu
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing 100020, China
| | - Runan Zhu
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing 100020, China
| | - Yong Zhang
- WHO WPRO Regional Polio Reference Laboratory, 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, No.155 Changbai Road, Changping District, Beijing 102206, People’s Republic of China
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing 100020, China
| | - Linqing Zhao
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing 100020, China
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Ji C, Zhang Y, Feng Y, Zhang X, Ma J, Pan Z, Kawaguchi A, Yao H. Systematic Surveillance of an Emerging Picornavirus among Cattle and Sheep in China. Microbiol Spectr 2023; 11:e0504022. [PMID: 37162348 PMCID: PMC10269770 DOI: 10.1128/spectrum.05040-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/09/2023] [Indexed: 05/11/2023] Open
Abstract
Emerging viruses are a constant threat to human and animal health. Boosepivirus is a novel picornavirus considered a gastrointestinal pathogen and has broken out in recent years. In 2020, we identified a strain of boosepivirus NX20-1 from Chinese calf feces and performed genetic characterization and evolutionary analysis. NX20-1 was closely related to the Japanese strain Bo-12-38/2009/JPN and belonged to Boosepivirus B. We found that 64 of 603 samples (10.6%) from 20 different provinces across the country were positive for boosepivirus by reverse transcription (RT)-PCR. Further, coinfection with other diarrheal pathogens was also present in 35 of these positive samples. Importantly, we found the prevalence of boosepivirus in sheep as well, indicating that Boosepivirus can infect different domestic animals. Our data suggest that boosepivirus is a potential diarrheal pathogen, but the pathogenicity and the mechanism of pathogenesis need further study. IMPORTANCE We identified a novel picornavirus, boosepivirus, for the first time in China. Genetic evolutionary analysis revealed that NX20-1 strain was closely related to the Japanese strain Bo-12-38/2009/JPN and belonged to Boosepivirus B. In addition, we found that the virus was prevalent in China with an overall positivity rate of 10.6% (64 of 603 samples), and there was significant coinfection with other pathogens. Importantly, we found the prevalence of boosepivirus in sheep as well, suggesting that boosepivirus has a risk of spillover and can be transmitted across species.
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Affiliation(s)
- Chengyuan Ji
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yao Zhang
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yiqiu Feng
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xinqin Zhang
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jiale Ma
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Zihao Pan
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Atsushi Kawaguchi
- Department of Infection Biology, Faculty of Medicine and Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Huochun Yao
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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3
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Alsayed AR, Abed A, Abu-Samak M, Alshammari F, Alshammari B. Etiologies of Acute Bronchiolitis in Children at Risk for Asthma, with Emphasis on the Human Rhinovirus Genotyping Protocol. J Clin Med 2023; 12:3909. [PMID: 37373604 DOI: 10.3390/jcm12123909] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/22/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
This research aims to determine acute bronchiolitis' causative virus(es) and establish a viable protocol to classify the Human Rhinovirus (HRV) species. During 2021-2022, we included children 1-24 months of age with acute bronchiolitis at risk for asthma. The nasopharyngeal samples were taken and subjected to a quantitative polymerase chain reaction (qPCR) in a viral panel. For HRV-positive samples, a high-throughput assay was applied, directing the VP4/VP2 and VP3/VP1 regions to confirm species. BLAST searching, phylogenetic analysis, and sequence divergence took place to identify the degree to which these regions were appropriate for identifying and differentiating HRV. HRV ranked second, following RSV, as the etiology of acute bronchiolitis in children. The conclusion of the investigation of all available data in this study distributed sequences into 7 HRV-A, 1 HRV-B, and 7 HRV-C types based on the VP4/VP2 and VP3/VP1 sequences. The nucleotide divergence between the clinical samples and the corresponding reference strains was lower in the VP4/VP2 region than in the VP3/VP1 region. The results demonstrated the potential utility of the VP4/VP2 region and the VP3/VP1 region for differentiating HRV genotypes. Confirmatory outcomes were yielded, indicating how nested and semi-nested PCR can establish practical ways to facilitate HRV sequencing and genotyping.
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Affiliation(s)
- Ahmad R Alsayed
- Department of Clinical Pharmacy and Therapeutics, Applied Science Private University, Amman 11931, Jordan
| | - Anas Abed
- Pharmacological and Diagnostic Research Centre, Faculty of Pharmacy, Al-Ahliyya Amman University, Amman 11931, Jordan
| | - Mahmoud Abu-Samak
- Department of Clinical Pharmacy and Therapeutics, Applied Science Private University, Amman 11931, Jordan
| | - Farhan Alshammari
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 2440, Saudi Arabia
| | - Bushra Alshammari
- Department of Medical Surgical Nursing, College of Nursing, University of Hail, Hail 2440, Saudi Arabia
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4
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Lu L, Ashworth J, Nguyen D, Li K, Smith DB, Woolhouse M. No Exchange of Picornaviruses in Vietnam between Humans and Animals in a High-Risk Cohort with Close Contact despite High Prevalence and Diversity. Viruses 2021; 13:v13091709. [PMID: 34578290 PMCID: PMC8473303 DOI: 10.3390/v13091709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 02/03/2023] Open
Abstract
Hospital-based and community-based 'high-risk cohort' studies investigating humans at risk of zoonotic infection due to occupational or residential exposure to animals were conducted in Vietnam, with diverse viruses identified from faecal samples collected from humans, domestic and wild animals. In this study, we focus on the positive-sense RNA virus family Picornaviridae, investigating the prevalence, diversity, and potential for cross-species transmission. Through metagenomic sequencing, we found picornavirus contigs in 23% of samples, belonging to 15 picornavirus genera. Prevalence was highest in bats (67%) while diversity was highest in rats (nine genera). In addition, 22% of the contigs were derived from novel viruses: Twelve phylogenetically distinct clusters were observed in rats of which seven belong to novel species or types in the genera Hunnivirus, Parechovirus, Cardiovirus, Mosavirus and Mupivirus; four distinct clusters were found in bats, belonging to one novel parechovirus species and one related to an unclassified picornavirus. There was no evidence for zoonotic transmission in our data. Our study provides an improved knowledge of the diversity and prevalence of picornaviruses, including a variety of novel picornaviruses in rats and bats. We highlight the importance of monitoring the human-animal interface for possible spill-over events.
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Affiliation(s)
- Lu Lu
- Usher Institute, University of Edinburgh, Edinburgh EH9 3FL, UK; (J.A.); (M.W.)
- Correspondence:
| | - Jordan Ashworth
- Usher Institute, University of Edinburgh, Edinburgh EH9 3FL, UK; (J.A.); (M.W.)
| | - Dung Nguyen
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; (D.N.); (D.B.S.)
| | - Kejin Li
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK;
| | - Donald B. Smith
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; (D.N.); (D.B.S.)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK;
| | - Mark Woolhouse
- Usher Institute, University of Edinburgh, Edinburgh EH9 3FL, UK; (J.A.); (M.W.)
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5
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Boros Á, László Z, Pankovics P, Marosi A, Albert M, Cságola A, Bíró H, Fahsbender E, Delwart E, Reuter G. High prevalence, genetic diversity and a potentially novel genotype of Sapelovirus A ( Picornaviridae) in enteric and respiratory samples in Hungarian swine farms. J Gen Virol 2020; 101:609-621. [PMID: 32255421 DOI: 10.1099/jgv.0.001410] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
All of the known porcine sapeloviruses (PSVs) currently belong to a single genotype in the genus Sapelovirus (family Picornaviridae). Here, the complete genome of a second, possibly recombinant, genotype of PSV strain SZ1M-F/PSV/HUN2013 (MN807752) from a faecal sample of a paraplegic pig in Hungary was characterized using viral metagenomics and RT-PCR. This sapelovirus strain showed only 64 % nucleotide identity in the VP1 region to its closest PSV-1 relative. Complete VP1 sequence-based epidemiological investigations of PSVs circulating in Hungary showed the presence of diverse strains found in high prevalence in enteric and respiratory samples collected from both asymptomatic and paraplegic pigs from 12 swine farms. Virus isolation attempts using PK-15 cell cultures were successful in 3/8 cases for the classic but not the novel PSV genotype. Sequence comparisons of faeces and isolate strains derived VP1 showed that cultured PSV strains not always represent the dominant PSVs found in vivo.
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Affiliation(s)
- Ákos Boros
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Zoltán László
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Péter Pankovics
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - András Marosi
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, Budapest, Hungary
| | | | | | | | | | - Eric Delwart
- University of California, San Francisco, CA, USA.,Vitalant Research Institute, San Francisco, CA, USA
| | - Gábor Reuter
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
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6
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Zhang W, Kataoka M, Doan HY, Ami Y, Suzaki Y, Takeda N, Muramatsu M, Li TC. Characterization of a Novel Simian Sapelovirus Isolated from a Cynomolgus Monkey using PLC/PRF/5 Cells. Sci Rep 2019; 9:20221. [PMID: 31882888 PMCID: PMC6934677 DOI: 10.1038/s41598-019-56725-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/16/2019] [Indexed: 01/27/2023] Open
Abstract
We isolated a novel simian sapelovirus (SSV), Cam13, from fecal specimen of a cynomolgus monkey by using PLC/PRF/5 cells. The SSV infection of the cells induced an extensive cytopathic effect. Two types of virus particles with identical diameter (~32 nm) but different densities (1.348 g/cm3 and 1.295 g/cm3) were observed in the cell culture supernatants. The RNA genome of Cam13 possesses 8,155 nucleotides and a poly(A) tail, and it has a typical sapelovirus genome organization consisting of a 5’ terminal untranslated region, a large open reading frame (ORF), and a 3’ terminal untranslated region. The ORF encodes a single polyprotein that is subsequently processed into a leader protein (L), four structural proteins (VP1, VP2, VP3, and VP4) and seven functional proteins (2A, 2B, 2C, 3A, 3B, 3C, and 3D). We confirmed that 293 T, HepG2/C3A, Hep2C, Huh7 and primary cynomolgus monkey kidney cells were susceptible to SSV infection. In contrast, PK-15, Vero, Vero E6, RD-A, A549, and primary green monkey kidney cells were not susceptible to SSV infection. We established an ELISA for the detection of IgG antibodies against SSV by using the virus particles as the antigen. A total of 327 serum samples from cynomolgus monkeys and 61 serum samples from Japanese monkeys were examined, and the positive rates were 88.4% and 18%, respectively. These results demonstrated that SSV infection occurred frequently in the monkeys. Since Cam13 shared 76.54%–79.52% nucleotide sequence identities with other known SSVs, and constellated in a separate lineage in the phylogeny based on the entire genome sequence, we propose that Cam13 is a new genotype of the simian sapelovirus species.
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Affiliation(s)
- Wenjing Zhang
- Blood Center of Shandong Province, East Shanshi Road 22, Jinan, Shandong, 250014, China.,Department of Virology II, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashi-murayama, Tokyo, 208-0011, Japan
| | - Michiyo Kataoka
- Department of Pathology, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashi-murayama, Tokyo, 208-0011, Japan
| | - Hai Yen Doan
- Department of Virology II, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashi-murayama, Tokyo, 208-0011, Japan
| | - Yasushi Ami
- Division of Experimental Animals Research, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashi-murayama, Tokyo, 208-0011, Japan
| | - Yuriko Suzaki
- Division of Experimental Animals Research, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashi-murayama, Tokyo, 208-0011, Japan
| | - Naokazu Takeda
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0781, Japan
| | - Masamichi Muramatsu
- Department of Virology II, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashi-murayama, Tokyo, 208-0011, Japan
| | - Tian-Cheng Li
- Department of Virology II, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashi-murayama, Tokyo, 208-0011, Japan.
