1
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Deng H, Cong G, Wang H, Hu Z, Shi D, Shi H, Xia C, Fu F, Feng L. Isolation, characterization, and phylogenetic analysis of two new porcine parvovirus 1 isolates from Northern China. Virus Res 2024; 339:199247. [PMID: 37923168 PMCID: PMC10751695 DOI: 10.1016/j.virusres.2023.199247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/19/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023]
Abstract
Porcine parvovirus (PPV) is a pathogen of infectious reproductive disease, which can cause stillbirth, mummification, embryo death, and infertility (SMEDI) syndrome in pigs. The objective of this study was to gain new insights into the evolution and phylogeny of the PPV1 genome. In this study, we isolated two new PPV1 (HLJ202108-Y and SDLC202109) from northern China and sequenced their whole genomes. The new isolates were found to have three amino acid substitutions (K195R, K562R, and S578P) in nonstructural protein 1. The VP2 amino acid site contained nine nonsynonymous substitutions, including six substitutions of the Kresse strain corresponding to the NADL-2 strain and three substitutions of A414S, S436T, and N555K. Genetic evolution analysis was conducted on 107 reference sequences available in the GenBank database, and 4-5 PPV1 taxa were defined. The new isolates were in the same phylogenetic cluster as strain 27a. The changes in the cluster, specifically marker amino acids, and their potential role in enhancing pathogenicity are discussed in this study. Furthermore, the evolutionary tree map results showed that the strains in China were evolving in two directions: one was becoming increasingly similar to early NADL-2 strains, while the other was evolving toward 27a-like strains. We also compared the proliferation ability of the isolated strains in susceptible cells by analyzing the multistep growth curves. The results showed that the virulence titer of the mutant strain was high. In summary, this study introduced the latest changes in PPV and discussed the virus characteristics that were considered to affect virulence.
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Affiliation(s)
- Huiwei Deng
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Guangyi Cong
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Hongfeng Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Zedong Hu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Da Shi
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Hongyan Shi
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Changyou Xia
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Fang Fu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China.
| | - Li Feng
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China.
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2
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Sutherland M, Sarker S. Liver virome of a Little Corella (Cacatua sanguinea) reveals coinfection with a novel parvovirus and two beak and feather disease viruses. Aust Vet J 2023; 101:366-372. [PMID: 37497656 DOI: 10.1111/avj.13271] [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: 04/27/2023] [Accepted: 07/07/2023] [Indexed: 07/28/2023]
Abstract
Emerging diseases are acknowledged as a growing threat to wildlife, with the continued identification of pathogenic and potentially pathogenic viruses in avian species resulting from ongoing advances in molecular diagnostic techniques. Parvoviruses under the genus Chaphamaparvovirus (subfamily Hamaparvovirinae) are highly divergent. The detection and characterisation of parvoviruses in psittacine birds is limited. This study reports a novel parvovirus, tentatively named psittaciform chaphamaparvovirus 3 (PsChV-3) under the genus Chaphamaparvovirus, identified in an Australian free-ranging little corella (Cacatua sanguinea). The PsChV-3 genome is 4277 bp in length and encompasses four predicted open-reading frames, including two major genes, a nonstructural replicase gene (NS1), and a structural capsid gene (VP1). The NS1 and VP1 genes showed the closest amino acid identities of 78.8% and 69.7%, respectively, with a recently sequenced psittaciform chaphamaparvovirus 2 from Australian Neophema species grass parrots. In addition, the presence of two complete novel beak and feather disease (BFDV) genomes, 1993 and 1868 nt in length, respectively, were detected from the same bird. Both these BFDV genomes contained two bidirectional ORFs encoding the putative Rep and Cap proteins. Phylogenetic analysis showed that the sequenced novel BFDV genomes clustered in a distinct subclade with other BFDVs isolated from Australian cockatoos. This study contributes to the characterisation chaphamaparvoviruses and BFDV in Australian parrots and supports the need for ongoing monitoring and molecular studies into the avian virome in native Australian psittacine bird species.
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Affiliation(s)
- M Sutherland
- The Unusual Pet Vets, 210 Karingal Drive, Frankston, Victoria, 3930, Australia
| | - S Sarker
- Dept. of Microbiology, Anatomy, Physiology, and Pharmacology, School of Agriculture, Biomedicine and Environment, LaTrobe University, Melbourne, Victoria, 3086, Australia
- Biomedical Sciences & Molecular Biology, Australian Institute of Tropical Health and Medicine, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia
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3
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Zhang Y, Feng B, Xie Z, Zhang M, Fan Q, Deng X, Xie Z, Li M, Zeng T, Xie L, Luo S, Huang J, Wang S. Molecular characterization of emerging chicken and turkey parvovirus variants and novel strains in Guangxi, China. Sci Rep 2023; 13:13083. [PMID: 37567941 PMCID: PMC10421884 DOI: 10.1038/s41598-023-40349-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/09/2023] [Indexed: 08/13/2023] Open
Abstract
Avian parvoviruses cause several enteric poultry diseases that have been increasingly diagnosed in Guangxi, China, since 2014. In this study, the whole-genome sequences of 32 strains of chicken parvovirus (ChPV) and 3 strains of turkey parvovirus (TuPV) were obtained by traditional PCR techniques. Phylogenetic analyses of 3 genes and full genome sequences were carried out, and 35 of the Guangxi ChPV/TuPV field strains were genetically different from 17 classic ChPV/TuPV reference strains. The nucleotide sequence alignment between ChPVs/TuPVs from Guangxi and other countries revealed 85.2-99.9% similarity, and the amino acid sequences showed 87.8-100% identity. The phylogenetic tree of these sequences could be divided into 6 distinct ChPV/TuPV groups. More importantly, 3 novel ChPV/TuPV groups were identified for the first time. Recombination analysis with RDP 5.0 revealed 15 recombinants in 35 ChPV/TuPV isolates. These recombination events were further confirmed by Simplot 3.5.1 analysis. Phylogenetic analysis based on full genomes showed that Guangxi ChPV/TuPV strains did not cluster according to their geographic origin, and the identified Guangxi ChPV/TuPV strains differed from the reference strains. Overall, whole-genome characterizations of emerging Guangxi ChPV and TuPV field strains will provide more detailed insights into ChPV/TuPV mutations and recombination and their relationships with molecular epidemiological features.