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A novel picornavirus identified in wild Macaca mulatta in China. Arch Virol 2019; 165:495-504. [PMID: 31845155 DOI: 10.1007/s00705-019-04442-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 09/19/2019] [Indexed: 02/06/2023]
Abstract
The discovery of novel viruses in wild animals allows the prediction of their potential threat to the health of humans and other animals. We report a highly divergent picornavirus (tentatively named "mobovirus A"), identified in a fecal sample from Macaca mulatta in Yunnan province, China, using viral metagenomic analysis, with viral loads of 2 × 107 copies/g. The complete genomic sequence of mobovirus A is 8,325 nucleotides in length. Phylogenetic analysis showed that it clustered with Guangxi changeable lizard picornavirus 1 and Guangxi Chinese leopard gecko picornavirus, with less than 38%, 40%, and 40% amino acid identity in the P1, P2, and P3 protein, respectively. The viruses in this cluster were most closely related to members of the genera Harkavirus, Tremovirus and Hepatovirus. Genomic analysis revealed that mobovirus A has the typical genomic organization and motifs of a picornavirus. Additionally, its codon usage bias complements that of M. mulatta, suggesting that this feature is not restricted only to hepatoviruses. Thus, according to the guidelines of the Picornaviridae Study Group of the International Committee on Taxonomy of Viruses, mobovirus A should be considered a member of a new genus (tentatively named for Monkey-borne virus, "Mobovirus") in the family Picornaviridae. These data will facilitate the understanding of the genetic diversity and evolution of picornaviruses. Further studies are needed to understand the epidemiology and potential pathogenicity of the virus in M. mulatta.
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8
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Jayawardena N, Burga LN, Poirier JT, Bostina M. Virus-Receptor Interactions: Structural Insights For Oncolytic Virus Development. Oncolytic Virother 2019; 8:39-56. [PMID: 31754615 PMCID: PMC6825474 DOI: 10.2147/ov.s218494] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/02/2019] [Indexed: 12/11/2022] Open
Abstract
Recent advancements in oncolytic virotherapy commend a special attention to developing new strategies for targeting cancer cells with oncolytic viruses (OVs). Modifications of the viral envelope or coat proteins serve as a logical mean of repurposing viruses for cancer treatment. In this review, we discuss how detailed structural knowledge of the interactions between OVs and their natural receptors provide valuable insights into tumor specificity of some viruses and re-targeting of alternate receptors for broad tumor tropism or improved tumor selectivity.
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Affiliation(s)
- Nadishka Jayawardena
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Laura N Burga
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - John T Poirier
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Mihnea Bostina
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Otago Micro and Nano Imaging, University of Otago, Dunedin, New Zealand
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9
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Li Y, Du L, Jin T, Cheng Y, Zhang X, Jiao S, Huang T, Zhang Y, Yan Y, Gu J, Zhou J. Characterization and epidemiological survey of porcine sapelovirus in China. Vet Microbiol 2019; 232:13-21. [PMID: 31030837 DOI: 10.1016/j.vetmic.2019.02.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 02/06/2019] [Accepted: 02/10/2019] [Indexed: 01/19/2023]
Abstract
Porcine sapelovirus (PSV) is a causative agent of acute diarrhoea, respiratory distress, reproductive failure, and polioencephalomyelitis in swine. Here, we report the isolation, genomic sequence, and biological characterization of PSV isolated from pig diarrhoeal samples. In our study, two PSV strains were identified with a diameter of approximately 25 nm, and their full genomes were 7564 nucleotides in length. We named the strains PSV-JXXY-a2 and PSV-JXXY-c. Phylogenetic analysis showed that the two virus isolates were classified into the China cluster. Moreover, the PSV-JXXY-a2 strain could be inactivated quickly at 54℃ and adapted to grow on different cell lines of porcine, human, and baby hamster origin. Pathogenicity investigation showed that the isolated PSV could infect neonatal piglets efficiently and caused diarrhoea in piglets. Further epidemiological investigation revealed a high prevalence of PSV in pig herds, and the PSV-positive rates in pigs with diarrhoea were much higher than in asymptomatic samples in China. Together, our findings demonstrate that PSV-JXXY-a2 is pathogenic to neonatal piglets and advance knowledge on the prevalence of PSV infection.
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Affiliation(s)
- Ying Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Institute of Immunology, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Liuyang Du
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Institute of Immunology, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Tao Jin
- China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yao Cheng
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Institute of Immunology, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Zhang
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of the Chinese Academy of Agriculture Sciences, Harbin 150069, China
| | - Shaoyong Jiao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Institute of Immunology, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Tong Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Institute of Immunology, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu Zhang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Institute of Immunology, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Yan
- Key Laboratory of Animal Virology of Ministry of Agriculture, Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China
| | - Jinyan Gu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Institute of Immunology, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Animal Virology of Ministry of Agriculture, Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China; Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jiyong Zhou
- Key Laboratory of Animal Virology of Ministry of Agriculture, Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China
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10
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Lukashev AN, Vakulenko YA, Turbabina NA, Deviatkin AA, Drexler JF. Molecular epidemiology and phylogenetics of human enteroviruses: Is there a forest behind the trees? Rev Med Virol 2018; 28:e2002. [PMID: 30069956 DOI: 10.1002/rmv.2002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/28/2018] [Accepted: 07/01/2018] [Indexed: 11/05/2022]
Abstract
Enteroviruses are among the best studied small non-enveloped enteric RNA viruses. Most enteroviruses are easy to isolate in cell culture, and many non-polio enterovirus strains were archived worldwide as a byproduct of the WHO poliovirus surveillance system. Common outbreaks and epidemics, most prominently the epidemic of hand-foot-and-mouth disease with severe neurological complications in East and South-East Asia, justify practical interest of non-polio enteroviruses. As a result, there are over 50 000 enterovirus nucleotide sequences available in GenBank. Technical possibilities have been also improving, as Bayesian phylogenetic methods with an integrated molecular clock were introduced a decade ago and provided unprecedented opportunities for phylogenetic analysis. As a result, hundreds of papers were published on the molecular epidemiology of enteroviruses. This review covers the modern methodology, structure, and biases of the sequence dataset available in GenBank. The relevance of the subtype classification, findings of co-circulation of multiple genetic variants, previously unappreciated complexity of viral populations, and global evolutionary patterns are addressed. The most relevant conclusions and prospects for further studies on outbreak emergence mechanisms are discussed.
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Affiliation(s)
- Alexander N Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia.,Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Preparations, Moscow, Russia
| | - Yulia A Vakulenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia.,Virology Department, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Natalia A Turbabina
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia
| | | | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
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Case-Control Comparison of Enteric Viromes in Captive Rhesus Macaques with Acute or Idiopathic Chronic Diarrhea. J Virol 2017; 91:JVI.00952-17. [PMID: 28659484 DOI: 10.1128/jvi.00952-17] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 06/13/2017] [Indexed: 12/12/2022] Open
Abstract
Diarrhea is the major cause of non-research-associated morbidity and mortality affecting the supply of rhesus macaques and, potentially, their responses to experimental treatments. Idiopathic chronic diarrhea (ICD) in rhesus macaques also resembles ulcerative colitis, one form of human inflammatory bowel disease. To test for viral etiologies, we characterized and compared the fecal viromes from 32 healthy animals, 31 animals with acute diarrhea, and 29 animals with ICD. The overall fractions of eukaryotic viral reads were 0.063% for the healthy group, 0.131% for the acute-diarrhea group, and 0.297% for the chronic-diarrhea group. Eukaryotic viruses belonging to 6 viral families, as well as numerous circular Rep-encoding single-stranded DNA (CRESS DNA) viral genomes, were identified. The most commonly detected sequences were from picornaviruses, making up 59 to 88% of all viral reads, followed by 9 to 17% for CRESS DNA virus sequences. The remaining 5 virus families, Adenoviridae, Astroviridae, Anelloviridae, Picobirnaviridae, and Parvoviridae, collectively made up 1 to 3% of the viral reads, except for parvoviruses, which made up 23% of the viral reads in the healthy group. Detected members of the families Picornaviridae and Parvoviridae were highly diverse, consisting of multiple genera, species, and genotypes. Coinfections with members of up to six viral families were detected. Complete and partial viral genomes were assembled and used to measure the number of matching short sequence reads in feces from the 92 animals in the two clinical and the healthy control groups. Several enterovirus genotypes and CRESS DNA genomes were associated with ICD relative to healthy animals. Conversely, higher read numbers from different parvoviruses were associated with healthy animals. Our study reveals a high level of enteric coinfections with diverse viruses in a captive rhesus macaque colony and identifies several viruses positively or negatively associated with ICD.
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12
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Zou L, Yi L, Song Y, Zhang X, Liang L, Ni H, Ke C, Wu J, Lu J. A cluster of coxsackievirus A21 associated acute respiratory illness: the evidence of efficient transmission of CVA21. Arch Virol 2016; 162:1057-1059. [PMID: 28025712 PMCID: PMC7087265 DOI: 10.1007/s00705-016-3201-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 12/07/2016] [Indexed: 11/28/2022]
Abstract
In March 2016, a cluster of unexplained respiratory illnesses was reported by the acute respiratory infections (ARI) surveillance system of Guangdong Province, China. Twenty-three high school students and one teacher from the four neighboring classes were admitted to a hospital. CVA21 was found in eight of fourteen patients. Phylogenetic analysis suggested that the CVA21 outbreak was most likely caused by transmission of the virus from person to person. This is the first report of an ARI outbreak caused by CVA21, which suggests that CVA21 has the potential to be transmitted efficiently from person to person and should be closely monitored by clinicians and public health agencies.
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Affiliation(s)
- Lirong Zou
- Guangdong Provincial Centre for Disease Control and Prevention, Guangdong, 514300, China
| | - Lina Yi
- Guangdong Provincial Centre for Disease Control and Prevention, Guangdong, 514300, China.,Guangdong Provincial Institutes of Public Health, Guangdong Provincial Centre for Disease Control and Prevention, Guangdong, 514300, China
| | - Yingchao Song
- Guangdong Provincial Centre for Disease Control and Prevention, Guangdong, 514300, China
| | - Xin Zhang
- Guangdong Provincial Centre for Disease Control and Prevention, Guangdong, 514300, China
| | - Lijun Liang
- Guangdong Provincial Centre for Disease Control and Prevention, Guangdong, 514300, China
| | - Hanzhong Ni
- Guangdong Provincial Centre for Disease Control and Prevention, Guangdong, 514300, China
| | - Changwen Ke
- Guangdong Provincial Centre for Disease Control and Prevention, Guangdong, 514300, China
| | - Jie Wu
- Guangdong Provincial Centre for Disease Control and Prevention, Guangdong, 514300, China
| | - Jing Lu
- Guangdong Provincial Centre for Disease Control and Prevention, Guangdong, 514300, China. .,Guangdong Provincial Institutes of Public Health, Guangdong Provincial Centre for Disease Control and Prevention, Guangdong, 514300, China.
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13
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Wang X, Shao S, Wang H, Shen Q, Yang S, Zhang W. An enterovirus from a captive primate in China. SPRINGERPLUS 2016; 5:1281. [PMID: 27547656 PMCID: PMC4977230 DOI: 10.1186/s40064-016-2966-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 07/29/2016] [Indexed: 11/23/2022]
Abstract
Background Enteroviruses (EVs) are a genetically and antigenically diverse group of viruses infecting humans and a variety of animals including non-human primates (NHPs). The present study was to investigate EVs in the fecal samples from captive NHPs in zoos in China using classic RT-PCR and viral metagenomics methods. Findings An EV strain was detected in a fecal sample collected from a captive NHP of a zoo in eastern China. The complete genome of this EV strain (named Sev-nj1) was determined and characterized. Sequence analysis indicated Sev-nj1 shared the highest sequence identity (75.6 %) with an EV-J strain, Poo-1, based on the complete genome. Phylogenetic analysis showed Sev-nj1 clustered with the other EV-J strains, forming a separate clade. Discussion According to the genetic distance-based criteria, Sev-nj1 belonged to a new type within the species EV-J. This is the first study detecting EV-J from a NHP in China, which will be helpful for the future epidemiology study of EVs in NHPs.
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Affiliation(s)
- Xiaochun Wang
- Department of Pathogenic Biology, School of Medical Science, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Shihe Shao
- Department of Pathogenic Biology, School of Medical Science, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Hua Wang
- Department of Pathogenic Biology, School of Medical Science, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Quan Shen
- Department of Pathogenic Biology, School of Medical Science, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Shixing Yang
- Department of Pathogenic Biology, School of Medical Science, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Wen Zhang
- Department of Pathogenic Biology, School of Medical Science, Jiangsu University, Zhenjiang, 212013 Jiangsu China
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14
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Kim DS, Kang MI, Son KY, Bak GY, Park JG, Hosmillo M, Seo JY, Kim JY, Alfajaro MM, Soliman M, Baek YB, Cho EH, Lee JH, Kwon J, Choi JS, Goodfellow I, Cho KO. Pathogenesis of Korean SapelovirusA in piglets and chicks. J Gen Virol 2016; 97:2566-2574. [PMID: 27487773 PMCID: PMC5078829 DOI: 10.1099/jgv.0.000571] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Sapelovirus A (SV-A), formerly known as porcine sapelovirus as a member of a new genus Sapelovirus, is known to cause enteritis, pneumonia, polioencephalomyelitis and reproductive disorders in pigs. We have recently identified α2,3-linked sialic acid on GD1a ganglioside as a functional SV-A receptor rich in the cells of pigs and chickens. However, the role of GD1a in viral pathogenesis remains elusive. Here, we demonstrated that a Korean SV-A strain could induce diarrhoea and intestinal pathology in piglets but not in chicks. Moreover, this Korean SV-A strain had mild extra-intestinal tropisms appearing as mild, non-suppurative myelitis, encephalitis and pneumonia in piglets, but not in chicks. By real-time reverse transcription (RT) PCR, higher viral RNA levels were detected in faecal samples than in sera or extra-intestinal organs from virus-inoculated piglets. Immunohistochemistry confirmed that high viral antigens were detected in the epithelial cells of intestines from virus-inoculated piglets but not from chicks. This Korean SV-A strain could bind the cultured cell lines originated from various species, but replication occurred only in cells of porcine origin. These data indicated that this Korean SV-A strain could replicate and induce pathology in piglets but not in chicks, suggesting that additional porcine-specific factors are required for virus entry and replication. In addition, this Korean SV-A strain is enteropathogenic, but could spread to the bloodstream from the gut and disseminate to extra-intestinal organs and tissues. These results will contribute to our understanding of SV-A pathogenesis so that efficient anti-sapelovirus drugs and vaccines could be developed in the future.
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Affiliation(s)
- Deok-Song Kim
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
| | - Mun-Il Kang
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
| | - Kyu-Yeol Son
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
| | - Geon-Yong Bak
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
| | - Jun-Gyu Park
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
| | - Myra Hosmillo
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
| | - Ja-Young Seo
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
| | - Ji-Yun Kim
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
| | - Mia Madel Alfajaro
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
| | - Mahmoud Soliman
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
| | - Yeong-Bin Baek
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
| | - Eun-Hyo Cho
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
| | - Ju-Hwan Lee
- Chonnam National University Veterinary Teaching Hospital, Gwangju, Republic of Korea
| | - Joseph Kwon
- Division of Life Science, Korea Basic Science Institute, 169-148 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Jong-Soon Choi
- Division of Life Science, Korea Basic Science Institute, 169-148 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Ian Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
- Correspondence Ian Goodfellow
| | - Kyoung-Oh Cho
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
- Kyoung-Oh Cho
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15
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Ao YY, Yu JM, Zhang CY, Xin YY, Li LL, Duan ZJ. Identification of a Novel Enterovirus Species in Rhesus Macaque in China. Sci Rep 2016; 6:28526. [PMID: 27329349 PMCID: PMC4916455 DOI: 10.1038/srep28526] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 06/02/2016] [Indexed: 11/30/2022] Open
Abstract
Recent studies of Enterovirus (EV) in nonhuman primates (NHPs), which could act as a source of future emerging human viral diseases, have boosted interest in the search for novel EVs. Here, a highly divergent strain of EV, tentatively named SEV-gx, was identified by viral metagenomic analysis from stool samples of rhesus macaques in China. In total, 27 of 280 (9.6%) faecal samples from rhesus macaques were positive for SEV-gx. Its complete genomic sequence is 7,367 nucleotide (nt). Genomic analyses showed that it has a standard genomic organisation for EVs, being more closely related to EV-J strains (approximately 54.0%, 43.0–44.1%, 52.3–55.2%, 61.1–62.7% and 64.0% amino acids identity in polyprotein, P1, P2 and P3 and combined 2C/3CD regions, respectively). It was also shown to have genome characteristics typical of EVs. Phylogenetic analysis of P1, 2C and 3CD aa indicated that SEV-gx can be classified as a distinct cluster in the EVs. All of this evidence demonstrates SEV-gx is a novel species (tentatively named EV-K) in the EV genus, which contributes to our understanding of the genetic diversity and evolution of EVs. Further studies are needed to investigate the potential pathogenicity of SEV-gx in NHPs and humans.
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Affiliation(s)
- Yuan-Yun Ao
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing 100052, China
| | - Jie-Mei Yu
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing 100052, China
| | - Cui-Yuan Zhang
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing 100052, China
| | - Yun-Yun Xin
- The First affiliated Hospital of Hunan Normal University, Changsha 410000, Hunan, China
| | - Li-Li Li
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing 100052, China
| | - Zhao-Jun Duan
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing 100052, China
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16
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Sin J, Mangale V, Thienphrapa W, Gottlieb RA, Feuer R. Recent progress in understanding coxsackievirus replication, dissemination, and pathogenesis. Virology 2015; 484:288-304. [PMID: 26142496 DOI: 10.1016/j.virol.2015.06.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 04/23/2015] [Accepted: 06/03/2015] [Indexed: 01/01/2023]
Abstract
Coxsackieviruses (CVs) are relatively common viruses associated with a number of serious human diseases, including myocarditis and meningo-encephalitis. These viruses are considered cytolytic yet can persist for extended periods of time within certain host tissues requiring evasion from the host immune response and a greatly reduced rate of replication. A member of Picornaviridae family, CVs have been historically considered non-enveloped viruses - although recent evidence suggest that CV and other picornaviruses hijack host membranes and acquire an envelope. Acquisition of an envelope might provide distinct benefits to CV virions, such as resistance to neutralizing antibodies and efficient nonlytic viral spread. CV exhibits a unique tropism for progenitor cells in the host which may help to explain the susceptibility of the young host to infection and the establishment of chronic disease in adults. CVs have also been shown to exploit autophagy to maximize viral replication and assist in unconventional release from target cells. In this article, we review recent progress in clarifying virus replication and dissemination within the host cell, identifying determinants of tropism, and defining strategies utilized by the virus to evade the host immune response. Also, we will highlight unanswered questions and provide future perspectives regarding the potential mechanisms of CV pathogenesis.
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Affiliation(s)
- Jon Sin
- Cedars-Sinai Heart Institute, 8700 Beverly Blvd., Los Angeles, CA 90048, USA
| | - Vrushali Mangale
- The Integrated Regenerative Research Institute (IRRI) at San Diego State University, Cell & Molecular Biology Joint Doctoral Program, Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
| | - Wdee Thienphrapa
- The Integrated Regenerative Research Institute (IRRI) at San Diego State University, Cell & Molecular Biology Joint Doctoral Program, Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
| | - Roberta A Gottlieb
- Cedars-Sinai Heart Institute, 8700 Beverly Blvd., Los Angeles, CA 90048, USA
| | - Ralph Feuer
- The Integrated Regenerative Research Institute (IRRI) at San Diego State University, Cell & Molecular Biology Joint Doctoral Program, Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA.
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17
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Jonsson N, Sävneby A, Gullberg M, Evertsson K, Klingel K, Lindberg AM. Efficient replication of recombinant Enterovirus B types, carrying different P1 genes in the coxsackievirus B5 replicative backbone. Virus Genes 2015; 50:351-7. [PMID: 25663145 DOI: 10.1007/s11262-015-1177-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 01/27/2015] [Indexed: 11/29/2022]
Abstract
Recombination is an important feature in the evolution of the Enterovirus genus. Phylogenetic studies of enteroviruses have revealed that the capsid genomic region (P1) is type specific, while the parts of the genome coding for the non-structural proteins (P2-P3) are species specific. Hence, the genome may be regarded as consisting of two modules that evolve independently. In this study, it was investigated whether the non-structural coding part of the genome in one type could support replication of a virus with a P1 region from another type of the same species. A cassette vector (pCas) containing a full-length cDNA copy of coxsackievirus B5 (CVB5) was used as a replicative backbone. The P1 region of pCas was replaced with the corresponding part from coxsackievirus B3 Nancy (CVB3N), coxsackievirus B6 Schmitt (CVB6S), and echovirus 7 Wallace (E7W), all members of the Enterovirus B species. The replication efficiency after transfection with clone-derived in vitro transcribed RNA was studied and compared with that of pCas. All the recombinant viruses replicated with similar efficiencies and showed threshold cycle (Ct) values, tissue culture infectivity dose 50 %, and plaque-forming unit titers comparable to viruses generated from the pCas construct. In addition to this, a clone without the P1 region was also constructed, and Western Blot and immunofluorescence staining analysis showed that the viral genome could be translated and replicated despite the lack of the structural protein-coding region. To conclude, the replicative backbone of the CVB5 cassette vector supports replication of intraspecies constructs with P1 regions derived from other members of the Enterovirus B species. In addition to this, the replicative backbone can be both translated and replicated without the presence of a P1 region.
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Affiliation(s)
- Nina Jonsson
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden
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18
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Son KY, Kim DS, Kwon J, Choi JS, Kang MI, Belsham GJ, Cho KO. Full-length genomic analysis of Korean porcine Sapelovirus strains. PLoS One 2014; 9:e107860. [PMID: 25229940 PMCID: PMC4168140 DOI: 10.1371/journal.pone.0107860] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 08/07/2014] [Indexed: 12/17/2022] Open
Abstract
Porcine sapelovirus (PSV), a species of the genus Sapelovirus within the family Picornaviridae, is associated with diarrhea, pneumonia, severe neurological disorders, and reproductive failure in pigs. However, the structural features of the complete PSV genome remain largely unknown. To analyze the structural features of PSV genomes, the full-length nucleotide sequences of three Korean PSV strains were determined and analyzed using bioinformatic techniques in comparison with other known PSV strains. The Korean PSV genomes ranged from 7,542 to 7,566 nucleotides excluding the 3′ poly(A) tail, and showed the typical picornavirus genome organization; 5′untranslated region (UTR)-L-VP4-VP2-VP3-VP1-2A-2B-2C-3A-3B-3C-3D-3′UTR. Three distinct cis-active RNA elements, the internal ribosome entry site (IRES) in the 5′UTR, a cis-replication element (CRE) in the 2C coding region and 3′UTR were identified and their structures were predicted. Interestingly, the structural features of the CRE and 3′UTR were different between PSV strains. The availability of these first complete genome sequences for PSV strains will facilitate future investigations of the molecular pathogenesis and evolutionary characteristics of PSV.