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Affiliation(s)
- Yanfang Zhang
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, 530000, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, 530000, Guangxi, China
| | - Bin Feng
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, 530000, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, 530000, Guangxi, China
| | - Zhixun Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, 530000, Guangxi, China.
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, 530000, Guangxi, China.
| | - Minxiu Zhang
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, 530000, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, 530000, Guangxi, China
| | - Qing Fan
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, 530000, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, 530000, Guangxi, China
| | - Xianwen Deng
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, 530000, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, 530000, Guangxi, China
| | - Zhiqin Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, 530000, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, 530000, Guangxi, China
| | - Meng Li
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, 530000, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, 530000, Guangxi, China
| | - Tingting Zeng
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, 530000, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, 530000, Guangxi, China
| | - Liji Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, 530000, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, 530000, Guangxi, China
| | - Sisi Luo
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, 530000, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, 530000, Guangxi, China
| | - Jiaoling Huang
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, 530000, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, 530000, Guangxi, China
| | - Sheng Wang
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, 530000, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, 530000, Guangxi, China
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4
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Schulz M, Levy DI, Petropoulos CJ, Bashirians G, Winburn I, Mahn M, Somanathan S, Cheng SH, Byrne BJ. Binding and neutralizing anti-AAV antibodies: Detection and implications for rAAV-mediated gene therapy. Mol Ther 2023; 31:616-630. [PMID: 36635967 PMCID: PMC10014285 DOI: 10.1016/j.ymthe.2023.01.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/21/2022] [Accepted: 01/06/2023] [Indexed: 01/13/2023] Open
Abstract
Assessment of anti-adeno-associated virus (AAV) antibodies in patients prior to systemic gene therapy administration is an important consideration regarding efficacy and safety of the therapy. Approximately 30%-60% of individuals have pre-existing anti-AAV antibodies. Seroprevalence is impacted by multiple factors, including geography, age, capsid serotype, and assay type. Anti-AAV antibody assays typically measure (1) transduction inhibition by detecting the neutralizing capacity of antibodies and non-antibody neutralizing factors, or (2) total anti-capsid binding antibodies, regardless of neutralizing activity. Presently, there is a paucity of head-to-head data and standardized approaches associating assay results with clinical outcomes. In addition, establishing clinically relevant screening titer cutoffs is complex. Thus, meaningful comparisons across assays are nearly impossible. Although complex, establishing screening assays in routine clinical practice to identify patients with antibody levels that may impact favorable treatment outcomes is achievable for both transduction inhibition and total antibody assays. Formal regulatory approval of such assays as companion diagnostic tests will confirm their suitability for specific recombinant AAV gene therapies. This review covers current approaches to measure anti-AAV antibodies in patient plasma or serum, their potential impact on therapeutic safety and efficacy, and investigative strategies to mitigate the effects of pre-existing anti-AAV antibodies in patients.
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Affiliation(s)
- Martin Schulz
- Pfizer, 235 East 42nd Street, New York, NY 10017, USA
| | - Daniel I Levy
- Pfizer, 235 East 42nd Street, New York, NY 10017, USA
| | | | | | - Ian Winburn
- Pfizer, 235 East 42nd Street, New York, NY 10017, USA
| | - Matthias Mahn
- Pfizer, 235 East 42nd Street, New York, NY 10017, USA
| | | | - Seng H Cheng
- Pfizer, 235 East 42nd Street, New York, NY 10017, USA
| | - Barry J Byrne
- University of Florida, 1600 SW Archer Road, Gainesville, FL 32610, USA.