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Affiliation(s)
- Kyu-Yeol Son
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
| | - Deok-Song Kim
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
| | - Joseph Kwon
- Division of Life Science, Korea Basic Science Institute, Yuseong-gu, Daejeon, Republic of Korea
| | - Jong-Soon Choi
- Division of Life Science, Korea Basic Science Institute, Yuseong-gu, Daejeon, Republic of Korea
| | - Mun-Il Kang
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
| | - Graham J. Belsham
- National Veterinary Institute, Technical University of Denmark, Kalvehave, Denmark
- * E-mail: (GJB); (KOC)
| | - Kyoung-Oh Cho
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
- * E-mail: (GJB); (KOC)
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Sadeuh-Mba SA, Bessaud M, Joffret ML, Endegue Zanga MC, Balanant J, Mpoudi Ngole E, Njouom R, Reynes JM, Delpeyroux F, Rousset D. Characterization of Enteroviruses from non-human primates in cameroon revealed virus types widespread in humans along with candidate new types and species. PLoS Negl Trop Dis 2014; 8:e3052. [PMID: 25079078 PMCID: PMC4117447 DOI: 10.1371/journal.pntd.0003052] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 06/14/2014] [Indexed: 12/28/2022] Open
Abstract
Enteroviruses (EVs) infecting African Non-Human Primates (NHP) are still poorly documented. This study was designed to characterize the genetic diversity of EVs among captive and wild NHP in Cameroon and to compare this diversity with that found in humans. Stool specimens were collected in April 2008 in NHP housed in sanctuaries in Yaounde and neighborhoods. Moreover, stool specimens collected from wild NHP from June 2006 to October 2008 in the southern rain forest of Cameroon were considered. RNAs purified directly from stool samples were screened for EVs using a sensitive RT-nested PCR targeting the VP1 capsid coding gene whose nucleotide sequence was used for molecular typing. Captive chimpanzees (Pan troglodytes) and gorillas (Gorilla gorilla) were primarily infected by EV types already reported in humans in Cameroon and elsewhere: Coxsackievirus A13 and A24, Echovirus 15 and 29, and EV-B82. Moreover EV-A119, a novel virus type recently described in humans in central and west Africa, was also found in a captive Chimpanzee. EV-A76, which is a widespread virus in humans, was identified in wild chimpanzees, thus suggesting its adaptation and parallel circulation in human and NHP populations in Cameroon. Interestingly, some EVs harbored by wild NHP were genetically distinct from all existing types and were thus assigned as new types. One chimpanzee-derived virus was tentatively assigned as EV-J121 in the EV-J species. In addition, two EVs from wild monkeys provisionally registered as EV-122 and EV-123 were found to belong to a candidate new species. Overall, this study indicates that the genetic diversity of EVs among NHP is more important than previously known and could be the source of future new emerging human viral diseases.
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Affiliation(s)
| | - Maël Bessaud
- Institut Pasteur, Unité de Biologie des Virus Entériques, Paris, France
- INSERM, U994, Paris, France
| | - Marie-Line Joffret
- Institut Pasteur, Unité de Biologie des Virus Entériques, Paris, France
- INSERM, U994, Paris, France
| | | | - Jean Balanant
- Institut Pasteur, Unité de Biologie des Virus Entériques, Paris, France
- INSERM, U994, Paris, France
| | | | - Richard Njouom
- Service de Virologie, Centre Pasteur du Cameroun, Yaounde, Cameroon
| | - Jean-Marc Reynes
- Service de Virologie, Centre Pasteur du Cameroun, Yaounde, Cameroon
| | - Francis Delpeyroux
- Institut Pasteur, Unité de Biologie des Virus Entériques, Paris, France
- INSERM, U994, Paris, France
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Son KY, Kim DS, Matthijnssens J, Kwon HJ, Park JG, Hosmillo M, Alfajaro MM, Ryu EH, Kim JY, Kang MI, Cho KO. Molecular epidemiology of Korean porcine sapeloviruses. Arch Virol 2014; 159:1175-80. [PMID: 24232913 PMCID: PMC7087272 DOI: 10.1007/s00705-013-1901-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 10/16/2013] [Indexed: 10/26/2022]
Abstract
To evaluate the prevalence and genetic diversity of porcine sapeloviruses (PSVs) in Korea, a total of 100 diarrhea fecal samples from pigs were analyzed by RT-PCR and nested PCR assays with primer pairs specific for the VP1 gene. Overall, 34 % of the diarrhea samples tested positive for PSV, and a high proportion of infections occurred along with a variety of other enteric viruses and bacteria. Genomic and phylogenetic analysis of the VP1 genes revealed pronounced genetic diversities between PSVs from Korean and elsewhere. Our results indicate that PSV infections are very common in Korean pigs with diarrhea. The infecting strains are genetically diverse.
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High rates of infection with novel enterovirus variants in wild populations of mandrills and other old world monkey species. J Virol 2014; 88:5967-76. [PMID: 24623420 DOI: 10.1128/jvi.00088-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
UNLABELLED Enteroviruses (EVs) are a genetically and antigenically diverse group of viruses infecting humans. A mostly distinct set of EV variants have additionally been documented to infect wild apes and several, primarily captive, Old World monkey (OWM) species. To investigate the prevalence and genetic characteristics of EVs infecting OWMs in the wild, fecal samples from mandrills (Mandrillus sphinx) and other species collected in remote regions of southern Cameroon were screened for EV RNA. Remarkably high rates of EV positivity were detected in M. sphinx (100 of 102 screened), Cercocebus torquatus (7/7), and Cercopithecus cephus (2/4), with high viral loads indicative of active infection. Genetic characterization in VP4/VP2 and VP1 regions allowed EV variants to be assigned to simian species H (EV-H) and EV-J (including one or more new types), while seven matched simian EV-B variants, SA5 and EV110 (chimpanzee). Sequences from the remaining 70 formed a new genetic group distinct in VP4/2 and VP1 region from all currently recognized human or simian EV species. Complete genome sequences were obtained from three to determine their species assignment. In common with EV-J and the EV-A A13 isolate, new group sequences were chimeric, being most closely related to EV-A in capsid genes and to EV-B in the nonstructural gene region. Further recombination events created different groupings in 5' and 3' untranslated regions. While clearly a distinct EV group, the hybrid nature of new variants prevented their unambiguous classification as either members of a new species or as divergent members of EV-A using current International Committee on Taxonomy of Viruses (ICTV) assignment criteria. IMPORTANCE This study is the first large-scale investigation of the frequency of infection and diversity of enteroviruses (EVs) infecting monkeys (primarily mandrills) in the wild. Our findings demonstrate extremely high frequencies of active infection (95%) among mandrills and other Old World monkey species inhabiting remote regions of Cameroon without human contact. EV variants detected were distinct from those infecting human populations, comprising members of enterovirus species B, J, and H and a large novel group of viruses most closely related to species A in the P1 region. The viral sequences obtained contribute substantially to our growing understanding of the genetic diversity of EVs and the existence of interspecies chimerism that characterizes the novel variants in the current study, as well as in previously characterized species A and J viruses infecting monkeys. The latter findings will contribute to future development of consensus criteria for species assignments in enteroviruses and other picornavirus genera.
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22
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Epidemiology of Sporadic Cases of Human Enterovirus 92 in Captivated Primates with Acute Diarrhea. Jundishapur J Microbiol 2013. [DOI: 10.5812/jjm.7812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Prevalence of nonpolio enteroviruses in the sewage of Guangzhou city, China, from 2009 to 2012. Appl Environ Microbiol 2013; 79:7679-83. [PMID: 24096418 DOI: 10.1128/aem.02058-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human-pathogenic viruses in urban sewage have been extensively monitored to obtain information on circulating viruses in human communities. Enteroviruses (EVs) excreted by patients who present with diverse clinical syndromes can remain infectious in the environment for several weeks, and limited data on circulating environmental EVs are available. A 4-year (2009 to 2012) surveillance study was conducted to detect nonpolio enteroviruses (NPEVs) in the urban sewage of Guangzhou city, China. After the viruses in the sewage samples were concentrated and isolated, molecular identification was used to detect and type the NPEVs. During the 4-year study, 17 different NPEV serotypes were identified in the sewage of Guangzhou city. The most common serotypes were echovirus 11 (ECHO11), ECHO6, ECHO7, and ECHO12 and coxsackie group B viruses 5 (CVB5) and CVB3. The predominant serotypes were influenced by spatial and temporal factors and differed each year. CVB5 was commonly detected in 2009 and 2010 but was rarely isolated in 2011 and 2012. In contrast, CVB3 was not observed in 2009 and 2010 but was increasingly detected in 2011 and 2012. Our study provides an overview of the serotype distribution and circulation patterns of NPEVs in the sewage of Guangzhou, China. In the absence of a systematic EV disease surveillance system, the detection and characterization of sewage-borne NPEVs will help us better understand the changes in EV disease trends and the epidemic background of circulating EVs, which could help interpret the EV trends and warn of future outbreaks in this area.
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Lu J, Yi L, Ke C, Zhang Y, Liu R, Chen J, Kung HF, He ML. The interaction between human enteroviruses and type I IFN signaling pathway. Crit Rev Microbiol 2013; 41:201-7. [PMID: 23919297 DOI: 10.3109/1040841x.2013.813903] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Human enteroviruses (HEV), very common and important human pathogens, cause infections in diverse ways. Recently, the large epidemic of HFMD caused by HEV infection became a growing threat to public health in China. As the first line of immune response, the type I interferon (IFN-α/β) pathway plays an essential role in antiviral infection, particularly in limiting both the early and late stages of infection. Because of co-evolution with the host, the viruses have evolved multiple strategies to evade or subvert the host immunity to ensure their survival. In this paper, we systematically reviewed and summarized the interaction between HEV infections and host type I IFN responses. We firstly described the recent findings of HEV recognition and IFN induction, specifically on host pattern-recognition receptors (PRRs) in HEV infection. Then we discussed the antiviral effect of IFN in HEV infection. Finally, we timely summarized the mechanisms of HEV to circumvent the IFN responses. Clarification of the complexity in this battle may provide us new strategies for prevention and antiviral treatment.
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Affiliation(s)
- Jing Lu
- Center for Diseases Control and Prevention of Guangdong Province , Guangzhou , China
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25
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McIntyre CL, Knowles NJ, Simmonds P. Proposals for the classification of human rhinovirus species A, B and C into genotypically assigned types. J Gen Virol 2013; 94:1791-1806. [PMID: 23677786 PMCID: PMC3749525 DOI: 10.1099/vir.0.053686-0] [Citation(s) in RCA: 165] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Human rhinoviruses (HRVs) frequently cause mild upper respiratory tract infections and more severe disease manifestations such as bronchiolitis and asthma exacerbations. HRV is classified into three species within the genus Enterovirus of the family Picornaviridae. HRV species A and B contain 75 and 25 serotypes identified by cross-neutralization assays, although the use of such assays for routine HRV typing is hampered by the large number of serotypes, replacement of virus isolation by molecular methods in HRV diagnosis and the poor or absent replication of HRV species C in cell culture. To address these problems, we propose an alternative, genotypic classification of HRV-based genetic relatedness analogous to that used for enteroviruses. Nucleotide distances between 384 complete VP1 sequences of currently assigned HRV (sero)types identified divergence thresholds of 13, 12 and 13 % for species A, B and C, respectively, that divided inter- and intra-type comparisons. These were paralleled by 10, 9.5 and 10 % thresholds in the larger dataset of >3800 VP4 region sequences. Assignments based on VP1 sequences led to minor revisions of existing type designations (such as the reclassification of serotype pairs, e.g. A8/A95 and A29/A44, as single serotypes) and the designation of new HRV types A101–106, B101–103 and C34–C51. A protocol for assignment and numbering of new HRV types using VP1 sequences and the restriction of VP4 sequence comparisons to type identification and provisional type assignments is proposed. Genotypic assignment and identification of HRV types will be of considerable value in the future investigation of type-associated differences in disease outcomes, transmission and epidemiology.