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5
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Mendes Dos Santos MA, Dias LS, Ramirez Pavon JA, Viniski AE, Campos Souza CL, Pepato MA, Correa de Azevedo V, Teixeira Nunes MR, Slhessarenko RD. Regional mutations in CHIKV-ECSA genomes and detection of other viruses in the serum of acute febrile patients by a metagenomic approach in Mato Grosso, Central-Western Brazil, 2018. Virology 2022; 576:18-29. [PMID: 36126430 DOI: 10.1016/j.virol.2022.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/19/2022]
Abstract
Mato Grosso (MT) State is part of central western Brazil and has a tropical permissive environment that favors arbovirus outbreaks. A metagenomic approach was used to identify viral genomes in seven pools of serum from patients (n=65) with acute febrile disease. Seven chikungunya virus (CHIKV) genomes were determined, showing four amino acid changes found only in CHIKV genomes obtained in MT since 2018: nsP2:T31I, nsP3: A388V, E3:T201I and E3:H57R, in addition to other mutations in E1, nsP2 and nsP4. Six parvovirus B19 (B19V) genotype I genomes (4771-5131 nt) showed four aa alterations (NS1:N473D, R579Q; VP1:I716T; and 11 kDa:V44A) compared to most similar B19V from the USA. Coinfection between CHIKV and B19V was evidenced in 22/65 (33.8%) patients by RT‒PCR and PCR, respectively. Other viruses found in these pools include human pegivirus C, torque teno virus 3, an unclassified TTV and torque teno mini virus. Metagenomics represents a useful approach to detect viruses in the serum of acute febrile patients suspected of arbovirus disease.
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Affiliation(s)
- Marcelo Adriano Mendes Dos Santos
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil; Faculdade de Medicina, Universidade do Estado de Mato Grosso, Cáceres, MT, Brazil
| | - Lucas Silva Dias
- Curso de Graduação em Medicina, Faculdade de Medicina, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil
| | - Janeth Aracely Ramirez Pavon
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil
| | - Ana Elisa Viniski
- Laboratório Central do Estado de Mato Grosso, Secretaria Estadoual de Saúde, Cuiabá, MT, Brazil
| | | | - Marco Andrey Pepato
- Laboratório Central do Estado de Mato Grosso, Secretaria Estadoual de Saúde, Cuiabá, MT, Brazil; Hospital Universitário Júlio Muller, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil
| | | | | | - Renata Dezengrini Slhessarenko
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil.
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6
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Robust AAV Genotyping Based on Genetic Distances in Rep Gene That Are Maintained by Ubiquitous Recombination. Viruses 2022; 14:v14051038. [PMID: 35632781 PMCID: PMC9143360 DOI: 10.3390/v14051038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/04/2022] [Accepted: 05/09/2022] [Indexed: 02/01/2023] Open
Abstract
Adeno-associated viruses (AAVs) are a convenient tool for gene therapy delivery. According to the current classification, they are divided into the species AAV A and AAV B within the genus Dependoparvovirus. Historically AAVs were also subdivided on the intraspecies level into 13 serotypes, which differ in tissue tropism and targeted gene delivery capacity. Serotype, however, is not a universal taxonomic category, and their assignment is not always robust. Cross-reactivity has been shown, indicating that classification could not rely on the results of serological tests alone. Moreover, since the isolation of AAV4, all subsequent AAVs were subdivided into serotypes based primarily on genetic differences and phylogenetic reconstructions. An increased interest in the use of AAV as a gene delivery tool justifies the need to improve the existing classification. Here, we suggest genotype-based AAV classification below the species level based on the rep gene. A robust threshold was established as 10% nt differences within the 1248 nt genome fragment, with 4 distinct AAV genotypes identified. This distinct sub-species structure is maintained by ubiquitous recombination within, but not between, rep genes of the suggested genotypes.
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7
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Schindeler A, Lee LR, O'Donohue AK, Ginn SL, Munns CF. Curative Cell and Gene Therapy for Osteogenesis Imperfecta. J Bone Miner Res 2022; 37:826-836. [PMID: 35306687 PMCID: PMC9324990 DOI: 10.1002/jbmr.4549] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/03/2022] [Accepted: 02/27/2022] [Indexed: 11/17/2022]
Abstract
Osteogenesis imperfecta (OI) describes a series of genetic bone fragility disorders that can have a substantive impact on patient quality of life. The multidisciplinary approach to management of children and adults with OI primarily involves the administration of antiresorptive medication, allied health (physiotherapy and occupational therapy), and orthopedic surgery. However, advances in gene editing technology and gene therapy vectors bring with them the promise of gene-targeted interventions to provide an enduring or perhaps permanent cure for OI. This review describes emergent technologies for cell- and gene-targeted therapies, major hurdles to their implementation, and the prospects of their future success with a focus on bone disorders. © 2022 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Aaron Schindeler
- Bioengineering and Molecular Medicine Laboratory, the Children's Hospital at Westmead and the Westmead Institute for Medical Research, Westmead, Australia.,Children's Hospital Westmead Clinical School, University of Sydney, Camperdown, Australia
| | - Lucinda R Lee
- Bioengineering and Molecular Medicine Laboratory, the Children's Hospital at Westmead and the Westmead Institute for Medical Research, Westmead, Australia.,Children's Hospital Westmead Clinical School, University of Sydney, Camperdown, Australia
| | - Alexandra K O'Donohue
- Bioengineering and Molecular Medicine Laboratory, the Children's Hospital at Westmead and the Westmead Institute for Medical Research, Westmead, Australia.,Children's Hospital Westmead Clinical School, University of Sydney, Camperdown, Australia
| | - Samantha L Ginn
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Craig F Munns
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.,Department of Endocrinology and Diabetes, Queensland Children's Hospital, Brisbane, QLD, Australia.,Child Health Research Centre and Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
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8
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Kim JI, Park K, Shin H, Choi SM, Song KJ. Molecular Detection of Parvovirus in Manchurian Chipmunks (Tamias sibiricus asiaticus) Captured in Korea. Intervirology 2021; 65:160-166. [PMID: 34695823 PMCID: PMC9501794 DOI: 10.1159/000520388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/18/2021] [Indexed: 11/19/2022] Open
Abstract
Cross-species transmission of viral diseases alarms our global community for its potential of novel pandemic events. Of various viral pathogens noted recently, parvoviruses have posed public health threats not only to humans but also to wild animals. To investigate the prevalence of parvoviruses in wild Manchurian chipmunks, here we detected genetic fragments of the nonstructural protein of parvovirus by polymerase chain reaction in wild Manchurian chipmunk specimens captured in the central and southern regions of South Korea and compared their sequence homology with references. Of a total of 348 specimens examined, chipmunk parvovirus (ChpPV)-specific gene fragments were detected with a 31.32% rate (109 chipmunks of 348) in their kidney, liver, lung, and spleen samples, and the chipmunks captured in Gangwon Province exhibited the highest positive rate (45.37%), followed by Gyeongsang (35.29%), Gyeonggi (31.03%), Chungcheong (20.00%), and Jeolla (19.70%). When compared with the reference sequences, a partial ChpPV sequence showed 97.70% identity to the previously reported Korean strain at the nucleic acid level. In the phylogenetic analysis, ChpPV exhibited closer relationship to primate parvoviruses, erythroviruses, and bovine parvovirus than to adeno-associated viruses. Despite limited sample size and genetic sequences examined in this study, our results underline the prevalence of ChpPV in Korea and emphasize the need of close surveillance of parvoviruses in wild animals.