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Affiliation(s)
- Chloe L McIntyre
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH15 9RG, UK
| | - Nick J Knowles
- Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Peter Simmonds
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH15 9RG, UK
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26
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Lim BK, Ju ES, Lao DH, Yun SH, Lee YJ, Kim DK, Jeon ES. Development of a enterovirus diagnostic assay system for diagnosis of viral myocarditis in humans. Microbiol Immunol 2013; 57:281-7. [DOI: 10.1111/1348-0421.12028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 12/26/2012] [Accepted: 01/09/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Byung-Kwan Lim
- Division of Cardiology, Samsung Medical Center, Samsung Biomedical Research Institute; Sungkyunkwan University School of Medicine; 50 Irwon dong, Gangnam-gu, Seoul, 135-710; Korea
| | - Eun-Seon Ju
- Division of Cardiology, Samsung Medical Center, Samsung Biomedical Research Institute; Sungkyunkwan University School of Medicine; 50 Irwon dong, Gangnam-gu, Seoul, 135-710; Korea
| | - Dieu Hung Lao
- Department of Medicine; University of California, San Diego Department of Cardiology; San Diego, California; USA
| | - Soo-Hyeon Yun
- Research and Development Center; Celltrion, 13-6 Songdo-dong, Yeonsu-gu, Incheon 406-840; Korea
| | - Yoo-Jung Lee
- Division of Cardiology, Samsung Medical Center, Samsung Biomedical Research Institute; Sungkyunkwan University School of Medicine; 50 Irwon dong, Gangnam-gu, Seoul, 135-710; Korea
| | - Duk-Kyung Kim
- Division of Cardiology, Samsung Medical Center, Samsung Biomedical Research Institute; Sungkyunkwan University School of Medicine; 50 Irwon dong, Gangnam-gu, Seoul, 135-710; Korea
| | - Eun-Seok Jeon
- Division of Cardiology, Samsung Medical Center, Samsung Biomedical Research Institute; Sungkyunkwan University School of Medicine; 50 Irwon dong, Gangnam-gu, Seoul, 135-710; Korea
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27
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Handley SA, Thackray LB, Zhao G, Presti R, Miller AD, Droit L, Abbink P, Maxfield LF, Kambal A, Duan E, Stanley K, Kramer J, Macri SC, Permar SR, Schmitz JE, Mansfield K, Brenchley JM, Veazey RS, Stappenbeck TS, Wang D, Barouch DH, Virgin HW. Pathogenic simian immunodeficiency virus infection is associated with expansion of the enteric virome. Cell 2012; 151:253-66. [PMID: 23063120 DOI: 10.1016/j.cell.2012.09.024] [Citation(s) in RCA: 221] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Revised: 09/11/2012] [Accepted: 09/21/2012] [Indexed: 12/13/2022]
Abstract
Pathogenic simian immunodeficiency virus (SIV) infection is associated with enteropathy, which likely contributes to AIDS progression. To identify candidate etiologies for AIDS enteropathy, we used next-generation sequencing to define the enteric virome during SIV infection in nonhuman primates. Pathogenic, but not nonpathogenic, SIV infection was associated with significant expansion of the enteric virome. We identified at least 32 previously undescribed enteric viruses during pathogenic SIV infection and confirmed their presence by using viral culture and PCR testing. We detected unsuspected mucosal adenovirus infection associated with enteritis as well as parvovirus viremia in animals with advanced AIDS, indicating the pathogenic potential of SIV-associated expansion of the enteric virome. No association between pathogenic SIV infection and the family-level taxonomy of enteric bacteria was detected. Thus, enteric viral infections may contribute to AIDS enteropathy and disease progression. These findings underline the importance of metagenomic analysis of the virome for understanding AIDS pathogenesis.
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Affiliation(s)
- Scott A Handley
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
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28
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Characterizing the picornavirus landscape among synanthropic nonhuman primates in Bangladesh, 2007 to 2008. J Virol 2012; 87:558-71. [PMID: 23097448 DOI: 10.1128/jvi.00837-12] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The term synanthropic describes organisms that thrive in human-altered habitats. Where synanthropic nonhuman primates (NHP) share an ecological niche with humans, cross-species transmission of infectious agents can occur. In Bangladesh, synanthropic NHP are found in villages, densely populated cities, religious sites, and protected forest areas. NHP are also kept as performing monkeys and pets. To investigate possible transmission of enteric picornaviruses between humans and NHP, we collected fecal specimens from five NHP taxa at16 locations in Bangladesh during five field sessions, from January 2007 to June 2008. Specimens were screened using real-time PCR assays for the genera Enterovirus, Parechovirus, and Sapelovirus; PCR-positive samples were typed by VP1 sequencing. To compare picornavirus diversity between humans and NHP, the same assays were applied to 211 human stool specimens collected in Bangladesh in 2007 to 2008 for acute flaccid paralysis surveillance. Picornaviruses were detected in 78 of 677 (11.5%) NHP fecal samples. Twenty distinct human enterovirus (EV) serotypes, two bovine EV types, six human parechovirus serotypes, and one virus related to Ljungan virus were identified. Twenty-five additional enteroviruses and eight parechoviruses could not be typed. Comparison of the picornavirus serotypes detected in NHP specimens with those detected in human specimens revealed considerable overlap. Strikingly, no known simian enteroviruses were detected among these NHP populations. In conclusion, enteroviruses and parechoviruses may be transmitted between humans and synanthropic NHP in Bangladesh, but the directionality of transmission is unknown. These findings may have important implications for the health of both human and NHP populations.
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Gao J, Chen J, Si X, Xie Z, Zhu Y, Zhang X, Wang S, Jiang S. Genetic variation of the VP1 gene of the virulent duck hepatitis A virus type 1 (DHAV-1) isolates in Shandong province of China. Virol Sin 2012; 27:248-53. [PMID: 22899433 DOI: 10.1007/s12250-012-3255-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 06/28/2012] [Indexed: 11/27/2022] Open
Abstract
To investigate the relationship of the variation of virulence and the external capsid proteins of the pandemic duck hepatitis A virus type 1 (DHAV-1) isolates, the virulence, cross neutralization assays and the complete sequence of the virion protein 1 (VP1) gene of nine virulent DHAV-1 strains, which were isolated from infected ducklings with clinical symptoms in Shandong province of China in 2007-2008, were tested. The fifth generation duck embryo allantoic liquids of the 9 isolates were tested on 12-day-old duck embryos and on 7-day-old ducklings for the median embryonal lethal doses (ELD(50)s) and the median lethal doses (LD(50)s), respectively. The results showed that the ELD(50)s of embryonic duck eggs of the 9 DHAV-1 isolates were between 1.9 × 10(6)/mL to 1.44 × 10(7)/mL, while the LD(50)s were 2.39 × 10(5)/mL to 6.15 × 10(6)/mL. Cross-neutralization tests revealed that the 9 DHAV-1 isolates were completely neutralized by the standard serum and the hyperimmune sera against the 9 DHAV-1 isolates, respectively. Compared with other virulent, moderate virulent, attenuated vaccine and mild strains, the VP1 genes of the 9 strains shared 89.8%-99.7% similarity at the nucleotide level and 92.4%-99.6% at amino acid level with other DHAV-1 strains. There were three hypervariable regions at the C-terminus (aa 158-160, 180-193 and 205-219) and other variable points in VP1 protein, but which didn't cause virulence of DHAV-1 change.
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Affiliation(s)
- Jiming Gao
- College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, Shandong, China
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Toward genetics-based virus taxonomy: comparative analysis of a genetics-based classification and the taxonomy of picornaviruses. J Virol 2012; 86:3905-15. [PMID: 22278238 DOI: 10.1128/jvi.07174-11] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Virus taxonomy has received little attention from the research community despite its broad relevance. In an accompanying paper (C. Lauber and A. E. Gorbalenya, J. Virol. 86:3890-3904, 2012), we have introduced a quantitative approach to hierarchically classify viruses of a family using pairwise evolutionary distances (PEDs) as a measure of genetic divergence. When applied to the six most conserved proteins of the Picornaviridae, it clustered 1,234 genome sequences in groups at three hierarchical levels (to which we refer as the "GENETIC classification"). In this study, we compare the GENETIC classification with the expert-based picornavirus taxonomy and outline differences in the underlying frameworks regarding the relation of virus groups and genetic diversity that represent, respectively, the structure and content of a classification. To facilitate the analysis, we introduce two novel diagrams. The first connects the genetic diversity of taxa to both the PED distribution and the phylogeny of picornaviruses. The second depicts a classification and the accommodated genetic diversity in a standardized manner. Generally, we found striking agreement between the two classifications on species and genus taxa. A few disagreements concern the species Human rhinovirus A and Human rhinovirus C and the genus Aphthovirus, which were split in the GENETIC classification. Furthermore, we propose a new supergenus level and universal, level-specific PED thresholds, not reached yet by many taxa. Since the species threshold is approached mostly by taxa with large sampling sizes and those infecting multiple hosts, it may represent an upper limit on divergence, beyond which homologous recombination in the six most conserved genes between two picornaviruses might not give viable progeny.
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31
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Detection and genetic characterization of enteroviruses circulating among wild populations of chimpanzees in Cameroon: relationship with human and simian enteroviruses. J Virol 2011; 85:4480-6. [PMID: 21345956 DOI: 10.1128/jvi.02285-10] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enteroviruses (EVs), members of the family Picornaviridae, are a genetically and antigenically diverse range of viruses causing acute infections in humans and several Old World monkey (OWM) species. Despite their known wide distribution in primates, nothing is currently known about the occurrence, frequency, and genetic diversity of enteroviruses infecting apes. To investigate this, 27 chimpanzee and 27 gorilla fecal samples collected from undisturbed jungle areas with minimal human contact in Cameroon were screened for EVs. Four chimpanzee samples were positive, but none of the gorilla samples were positive. Genetic characterization of the VP1, VP4, and partial VP2 genes, the 5' untranslated region, and partial 3Dpol sequences enabled chimpanzee-derived EVs to be identified as (i) the species A type, EV76, (ii) a new species D type assigned as EV111, along with a human isolate from the Democratic Republic of Congo previously described by the International Committee on the Taxonomy of Viruses, and (iii) a new species B type (assigned as EV110) most closely related to, although a distinct type from, the SA5 isolate recovered from a vervet monkey. The identification of EVs infecting chimpanzees related to those circulating in human and OWM populations provides evidence for cross-species transmission of EVs between primates. However, the direction of transfer and the existence of primate sources of zoonotic enterovirus infections in humans require further investigation of population exposure and more extensive characterization of EVs circulating in wild ape populations.
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32
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Rhoades RE, Tabor-Godwin JM, Tsueng G, Feuer R. Enterovirus infections of the central nervous system. Virology 2011; 411:288-305. [PMID: 21251690 PMCID: PMC3060663 DOI: 10.1016/j.virol.2010.12.014] [Citation(s) in RCA: 148] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 12/08/2010] [Indexed: 12/15/2022]
Abstract
Enteroviruses (EV) frequently infect the central nervous system (CNS) and induce neurological diseases. Although the CNS is composed of many different cell types, the spectrum of tropism for each EV is considerable. These viruses have the ability to completely shut down host translational machinery and are considered highly cytolytic, thereby causing cytopathic effects. Hence, CNS dysfunction following EV infection of neuronal or glial cells might be expected. Perhaps unexpectedly given their cytolytic nature, EVs may establish a persistent infection within the CNS, and the lasting effects on the host might be significant with unanticipated consequences. This review will describe the clinical aspects of EV-mediated disease, mechanisms of disease, determinants of tropism, immune activation within the CNS, and potential treatment regimes.
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Affiliation(s)
| | | | | | - Ralph Feuer
- Corresponding author. Cell & Molecular Biology Joint Doctoral Program, Department of Biology, San Diego State University, 5500 Campanile Drive; San Diego, CA 92182-4614, USA. Fax: +1 619 594 0777.