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Affiliation(s)
- Jin Il Kim
- Department of Microbiology, The Institute for Viral Diseases and Korea Bank for Pathogenic Viruses, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kwangsook Park
- Department of Microbiology, The Institute for Viral Diseases and Korea Bank for Pathogenic Viruses, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hyunho Shin
- Department of Microbiology, The Institute for Viral Diseases and Korea Bank for Pathogenic Viruses, Korea University College of Medicine, Seoul, Republic of Korea
| | - Soo Min Choi
- Department of Microbiology, The Institute for Viral Diseases and Korea Bank for Pathogenic Viruses, Korea University College of Medicine, Seoul, Republic of Korea
| | - Ki-Joon Song
- Department of Microbiology, The Institute for Viral Diseases and Korea Bank for Pathogenic Viruses, Korea University College of Medicine, Seoul, Republic of Korea
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Sikdar A, Gupta R, Boura E. Reviewing Antiviral Research Against Viruses Causing Human Diseases - A Structure Guided Approach. Curr Mol Pharmacol 2021; 15:306-337. [PMID: 34348638 DOI: 10.2174/1874467214666210804152836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 11/22/2022]
Abstract
The littlest of all the pathogens, viruses have continuously been the foremost strange microorganisms to consider. Viral Infections can cause extreme sicknesses as archived by the HIV/AIDS widespread or the later Ebola or Zika episodes. Apprehensive framework distortions are too regularly watched results of numerous viral contaminations. Besides, numerous infections are oncoviruses, which can trigger different sorts of cancer. Nearly every year a modern infection species rises debilitating the world populace with an annihilating episode. Subsequently, the need of creating antivirals to combat such rising infections. In any case, from the innovation of to begin with antiviral medicate Idoxuridine in 1962 to the revelation of Baloxavir marboxil (Xofluza) that was FDA-approved in 2018, the hone of creating antivirals has changed significantly. In this article, different auxiliary science strategies have been described that can be referral for therapeutics innovation.
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Affiliation(s)
- Arunima Sikdar
- Department of Hematology and Oncology, School of Medicine, The University of Tennessee Health Science Center, 920 Madison Ave, P.O.Box-38103, Memphis, Tennessee. United States
| | - Rupali Gupta
- Department of Neurology, Duke University Medical Center, Durham, North Carolina. United States
| | - Evzen Boura
- Department of Molecular Biology and Biochemistry, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, P.O. Box:16000, Prague. Czech Republic
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10
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Large EE, Silveria MA, Zane GM, Weerakoon O, Chapman MS. Adeno-Associated Virus (AAV) Gene Delivery: Dissecting Molecular Interactions upon Cell Entry. Viruses 2021; 13:1336. [PMID: 34372542 PMCID: PMC8310307 DOI: 10.3390/v13071336] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/08/2021] [Accepted: 07/08/2021] [Indexed: 12/13/2022] Open
Abstract
Human gene therapy has advanced from twentieth-century conception to twenty-first-century reality. The recombinant Adeno-Associated Virus (rAAV) is a major gene therapy vector. Research continues to improve rAAV safety and efficacy using a variety of AAV capsid modification strategies. Significant factors influencing rAAV transduction efficiency include neutralizing antibodies, attachment factor interactions and receptor binding. Advances in understanding the molecular interactions during rAAV cell entry combined with improved capsid modulation strategies will help guide the design and engineering of safer and more efficient rAAV gene therapy vectors.
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Affiliation(s)
| | | | | | | | - Michael S. Chapman
- Department of Biochemistry, University of Missouri, Columbia, MO 65201, USA; (E.E.L.); (M.A.S.); (G.M.Z.); (O.W.)