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33
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Abstract
Several new enterovirus serotypes and a new human rhinovirus species have been characterized in the Enterovirus genus recently, raising a question about the origin of the new viruses. In this article we attempt to outline the general patterns of enterovirus evolution, ultimately leading to the emergence of new serotypes or species. Different evolutionary and epidemiological patterns can be deduced between different enterovirus species, between entero- and rhino-viruses and between different serotypes within a species. This article presents a hypothesis that the divergent evolution leading to a new serotype is likely to involve adaptation to a new ecological niche either within a single host species or due to interspecies transmission. By contrast, evolution within a serotype appears to occur primarily by genetic drift.
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Affiliation(s)
| | - Carita Savolainen-Kopra
- National Institute for Health and Welfare (THL), Division of Health Protection, Department of Infectious Disease Surveillance & Control, Intestinal Viruses Unit, P.O. Box 30, FI-00271 Helsinki, Finland; National Institute for Health & Welfare (THL), PO Box 30, FI-00271 Helsinki, Finland
| | - Merja Roivainen
- National Institute for Health and Welfare (THL), Division of Health Protection, Department of Infectious Disease Surveillance & Control, Intestinal Viruses Unit, P.O. Box 30, FI-00271 Helsinki, Finland; National Institute for Health & Welfare (THL), PO Box 30, FI-00271 Helsinki, Finland
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34
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Abstract
Picornaviruses are small non-enveloped positive strand RNA viruses that can cause a wide range of clinical manifestations in humans and animals. Many of these viruses are highly diversified and globally prevalent. Natural recombination has been reported in most picornavirus genera and is a key genetic feature of these infectious agents. In several socially relevant picornavirus genera, such as enteroviruses, aphthoviruses, parechoviruses and cardioviruses, recombination, combined with dynamic global epidemiology, maintains virus species as a worldwide pool of genetic information. It can be suggested that on a short time scale recombination acts to promote virus diversity, and new recombinant forms of picornaviruses emerge frequently as 'snapshots' of this global pool. On a longer time scale, recombination maintains stability of a gene pool of a species by shuffling sequences and thus limiting divergence and speciation. This review covers existing evidence of recombination in most genera of the family Picornaviridae and possible implications for diagnostics, epidemiology and classification.
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Affiliation(s)
- A N Lukashev
- M.P. Chumakov Institute of Poliomyelitis and Viral Encephalitides, Russian Academy of Medical Sciences, Moscow Region, Russia.
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35
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Chu PY, Ke GM, Chang CH, Lin JC, Sun CY, Huang WL, Tsai YC, Ke LY, Lin KH. Molecular epidemiology of coxsackie A type 24 variant in Taiwan, 2000-2007. J Clin Virol 2009; 45:285-91. [PMID: 19473877 DOI: 10.1016/j.jcv.2009.04.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Revised: 03/27/2009] [Accepted: 04/20/2009] [Indexed: 11/24/2022]
Abstract
BACKGROUND Epidemics of acute hemorrhagic conjunctivitis (AHC) caused by a coxsackievirus A24 variant (CA24v) appeared in Taiwan in 2000-2002 and again in 2006-2007. OBJECTIVE To analyze the molecular epidemiology of CA24v in recent outbreaks in Taiwan. STUDY DESIGN A 510bp fragment of 3C(pro) region was analyzed in 30 CA24v isolates during 2000-2007. Phylogenetic tree was constructed along with 130 CA24v isolates available from the GenBank. Moreover, the 235bp of 3'VP1 region was similarly analyzed in 15 randomly selected strains isolated during 1985-2007. Phylogenetic dendrogram was constructed for the 3'VP1 region in 105 CA24v strains worldwide. Genetic distances were calculated using Kimura 2-parameter model, and phylogenetic trees were constructed by neighbor-joining method. RESULTS The 3C(pro) dendrogram depicted genotype IV (GIV), a new genotype that can be further divided into three clusters (C1-C3). The 2000-2002 outbreaks were caused by genotype IV-cluster 1 (GIV-C1) and GIV-C2. Strains isolated in the 2006-2007 outbreak belong to GIV-C3, also in the same cluster as Singapore strains from 2005. Analysis on 3'VP1 revealed only GI, GIII and GIV in line with the classification in 3C(pro) dendrogram. All genotype IV strains were also divided into three clusters, though the GIV-C 2' were isolated from broader geographic areas and over a longer period of time. CONCLUSIONS Analysis of the 3C(pro) region is more insightful than the 3'VP1 region in the molecular epidemiology of CA24v. The 3C(pro) dendrogram accurately and chronologically identified all stains involved in the worldwide outbreaks.
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Affiliation(s)
- Pei-Yu Chu
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
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36
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Brown BA, Maher K, Flemister MR, Naraghi-Arani P, Uddin M, Oberste MS, Pallansch MA. Resolving ambiguities in genetic typing of human enterovirus species C clinical isolates and identification of enterovirus 96, 99 and 102. J Gen Virol 2009; 90:1713-1723. [PMID: 19264596 DOI: 10.1099/vir.0.008540-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Molecular methods, based on sequencing the region encoding the VP1 major capsid protein, have recently become the gold standard for enterovirus typing. In the most commonly used scheme, sequences more than 75% identical (>85% amino acid identity) in complete or partial VP1 sequence are considered to represent the same type. However, as sequence data have accumulated, it has become clear that the '75%/85% rule' may not be universally applicable. To address this issue, we have determined nucleotide sequences for the complete P1 capsid region of a collection of 53 isolates from the species Human enterovirus C (HEV-C), comparing them with each other and with those of 20 reference strains. Pairwise identities, similarity plots and phylogenetic reconstructions identified three potential new enterovirus types, EV96, EV99 and EV102. When pairwise sequence comparisons were considered in aggregate, there was overlap in percentage identity between comparisons of homotypic strains and heterotypic strains. In particular, the differences between coxsackievirus (CV) A13 and CVA17, CVA24 and EV99, and CVA20 and EV102 were difficult to discern, largely because of intratypic sequence diversity. Closer inspection revealed the minimum intratypic values and maximum intratypic values varied by type, suggesting that the rules were at least consistent within a type. By plotting VP1 amino acid identity vs nucleotide identity for each sequence pair and considering each type separately, members of each type were fully resolved from those of other types. This study suggests that a more stringent value of 88% VP1 amino acid identity is more appropriate for routine typing and that other criteria may need to be applied, on a case by case basis, where lower values are seen.
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Affiliation(s)
- Betty A Brown
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop G17, Atlanta, GA 30333, USA
| | - Kaija Maher
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop G17, Atlanta, GA 30333, USA
| | - Mary R Flemister
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop G17, Atlanta, GA 30333, USA
| | - Pejman Naraghi-Arani
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop G17, Atlanta, GA 30333, USA
| | - Moyez Uddin
- Institute of Public Health, Dhaka, Bangladesh
| | - M Steven Oberste
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop G17, Atlanta, GA 30333, USA
| | - Mark A Pallansch
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop G17, Atlanta, GA 30333, USA
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37
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Oberste MS, Jiang X, Maher K, Nix WA, Jiang B. The complete genome sequences for three simian enteroviruses isolated from captive primates. Arch Virol 2008; 153:2117-22. [PMID: 18941864 DOI: 10.1007/s00705-008-0225-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Accepted: 09/24/2008] [Indexed: 11/30/2022]
Abstract
In a recent study, we used RT-PCR and partial genome sequencing to detect simian enteroviruses SV6, SV19 and SV46, as well as two new enterovirus types (EV92 and EV103) in fecal specimens from rhesus macaques (Macaca mulatta), pigtail macaques (M. nemestrina), and sooty mangabeys (Cercocebus atys) with diarrheal disease at a US primate center. The complete genome sequences of representative SV46, EV92, and EV103 strains, presented here, show that SV46 and EV92 are typical of the simian enteroviruses classified within the species Human enterovirus A, while EV103 appears to belong to an unclassified species that also contains SV6 and N125/N203.
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Affiliation(s)
- M Steven Oberste
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop G-17, Atlanta, GA 30333, USA.
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38
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Victoria JG, Kapoor A, Dupuis K, Schnurr DP, Delwart EL. Rapid identification of known and new RNA viruses from animal tissues. PLoS Pathog 2008; 4:e1000163. [PMID: 18818738 PMCID: PMC2533695 DOI: 10.1371/journal.ppat.1000163] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2008] [Accepted: 08/27/2008] [Indexed: 12/13/2022] Open
Abstract
Viral surveillance programs or diagnostic labs occasionally obtain infectious samples that fail to be typed by available cell culture, serological, or nucleic acid tests. Five such samples, originating from insect pools, skunk brain, human feces and sewer effluent, collected between 1955 and 1980, resulted in pathology when inoculated into suckling mice. In this study, sequence-independent amplification of partially purified viral nucleic acids and small scale shotgun sequencing was used on mouse brain and muscle tissues. A single viral agent was identified in each sample. For each virus, between 16% to 57% of the viral genome was acquired by sequencing only 42–108 plasmid inserts. Viruses derived from human feces or sewer effluent belonged to the Picornaviridae family and showed between 80% to 91% amino acid identities to known picornaviruses. The complete polyprotein sequence of one virus showed strong similarity to a simian picornavirus sequence in the provisional Sapelovirus genus. Insects and skunk derived viral sequences exhibited amino acid identities ranging from 25% to 98% to the segmented genomes of viruses within the Reoviridae family. Two isolates were highly divergent: one is potentially a new species within the orthoreovirus genus, and the other is a new species within the orbivirus genus. We demonstrate that a simple, inexpensive, and rapid metagenomics approach is effective for identifying known and highly divergent new viruses in homogenized tissues of acutely infected mice. Viral surveillance programs aim to identify circulating viruses to safeguard the public and livestock from viral outbreaks. Occasionally, samples suspected of harboring a virus cause severe disease in laboratory animals, but the identity of the virus eludes researchers. Here, we applied a simple viral discovery technique to identify viruses directly from the tissues of inoculated symptomatic mice and found a single virus in each sample using a rapid viral particle purification and random nucleic acid amplification method. Two viruses appear to be closely related to the members of the Picornaviridae family. In three other samples, originally collected from pools of crushed mosquitoes and the brain of a sick skunk, a known and novel viruses related to members of the Reoviridiae family were identified. Reoviruses are considered major pathogens of livestock. Our studies provide the groundwork for further analysis of the prevalence and pathogenesis of these divergent viruses and illustrate the ease with which new viral species can be identified in tissues of acutely infected animals.
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Affiliation(s)
- Joseph G Victoria
- Department of Molecular Virology, Blood Systems Research Institute, San Francisco, California, USA.
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39
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Wei L, Chee LL, Wei T, Kwang J, Zhou J, Wang J, Shi L, Liu J. The VP1 protein of avian encephalomyelitis virus is a major host-protective immunogen that serves as diagnostic potential. J Virol Methods 2008; 149:56-62. [PMID: 18316131 DOI: 10.1016/j.jviromet.2008.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Revised: 12/22/2007] [Accepted: 01/10/2008] [Indexed: 10/22/2022]
Abstract
Avian encephalomyelitis virus (AEV) is an important pathogen of poultry and is classified as a member of Picornaviridae. To investigate the protective immunity induced by AEV structural proteins, recombinant VP1, VP0, and VP3 proteins were expressed in a baculovirus system. The result of in vivo protection assays shows that the VP1 protein is a major host-protective immunogen against AEV challenge and demonstrates further that the antibody raised against VP1 protein could neutralize more effectively AEV infection than antibody against VP3 or VP0 protein in a virus neutralization test. These purified recombinant proteins were subsequently evaluated as enzyme-linked immunosorbent assay (ELISA) antigens for detection of AEV infection. A total number of 50 positive sera and 30 negative sera were tested for ELISA validation. Results obtained by testing 193 sera from chickens suspected of being infected AEV further showed that the diagnostic sensitivities of the VP1, VP3, and VP0 protein-based ELISAs were 98.1, 80.6, and 51.9%, and their specificities were 100, 87.9, and 81.8%, respectively. Both sensitivity and specificity of the VP1 protein-based ELISA were comparable with a commercially available test, indicating that the VP1 protein has a highly promising and reliable diagnostic potential, and thus is a suitable antigen for ELISA detection of AEV antibodies in chickens.