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11
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Hardmeier I, Aeberhard N, Qi W, Schoenbaechler K, Kraettli H, Hatt JM, Fraefel C, Kubacki J. Metagenomic analysis of fecal and tissue samples from 18 endemic bat species in Switzerland revealed a diverse virus composition including potentially zoonotic viruses. PLoS One 2021; 16:e0252534. [PMID: 34133435 PMCID: PMC8208571 DOI: 10.1371/journal.pone.0252534] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 05/17/2021] [Indexed: 01/02/2023] Open
Abstract
Many recent disease outbreaks in humans had a zoonotic virus etiology. Bats in particular have been recognized as reservoirs to a large variety of viruses with the potential to cross-species transmission. In order to assess the risk of bats in Switzerland for such transmissions, we determined the virome of tissue and fecal samples of 14 native and 4 migrating bat species. In total, sequences belonging to 39 different virus families, 16 of which are known to infect vertebrates, were detected. Contigs of coronaviruses, adenoviruses, hepeviruses, rotaviruses A and H, and parvoviruses with potential zoonotic risk were characterized in more detail. Most interestingly, in a ground stool sample of a Vespertilio murinus colony an almost complete genome of a Middle East respiratory syndrome-related coronavirus (MERS-CoV) was detected by Next generation sequencing and confirmed by PCR. In conclusion, bats in Switzerland naturally harbour many different viruses. Metagenomic analyses of non-invasive samples like ground stool may support effective surveillance and early detection of viral zoonoses.
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Affiliation(s)
| | - Nadja Aeberhard
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | - Weihong Qi
- Functional Genomics Center Zurich, Zurich, Switzerland
| | | | | | - Jean-Michel Hatt
- Clinic for Zoo Animals, Exotic Pets and Wildlife, University of Zurich, Zurich, Switzerland
| | - Cornel Fraefel
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | - Jakub Kubacki
- Institute of Virology, University of Zurich, Zurich, Switzerland
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12
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Park GN, Song S, Cha RM, Choe S, Shin J, Kim SY, Hyun BH, Park BK, An DJ. Genetic analysis of porcine parvoviruses detected in South Korean wild boars. Arch Virol 2021; 166:2249-2254. [PMID: 33999261 DOI: 10.1007/s00705-021-05106-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/30/2021] [Indexed: 11/24/2022]
Abstract
Porcine parvovirus 1 (PPV1) is a major cause of reproductive failure in pigs. To date, six additional porcine parvoviruses (PPV2-PPV7) have been identified. In this study, we detected 11 PPV1 strains, five PPV3 strains, three PPV4 strains, six PPV5 strains, five PPV6 strains, and one PPV7 strain in Korean wild boars. PPV1, -3, and -5, and PPV6 from Korean wild boars harbor conserved motifs within the Ca2+ binding loop and the catalytic center of the PLA1 motif. Intra-species recombination among PPV7 strains was also identified. Genetic characterization revealed that PPV1 from Korean wild boars may be similar to virulent PPV strains.
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Affiliation(s)
- Gyu-Nam Park
- Virus Disease Division, Animal and Plant Quarantine Agency (APQA), Gimchen, Gyeongbuk-do, 39660, Republic of Korea
| | - Sok Song
- Virus Disease Division, Animal and Plant Quarantine Agency (APQA), Gimchen, Gyeongbuk-do, 39660, Republic of Korea
| | - Ra Mi Cha
- Virus Disease Division, Animal and Plant Quarantine Agency (APQA), Gimchen, Gyeongbuk-do, 39660, Republic of Korea
| | - SeEun Choe
- Virus Disease Division, Animal and Plant Quarantine Agency (APQA), Gimchen, Gyeongbuk-do, 39660, Republic of Korea
| | - Jihye Shin
- Virus Disease Division, Animal and Plant Quarantine Agency (APQA), Gimchen, Gyeongbuk-do, 39660, Republic of Korea
| | - Song-Yi Kim
- Virus Disease Division, Animal and Plant Quarantine Agency (APQA), Gimchen, Gyeongbuk-do, 39660, Republic of Korea
| | - Bang-Hun Hyun
- Virus Disease Division, Animal and Plant Quarantine Agency (APQA), Gimchen, Gyeongbuk-do, 39660, Republic of Korea
| | - Bong-Kyun Park
- Virus Disease Division, Animal and Plant Quarantine Agency (APQA), Gimchen, Gyeongbuk-do, 39660, Republic of Korea.,College of Veterinary Medicine, Seoul University, Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Dong-Jun An
- Virus Disease Division, Animal and Plant Quarantine Agency (APQA), Gimchen, Gyeongbuk-do, 39660, Republic of Korea.
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13
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Seetha D, Pillai HR, Nori SRC, Kalpathodi SG, Thulasi VP, Nair RR. Molecular-genetic characterization of human parvovirus B19 prevalent in Kerala State, India. Virol J 2021; 18:96. [PMID: 33952289 PMCID: PMC8097873 DOI: 10.1186/s12985-021-01569-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/30/2021] [Indexed: 01/21/2023] Open
Abstract
Background Human parvovirus B19V is a DNA virus, and a member of the family Parvoviridae, that causes various clinical manifestations, from asymptomatic to persistent infection that is associated with different autoimmune diseases. The parvovirus B19 evolves with a very high mutation rate that is closer to those of existing RNA viruses. Globally circulating B19V is currently classified into three genotypes, but their distribution is not spatially and temporally correlated. Except for a few recent reports on B19V entry into the human host and its genetic diversity, there is a lack of sufficient studies on this virus from distinct geographical locations and no clear understanding of its evolution has been documented. Methods To better understand the evolution of the Human parvo B19V virus from India's southern part, a geographically distinct location with no reports of B19V genomes, we have screened for B19V in 456 suspected cases using VP1/2 surface marker genes, and its characteristics were studied in detail. Amongst 456 clinically suspected B19V samples, 7.2% (33/456) were found positive by nested PCR (nPCR) were subsequently validated by real-time PCR, Sanger sequencing, and metagenome analysis. Results Human parvovirus B19 infection was shown among 33 of 456 patients when tested by nPCR; 30 among these were also positive by qPCR and were subsequently confirmed by sequencing 75% nPCR positive samples and 76% qPCR positive samples were from patients with age. ≥ 50 years respectively (Additional file 1: Table S1). The complete VP1/2 gene assembly from the South Indian strain showed three novel mutations (T122A, V128I, I283V), which might significantly impact the stability and virulence of the B19V virus circulating in this part of the world. These mutations might be crucial for its adaptive evolutionary strategies facilitating the spread and infectivity potential of the virus. In maximum likelihood phylogeny of VP1/2 sequences, the South Indian B19V strain forms a separate clade closer to the existing genotype two strains circulating worldwide. Conclusion Our study contributes to a better understanding of the human parvovirus's genetic and evolutionary characteristics in South India. Also, it highlights the possibility that a positive selection pressure acting on VP1/2 could increase the survival and replication capabilities of the viruses. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-021-01569-1.
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Affiliation(s)
- Dayakar Seetha
- Laboratory Medicine and Molecular Diagnostics Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695585, India
| | - Heera R Pillai
- Laboratory Medicine and Molecular Diagnostics Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695585, India
| | - Sai Ravi Chandra Nori
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Sanu Ghosh Kalpathodi
- Laboratory Medicine and Molecular Diagnostics Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695585, India
| | - Vineetha P Thulasi
- Laboratory Medicine and Molecular Diagnostics Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695585, India
| | - Radhakrishnan R Nair
- Laboratory Medicine and Molecular Diagnostics Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695585, India.
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14
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Abdelrahman D, Al-Sadeq DW, Smatti MK, Taleb SA, AbuOdeh RO, Al-Absi ES, Al-Thani AA, Coyle PV, Al-Dewik N, Qahtani AAA, Yassine HM, Nasrallah GK. Prevalence and Phylogenetic Analysis of Parvovirus (B19V) among Blood Donors with Different Nationalities Residing in Qatar. Viruses 2021; 13:v13040540. [PMID: 33805034 PMCID: PMC8063948 DOI: 10.3390/v13040540] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/12/2021] [Accepted: 03/14/2021] [Indexed: 12/16/2022] Open
Abstract
Human parvovirus (B19V) is the causative agent of erythema infectiosum in children and is linked to a wide range of clinical manifestations. Studies related to B19V prevalence in the Middle East and North Africa (MENA) region and other parts of Asia are very scarce. The objectives of this study were to estimate the seroprevalence (anti-B19V IgM and IgG), the viremia rate (B19V DNA), and the circulating genotypes of B19V among blood donors in Qatar. Methods: Donors’ blood samples (n = 5026) from different nationalities, mainly from the MENA region and South East Asia, were collected from 2014–2016. Samples were tested for the B19V DNA using RT-PCR. Furthermore, 1000 selected samples were tested to determine the seroprevalence of B19V antibodies using enzyme-linked immunosorbent assay (ELISA). Genotyping was performed on 65 DNA positive samples by sequencing of nested PCR fragments (NS1-VP1u region, 927 nt). Results: Only 1.4% (70/5026) of the samples had detectible B19V DNA in their blood. B19V DNA prevalence statistically decreased with age (p = 0.03). Anti-B19V IgG was detected in 60.3% (561/930) of the tested samples, while only 2.1% (20/930) were IgM-positive and 1.2% (11/930) were both IgM- and IgG-positive. B19V genotyping showed a predominance of Genotype 1 (100%). Sequence analysis of the NS1-VP1u region revealed 139 mutation sites, some of which were amino acid substitutions. Conclusion: Our results indicated a relatively high seroprevalence of B19V in Qatar. Most importantly, B19 DNA was detected among Qatari and non-Qatari blood donors. Therefore, blood banks in Qatar might need to consider screening for B19V, especially when transfusion is intended for high-risk populations, including immunocompromised patients.
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Affiliation(s)
| | - Duaa W. Al-Sadeq
- Biomedical Research Center, Member of QU Health, Qatar University, Doha, Qatar; (D.W.A.-S.); (M.K.S.); (E.S.A.-A.); (A.A.A.-T.); (H.M.Y.)
- College of Medicine, Member of QU Health, Qatar University, Doha, Qatar
| | - Maria K. Smatti
- Biomedical Research Center, Member of QU Health, Qatar University, Doha, Qatar; (D.W.A.-S.); (M.K.S.); (E.S.A.-A.); (A.A.A.-T.); (H.M.Y.)