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Affiliation(s)
- Li Wei
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Municipal Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Garden Central Road, Haidian District, Beijing 100097, People's Republic of China
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40
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Oberste MS, Maher K, Pallansch MA. Complete genome sequences for nine simian enteroviruses. J Gen Virol 2008; 88:3360-3372. [PMID: 18024906 DOI: 10.1099/vir.0.83124-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Analysis of the VP1 capsid-coding sequences of the simian picornaviruses has suggested that baboon enterovirus (BaEV), SV19, SV43 and SV46 belong to the species Human enterovirus A (HEV-A) and SA5 belongs to HEV-B, whereas SV4/A2 plaque virus (two isolates of a single serotype), SV6 and N125/N203 (two isolates of a single serotype) appear to represent new species in the genus. We have further characterized by complete genomic sequencing the genetic relationships among the simian enteroviruses serotypes (BaEV, N125/N203, SA5, SV4/A2 plaque virus, SV6, SV19, SV43 and SV46) and to other enteroviruses. Phylogenetic and pairwise sequence relationships for the P1 region paralleled those of VP1 alone, and confirmed that SV4/A-2 plaque virus, SV6 and N125/N203 represent unique genetic clusters that probably correspond to three new species. However, sequence relationships in the P2 and P3 regions were quite different. In 2C, SV19, SV43 and SV46 remain clustered with the human viruses of HEV-A, but BaEV, SV6 and N125/N203 cluster together; in 3CD, SA5 (HEV-B) also joined this cluster. The 3'-non-translated region (NTR) sequences are highly conserved within each of the four human enterovirus species, but the 3'-NTRs of the simian enteroviruses are distinct from those of all human enteroviruses and generally distinct from one another. These results suggest that host species may have a significant influence on the evolution of enterovirus non-capsid sequences.
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Affiliation(s)
- M Steven Oberste
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Kaija Maher
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Mark A Pallansch
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
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41
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Smura T, Blomqvist S, Paananen A, Vuorinen T, Sobotová Z, Buboviča V, Ivanova O, Hovi T, Roivainen M. Enterovirus surveillance reveals proposed new serotypes and provides new insight into enterovirus 5'-untranslated region evolution. J Gen Virol 2007; 88:2520-2526. [PMID: 17698662 DOI: 10.1099/vir.0.82866-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human enteroviruses are currently grouped into five species Human enterovirus A (HEV-A), HEV-B, HEV-C, HEV-D and Poliovirus. During surveillance for enteroviruses serologically non-typable enterovirus strains were found from acute flaccid paralysis patients and healthy individuals. In this study, we report isolates of recently described enterovirus types EV76 and EV90 of HEV-A species and characterize two new enterovirus type candidates, EV96 and EV97, to species HEV-C and HEV-B, respectively. Analysis of partial 3D regions of EV96 strains revealed sequence divergence consistent with several recombination events between EV96, other HEV-C viruses and polioviruses. Phylogenetic analysis of all available 5'-untranslated region sequences of human entero- and rhinovirus prototype strains and 10 simian enterovirus strains suggested interspecies recombination involving this region.
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Affiliation(s)
- Teemu Smura
- Enterovirus Laboratory, Department of Viral Diseases and Immunology, National Public Health Institute (KTL), Mannerheimintie 166, FIN-00300 Helsinki, Finland
| | - Soile Blomqvist
- Enterovirus Laboratory, Department of Viral Diseases and Immunology, National Public Health Institute (KTL), Mannerheimintie 166, FIN-00300 Helsinki, Finland
| | - Anja Paananen
- Enterovirus Laboratory, Department of Viral Diseases and Immunology, National Public Health Institute (KTL), Mannerheimintie 166, FIN-00300 Helsinki, Finland
| | - Tytti Vuorinen
- Department of Virology, University of Turku, Kiinamyllynkatu 13, FIN-20520 Turku, Finland
| | - Zdenka Sobotová
- National Reference Centres, Public Health Office of the Slovak Republic, Trnavska 52, 82645 Bratislava, Slovak Republic
| | - Veronika Buboviča
- State Agency 'Public Health Agency', Virology Laboratory, Klijanu Str. 7, LV-1012 Riga, Latvia
| | - Olga Ivanova
- M. P. Chumakov Institute of Poliomyelitis and Viral Encephalitides of Russian Academy of Medical Science, Kievskoe Shosse 27 km, 142782 Moscow Region, Russian Federation
| | - Tapani Hovi
- Enterovirus Laboratory, Department of Viral Diseases and Immunology, National Public Health Institute (KTL), Mannerheimintie 166, FIN-00300 Helsinki, Finland
| | - Merja Roivainen
- Enterovirus Laboratory, Department of Viral Diseases and Immunology, National Public Health Institute (KTL), Mannerheimintie 166, FIN-00300 Helsinki, Finland
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Tseng CH, Tsai HJ. Sequence analysis of a duck picornavirus isolate indicates that it together with porcine enterovirus type 8 and simian picornavirus type 2 should be assigned to a new picornavirus genus. Virus Res 2007; 129:104-14. [PMID: 17686542 DOI: 10.1016/j.virusres.2007.06.023] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2007] [Accepted: 06/26/2007] [Indexed: 11/15/2022]
Abstract
In a 1990 outbreak, a virus isolated in Taiwan from the intestines of ducks showing signs of hepatitis was tentatively classified as a picornavirus on the basis of physical, chemical, and morphological characteristics. The virus was cloned and then found not to be type 1 duck hepatitis virus (DHV-1) or a new serotype of duck hepatitis virus (N-DHV) by serum neutralization. Complete genome sequencing indicated that the virus genome had 8351 nucleotides and the typical picornavirus genome organization (i.e., 5' untranslated region (UTR)-L-P1 (VP 4-2-3-1)-P2 (2A-B-C)-P3 (3A-B-C-D)-3' UTR-poly A). One open reading frame encoded 2521 amino acids, which makes this virus one of the largest picornaviruses, second only to equine rhinitis B virus of the genus Erbovirus. Its L protein was the largest within the family Picornaviridae (451 amino acids) and suspected to be a trypsin-like protease. The 235-nucleotide 3' UTR region was of intermediate size, quite long compared to other picornaviruses but shorter than other picornaviruses of duck-origin (DHV-1 and N-DHV) and had four regions of secondary structure. The 2A protein was composed of only 12 amino acids, which is the shortest of any member of the family Picornaviridae. Phylogenetic analysis of the polyprotein and 3D sequences indicated that this virus (named duck picornavirus [DPV]) together with porcine enterovirus type 8 virus and several simian picornaviruses form a distinct branch of the family Picornaviridae and should be assigned to a new picornavirus genus.
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Affiliation(s)
- Chun-Hsien Tseng
- Graduate Institute of Veterinary Medicine, College of Bioresource and Agriculture, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 106, Taiwan
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43
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Sampath R, Hall TA, Massire C, Li F, Blyn LB, Eshoo MW, Hofstadler SA, Ecker DJ. Rapid identification of emerging infectious agents using PCR and electrospray ionization mass spectrometry. Ann N Y Acad Sci 2007; 1102:109-20. [PMID: 17470915 PMCID: PMC7167958 DOI: 10.1196/annals.1408.008] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
abstract: Newly emergent infectious diseases are a global public health problem. The population dense regions of Southeast Asia are the epicenter of many emerging diseases, as evidenced by the outbreak of Nipah, SARS, avian influenza (H5N1), Dengue, and enterovirus 71 in this region in the past decade. Rapid identification, epidemiologic surveillance, and mitigation of transmission are major challenges in ensuring public health safety. Here we describe a powerful new approach for infectious disease surveillance that is based on polymerase chain reaction (PCR) to amplify nucleic acid targets from large groupings of organisms, electrospray ionization mass spectrometry (ESI‐MS) for accurate mass measurements of the PCR products, and base composition signature analysis to identify organisms in a sample. This approach is capable of automated analysis of more than 1,500 PCR reactions a day. It is applicable to the surveillance of bacterial, viral, fungal, or protozoal pathogens and will facilitate rapid characterization of known and emerging pathogens.
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Affiliation(s)
- Rangarajan Sampath
- Ibis Biosciences Inc, Subsidiary of Isis Pharmaceuticals, Carlsbad, CA 92008, USA.
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44
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Hellen CUT, de Breyne S. A distinct group of hepacivirus/pestivirus-like internal ribosomal entry sites in members of diverse picornavirus genera: evidence for modular exchange of functional noncoding RNA elements by recombination. J Virol 2007; 81:5850-63. [PMID: 17392358 PMCID: PMC1900287 DOI: 10.1128/jvi.02403-06] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The 5' untranslated regions (UTRs) of the RNA genomes of Flaviviridae of the Hepacivirus and Pestivirus genera contain internal ribosomal entry sites (IRESs) that are unrelated to the two principal classes of IRESs of Picornaviridae. The mechanism of translation initiation on hepacivirus/pestivirus (HP) IRESs, which involves factor-independent binding to ribosomal 40S subunits, also differs fundamentally from initiation on these picornavirus IRESs. Ribosomal binding to HP IRESs requires conserved sequences that form a pseudoknot and the adjacent IIId and IIIe domains; analogous elements do not occur in the two principal groups of picornavirus IRESs. Here, comparative sequence analysis was used to identify a subset of picornaviruses from multiple genera that contain 5' UTR sequences with significant similarities to HP IRESs. They are avian encephalomyelitis virus, duck hepatitis virus 1, duck picornavirus, porcine teschovirus, porcine enterovirus 8, Seneca Valley virus, and simian picornavirus. Their 5' UTRs are predicted to form several structures, in some of which the peripheral elements differ from the corresponding HP IRES elements but in which the core pseudoknot, domain IIId, and domain IIIe elements are all closely related. These findings suggest that HP-like IRESs have been exchanged between unrelated virus families by recombination and support the hypothesis that RNA viruses consist of modular coding and noncoding elements that can exchange and evolve independently.
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Affiliation(s)
- Christopher U T Hellen
- Department of Microbiology and Immunology, SUNY Downstate Medical Center, 450 Clarkson Avenue, Box 44, Brooklyn, NY 11203, USA.
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45
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Tseng CH, Tsai HJ. Molecular characterization of a new serotype of duck hepatitis virus. Virus Res 2007; 126:19-31. [PMID: 17292992 DOI: 10.1016/j.virusres.2007.01.012] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2006] [Revised: 01/09/2007] [Accepted: 01/13/2007] [Indexed: 10/23/2022]
Abstract
Duck hepatitis strains 90D and 04G were determined to be antigenically unrelated to type 1 duck hepatitis virus (DHV-1) by in vitro cross-neutralization assay. The genome sequences of 90D and 04G revealed that both strains of the new serotype DHV (N-DHV) possessed a typical picornavirus genome organization apart from the unique possession of three in-tandem 2A genes present in DHV-1. The 2A1, 2A2, and 2A3 proteins represented an aphthovirus-like 2A protein, AIG1-like protein, and human parechovirus-like 2A protein, respectively. The N-DHV genome displayed unique features, compared to the DHV-1 genome. The 366 nt 3'UTR of N-DHV, the largest determined thus far among picornaviruses, was 52 nt longer than DHV-1. The pairwise percent identity of the nucleic acid and amino acid sequences at 1D region of N-DHV and DHV-1 were only 69.1-69.7 and 70.1-70.5%, respectively. Finally, phylogenetic and evolutionary analysis of N-DHV revealed that the N-DHV and DHV-1 belong to two different clusters of a novel genus in the Picornaviridae family.