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar;
| | - Sara A. Taleb
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar;
| | - Raed O AbuOdeh
- Medical Laboratory Sciences Department, College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates;
| | - Enas S. Al-Absi
- Biomedical Research Center, Member of QU Health, Qatar University, Doha, Qatar; (D.W.A.-S.); (M.K.S.); (E.S.A.-A.); (A.A.A.-T.); (H.M.Y.)
| | - Asmaa A. Al-Thani
- Biomedical Research Center, Member of QU Health, Qatar University, Doha, Qatar; (D.W.A.-S.); (M.K.S.); (E.S.A.-A.); (A.A.A.-T.); (H.M.Y.)
- Department of Biomedical Science, College of Health Sciences, Member of QU Health, Qatar University, Doha, Qatar
| | - Peter. V. Coyle
- Division of Virology, Department of Pathology and Laboratory Medicine, Hamad Medical Corporation, Doha, Qatar;
| | - Nader Al-Dewik
- Department of Pediatrics, Clinical and Metabolic Genetics, Hamad Medical Corporation, Doha, Qatar;
| | - Ahmed A. Al Qahtani
- Department of Infection and Immunity, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia;
- Department of Microbiology and Immunology, Alfaisal University School of Medicine, Riyadh 11533, Saudi Arabia
| | - Hadi M. Yassine
- Biomedical Research Center, Member of QU Health, Qatar University, Doha, Qatar; (D.W.A.-S.); (M.K.S.); (E.S.A.-A.); (A.A.A.-T.); (H.M.Y.)
- Department of Biomedical Science, College of Health Sciences, Member of QU Health, Qatar University, Doha, Qatar
| | - Gheyath K. Nasrallah
- Biomedical Research Center, Member of QU Health, Qatar University, Doha, Qatar; (D.W.A.-S.); (M.K.S.); (E.S.A.-A.); (A.A.A.-T.); (H.M.Y.)
- Department of Biomedical Science, College of Health Sciences, Member of QU Health, Qatar University, Doha, Qatar
- Correspondence:
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15
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Kim SC, Jeong CG, Nazki S, Lee SI, Baek YC, Jung YJ, Kim WI. Evaluation of a multiplex PCR method for the detection of porcine parvovirus types 1 through 7 using various field samples. PLoS One 2021; 16:e0245699. [PMID: 33508002 PMCID: PMC7842984 DOI: 10.1371/journal.pone.0245699] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/05/2021] [Indexed: 12/11/2022] Open
Abstract
Porcine parvoviruses (PPVs) are small, nonenveloped DNA viruses that are widespread in the global pig population. PPV type 1 (PPV1) is a major causative agent of reproductive failure and has been recognized since the 1960s. In recent decades, novel PPVs have been identified and designated as PPVs 2 through 7 (PPV2~PPV7). Although the epidemiological impacts of these newly recognized parvoviruses on pigs are largely unknown, continuous surveillance of these PPVs is needed. The aim of this study was to develop an improved and efficient detection tool for these PPVs and to assess the developed method with field samples. Using 7 sets of newly designed primers, a multiplex polymerase chain reaction (mPCR) protocol was developed for the simultaneous detection of the seven genotypes of PPV (PPV1~PPV7). The sensitivity of the mPCR assay was analyzed, and the detection limit was determined to be 3×103 viral copies. The assay was highly specific in detecting one or more of the viruses in various combinations in specimens. The mPCR method was evaluated with 80 serum samples, 40 lung or lymph node samples and 40 intestine or fecal samples. When applied to these samples, the mPCR method could detect the 7 viruses simultaneously, providing rapid results regarding infection and coinfection status. In conclusion, the developed mPCR assay can be utilized as an effective and accurate diagnostic tool for rapid differential detection and epidemiological surveillance of various PPVs in numerous types of field samples.
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Affiliation(s)
- Seung-Chai Kim
- College of Veterinary Medicine, Jeonbuk National University, Iksan, Korea
| | - Chang-Gi Jeong
- College of Veterinary Medicine, Jeonbuk National University, Iksan, Korea
| | - Salik Nazki
- College of Veterinary Medicine, Jeonbuk National University, Iksan, Korea
- The Pirbright Institute, Pirbright, United Kingdom
| | - Sim-In Lee
- College of Veterinary Medicine, Jeonbuk National University, Iksan, Korea
- Animal and Plant Quarantine Agency, Gimcheon, Korea
| | - Ye-Chan Baek
- College of Veterinary Medicine, Jeonbuk National University, Iksan, Korea
| | - Yong-Jin Jung
- College of Veterinary Medicine, Jeonbuk National University, Iksan, Korea
| | - Won-Il Kim
- College of Veterinary Medicine, Jeonbuk National University, Iksan, Korea
- * E-mail:
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16
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Zhang Y, Feng B, Xie Z, Deng X, Zhang M, Xie Z, Xie L, Fan Q, Luo S, Zeng T, Huang J, Wang S. Epidemiological Surveillance of Parvoviruses in Commercial Chicken and Turkey Farms in Guangxi, Southern China, During 2014-2019. Front Vet Sci 2020; 7:561371. [PMID: 33134348 PMCID: PMC7579407 DOI: 10.3389/fvets.2020.561371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/01/2020] [Indexed: 11/13/2022] Open
Abstract