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MESH Headings
- 5' Untranslated Regions
- Amino Acid Sequence
- Animals
- Antigens, Viral
- Base Sequence
- Cross Reactions
- DNA, Viral/genetics
- Ducks
- Evolution, Molecular
- Genome, Viral
- Hepatitis Virus, Duck/classification
- Hepatitis Virus, Duck/genetics
- Hepatitis Virus, Duck/immunology
- Hepatitis, Viral, Animal/virology
- Humans
- Molecular Sequence Data
- Neutralization Tests
- Nucleic Acid Conformation
- Phylogeny
- Picornaviridae Infections/veterinary
- Picornaviridae Infections/virology
- RNA, Viral/chemistry
- RNA, Viral/genetics
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
- Serotyping
- Viral Proteins/genetics
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Affiliation(s)
- Chun-Hsien Tseng
- Graduate Institute of Veterinary Medicine, College of Bioresource and Agriculture, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 106, Taiwan
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46
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Simmonds P, Welch J. Frequency and dynamics of recombination within different species of human enteroviruses. J Virol 2007; 80:483-93. [PMID: 16352572 PMCID: PMC1317522 DOI: 10.1128/jvi.80.1.483-493.2006] [Citation(s) in RCA: 212] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Enteroviruses are members of the family Picornaviridae that cause widespread infections in human and other mammalian populations. Enteroviruses are genetically and antigenically highly variable, and recombination within and between serotypes contributes to their genetic diversity. To investigate the dynamics of the recombination process, sequence phylogenies between three regions of the genome (VP4, VP1, and 3Dpol) were compared among species A and B enterovirus variants detected in a human population-based survey in Scotland between 2000 and 2001, along with contemporary virus isolates collected in the same geographical region. This analysis used novel bioinformatic methods to quantify phylogenetic compatibility and correlations with serotype assignments of evolutionary trees constructed for different regions of the enterovirus genome. Species B enteroviruses showed much more frequent, time-correlated recombination events than those found for species A, despite the equivalence in population sampling, concordant with a linkage analysis of previously characterized enterovirus sequences obtained over longer collection periods. An analysis of recombination among complete genome sequences by computation of a phylogenetic compatibility matrix (PCM) demonstrated sharply defined boundaries between the VP2/VP3/VP1 block and sequences to either side in phylogenetic compatibility. The PCM also revealed equivalent or frequently greater degrees of incompatibility between different parts within the nonstructural region (2A-3D), indicating the occurrence of extensive recombination events in the past evolution of this part of the genome. Together, these findings provide new insights into the dynamics of species A and B enterovirus recombination and evolution and into the contribution of structured sampling to documenting reservoirs, emergence, and spread of novel recombinant forms in human populations.
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Affiliation(s)
- Peter Simmonds
- Virus Evolution Group, Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, United Kingdom.
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47
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Nix WA, Oberste MS, Pallansch MA. Sensitive, seminested PCR amplification of VP1 sequences for direct identification of all enterovirus serotypes from original clinical specimens. J Clin Microbiol 2006; 44:2698-704. [PMID: 16891480 PMCID: PMC1594621 DOI: 10.1128/jcm.00542-06] [Citation(s) in RCA: 646] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A reverse transcription-seminested PCR (RT-snPCR) assay was developed for the detection and identification of enterovirus (EV) RNA in clinical specimens. Three conserved protein motifs were identified by aligning the VP3 and VP1 sequences of prototype EV strains. Consensus degenerate primers were designed from a conserved VP3 motif and a distal VP1 motif for the first PCR. Consensus-degenerate hybrid oligonucleotide primers were designed from an internal VP1 motif and used with the same distal VP1 motif for the second, seminested PCR step. The primers were designed for broad target specificity and amplified all recognized and proposed EV serotypes and other antigenic variant strains tested. The VP1 RT-snPCR assay was slightly more sensitive than our in-house EV 5' nontranslated region RT-snPCR assay, detecting as few as 10 RNA copies per reaction. As an example application, the VP1 RT-snPCR assay was used to identify EVs in clinical specimens. A product of the expected size was successfully amplified and sequenced from cerebrospinal fluid; serum; stool suspensions; and nasopharyngeal, eye, and rectal swab specimens, allowing unambiguous identification of the infecting virus in all cases. The VP1 sequences derived from the RT-snPCR products allow rapid phylogenetic and molecular epidemiologic analysis of strains circulating during the EV season and comparison with EV sequences from past seasons or from different locations around the world.
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Affiliation(s)
- W Allan Nix
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
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48
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Tseng CH, Knowles NJ, Tsai HJ. Molecular analysis of duck hepatitis virus type 1 indicates that it should be assigned to a new genus. Virus Res 2006; 123:190-203. [PMID: 17067712 DOI: 10.1016/j.virusres.2006.09.007] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2006] [Revised: 09/15/2006] [Accepted: 09/19/2006] [Indexed: 10/24/2022]
Abstract
The genome sequences of three duck hepatitis virus type 1 (DHV-1) strains were determined. Comparative sequence analyses showed that they possessed a typical picornavirus genome organization apart from the unique possession of three in-tandem 2A genes. The 2A1 protein of DHV-1 is an aphthovirus-like 2A protein; the 2A2 protein is not related to any known picornavirus protein; the 2A3 protein is a human parechovirus-like 2A protein. Several other features were found to be unique to the DHV-1 genome when compared with other picornaviruses: (i) the 3' UTR of DHV-1 was composed of 314 nt, the largest among the picornaviruses; (ii) pair-wise amino acid sequence identities between polyprotein of DHV-1 and other picornaviruses are all less than 30%. The pair-wise amino acid sequence identities in the 3D region of DHV-1 with LV and HPeV-1 is only 38.6 and 36.6%, respectively, and less than 30% with all other picornaviruses; (iii) the DHV-1 capsid polypeptide VP0 is not proteolytically cleaved into VP4 and VP2; and (iv) phylogenetic and evolutionary analysis of DHV-1 reveals a new picornavirus clade. It is therefore proposed that DHV-1 should be assigned to a new genus in the Picornaviridae.
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Affiliation(s)
- Chun-Hsien Tseng
- Graduate Institute of Veterinary Medicine, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 106, Taiwan
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49
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Jones LR, Zandomeni RO, Weber EL. A long distance RT-PCR able to amplify the Pestivirus genome. J Virol Methods 2006; 134:197-204. [PMID: 16497393 PMCID: PMC7112918 DOI: 10.1016/j.jviromet.2006.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2005] [Revised: 01/03/2006] [Accepted: 01/10/2006] [Indexed: 01/08/2023]
Abstract
A method to amplify long genomic regions (up to approximately 12.3 kb) from pestiviruses in one RT-PCR is described. The difficulty in designing conserved Pestivirus primers for the amplification of genomes from highly divergent isolates simply by means of overlapping segments is demonstrated using new bioinformatic tools. An alternative procedure consisting of optimizing the length of the genomic cDNA fragments and their subsequent amplification by polymerase chain reaction (PCR) using a limited set of specific primers is described. The amplification of long DNA fragments from a variety of sources, including genomic, mitochondrial, and viral DNAs as well as cDNA produced by reverse transcription (RT) has been achieved using this methodology, known as long distance PCR. In the case of viruses, it is necessary to obtain viral particles from infected cells prior to RT procedures. This work provides improvements in four steps of long distance RT-PCR (L-RT-PCR): (i) preparation of a viral stock, (ii) preparation of template RNA, (iii) reverse transcription and (iv) amplification of the cDNA by LD-PCR. The usefulness of L-RT-PCR is discussed in the light of current knowledge on pestivirus diversity. The genomic sequence of Singer_Arg reference strain obtained using this method is presented and characterized.
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Affiliation(s)
- Leandro R. Jones
- Instituto de Virología, CICVyA, INTA-Castelar, CC 25, (1712) Castelar, Buenos Aires, Argentina
| | - Rubén O. Zandomeni
- Instituto de Microbiología y Zoología Agrícola, CICVyA, INTA-Castelar, CC 25, (1712) Castelar, Buenos Aires, Argentina
| | - E. Laura Weber
- Instituto de Virología, CICVyA, INTA-Castelar, CC 25, (1712) Castelar, Buenos Aires, Argentina
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50
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Oberste MS, Maher K, Williams AJ, Dybdahl-Sissoko N, Brown BA, Gookin MS, Peñaranda S, Mishrik N, Uddin M, Pallansch MA. Species-specific RT-PCR amplification of human enteroviruses: a tool for rapid species identification of uncharacterized enteroviruses. J Gen Virol 2006; 87:119-128. [PMID: 16361424 DOI: 10.1099/vir.0.81179-0] [Citation(s) in RCA: 156] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The 65 serotypes of human enteroviruses are classified into four species, Human enterovirus (HEV) A to D, based largely on phylogenetic relationships in multiple genome regions. The 3'-non-translated region of enteroviruses is highly conserved within a species but highly divergent between species. From this information, species-specific RT-PCR primers were developed that can be used to rapidly screen collections of enterovirus isolates to identify species of interest. The four primer pairs were 100 % specific when tested against enterovirus prototype strains and panels of isolates of known serotype (a total of 193 isolates). For evaluation in a typical application, the species-specific primers were used to screen 186 previously uncharacterized non-polio enterovirus isolates. The HEV-B primers amplified 68.3 % of isolates, while the HEV-A and HEV-C primers accounted for 9.7 and 11.3 % of isolates, respectively; no isolates were amplified with the HEV-D primers. Twelve isolates (6.5 %) were amplified by more than one primer set and eight isolates (4.3 %) were not amplified by any of the four primer pairs. Serotypes were identified by partial sequencing of the VP1 capsid gene, and in every case sequencing confirmed that the species-specific PCR result was correct; the isolates that were amplified by more than one species-specific primer pair were mixtures of two (11 isolates) or three (one isolate) species of viruses. The eight isolates that were not amplified by the species-specific primers comprised four new serotypes (EV76, EV89, EV90 and EV91) that appear to be unique members of HEV-A based on VP1, 3D and 3'-non-translated region sequences.
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Affiliation(s)
- M Steven Oberste
- Respiratory and Enteric Viruses Branch, Division of Viral and Rickettsial Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop G-17, Atlanta, GA 30333, USA
| | - Kaija Maher
- Respiratory and Enteric Viruses Branch, Division of Viral and Rickettsial Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop G-17, Atlanta, GA 30333, USA
| | - Alford J Williams
- Respiratory and Enteric Viruses Branch, Division of Viral and Rickettsial Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop G-17, Atlanta, GA 30333, USA
| | - Naomi Dybdahl-Sissoko
- Respiratory and Enteric Viruses Branch, Division of Viral and Rickettsial Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop G-17, Atlanta, GA 30333, USA
| | - Betty A Brown
- Respiratory and Enteric Viruses Branch, Division of Viral and Rickettsial Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop G-17, Atlanta, GA 30333, USA
| | - Michelle S Gookin
- Respiratory and Enteric Viruses Branch, Division of Viral and Rickettsial Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop G-17, Atlanta, GA 30333, USA
| | - Silvia Peñaranda
- Respiratory and Enteric Viruses Branch, Division of Viral and Rickettsial Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop G-17, Atlanta, GA 30333, USA
| | - Nada Mishrik
- Respiratory and Enteric Viruses Branch, Division of Viral and Rickettsial Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop G-17, Atlanta, GA 30333, USA
| | - Moyez Uddin
- Institute of Public Health, Dhaka, Bangladesh
| | - Mark A Pallansch
- Respiratory and Enteric Viruses Branch, Division of Viral and Rickettsial Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop G-17, Atlanta, GA 30333, USA
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