A previously unidentified chicken parvovirus (ChPV) and turkey parvovirus (TuPV) strain, associated with runting-stunting syndrome (RSS) and poultry enteritis and mortality syndrome (PEMS) in turkeys, is now prevalent among chickens in China. In this study, a large-scale surveillance of parvoviruses in chickens and turkeys using conserved PCR assays was performed. We assessed the prevalence of ChPV/TuPV in commercial chicken and turkey farms in China between 2014 and 2019. Parvoviruses were prevalent in 51.73% (1,795/3,470) of commercial chicken and turkey farms in Guangxi, China. The highest frequency of ChPV positive samples tested by PCR occurred in chickens that were broiler chickens 64.18% (1,041/1,622) compared with breeder chickens 38.75% (572/1,476) and layer hens 38.89% (112/288), and TuPV was detected in 70/84 (83.33%). Native and exotic chicken species were both prevalent in commercial farms in southern China, and exotic broiler chickens had a higher positive rate with 88.10% (148/168), while native chickens were 50.00% (1,465/2,930). The environmental samples from poultry houses tested positive for ChPV and TuPV were 47.05% (415/874). Samples from open house flocks had higher prevalence rates of ChPV than those of closed house flocks (Table 5), among which those from the open house showed 84.16% (85/101) positivity, those from litter showed 62.86% (44/70) positivity, and those from drinking water showed 50.00% (56/112) positivity, whereas those from the closed house litter were 53.57% (60/112), those from swabs were 50.18% (138/275), and those from drinking water were 15.69% (32/204). Samples collected during spring were more frequently ChPV/ TuPV positive than those collected during other seasons. This study is the first report regarding the epidemiological surveillance of ChPV and TuPV in chicken/turkey flocks in Guangxi, China. Our results suggest that ChPV and TuPV are widely distributed in commercial fowl in Guangxi. These findings highlight the need for further epidemiological and genetic research on ChPV and TuPV in this area.
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Affiliation(s)
- Yanfang Zhang
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Bin Feng
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Zhixun Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Xianwen Deng
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Minxiu Zhang
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Zhiqin Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Liji Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Qing Fan
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Sisi Luo
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Tingting Zeng
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Jiaoling Huang
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Sheng Wang
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
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17
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Ogden PJ, Kelsic ED, Sinai S, Church GM. Comprehensive AAV capsid fitness landscape reveals a viral gene and enables machine-guided design. Science 2020; 366:1139-1143. [PMID: 31780559 DOI: 10.1126/science.aaw2900] [Citation(s) in RCA: 188] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 11/05/2019] [Indexed: 12/11/2022]
Abstract
Adeno-associated virus (AAV) capsids can deliver transformative gene therapies, but our understanding of AAV biology remains incomplete. We generated the complete first-order AAV2 capsid fitness landscape, characterizing all single-codon substitutions, insertions, and deletions across multiple functions relevant for in vivo delivery. We discovered a frameshifted gene in the VP1 region that expresses a membrane-associated accessory protein that limits AAV production through competitive exclusion. Mutant biodistribution revealed the importance of both surface-exposed and buried residues, with a few phenotypic profiles characterizing most variants. Finally, we algorithmically designed and experimentally verified a diverse in vivo targeted capsid library with viability far exceeding random mutagenesis approaches. These results demonstrate the power of systematic mutagenesis for deciphering complex genomes and the potential of empirical machine-guided protein engineering.
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Affiliation(s)
- Pierce J Ogden
- Harvard Medical School, Boston, MA 02115, USA.,Wyss Institute for Biomedically Inspired Engineering, Boston, MA 02115, USA.,Harvard Graduate Program in Biological and Biomedical Sciences, Boston, MA 02115, USA
| | - Eric D Kelsic
- Harvard Medical School, Boston, MA 02115, USA. .,Wyss Institute for Biomedically Inspired Engineering, Boston, MA 02115, USA.,Dyno Therapeutics, Inc., Cambridge, MA 02139, USA
| | - Sam Sinai
- Harvard Medical School, Boston, MA 02115, USA.,Wyss Institute for Biomedically Inspired Engineering, Boston, MA 02115, USA.,Dyno Therapeutics, Inc., Cambridge, MA 02139, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - George M Church
- Harvard Medical School, Boston, MA 02115, USA. .,Wyss Institute for Biomedically Inspired Engineering, Boston, MA 02115, USA.,Harvard Graduate Program in Biological and Biomedical Sciences, Boston, MA 02115, USA.,Dyno Therapeutics, Inc., Cambridge, MA 02139, USA
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18
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Li X, Lin Z, Liu J, Tang Y, Yuan X, Li N, Lin Z, Chen Y, Liu A. Overall prevalence of human parvovirus B19 among blood donors in mainland China: A PRISMA-compliant meta-analysis. Medicine (Baltimore) 2020; 99:e19832. [PMID: 32332630 PMCID: PMC7220778 DOI: 10.1097/md.0000000000019832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Human parvovirus B19 (B19V) infection exhibits a broad range of clinical outcomes. Blood transfusion is a common route of B19V transmission. However, information about the overall prevalence of B19V infection and B19V genotypes among blood donors in mainland China is lacking. METHODS This meta-analysis was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. A literature search for studies reporting the B19V prevalence among blood donors in mainland China from 2000 to 2018 was performed. The prevalence of B19V was estimated through a meta-analysis of the relevant literature. A comprehensive meta-analysis program was used for data processing and statistical analysis. RESULTS Twenty-one eligible articles were included, involving 48,923 participants assessed for B19V-DNA, 12,948 participants assessed for anti-B19V immunoglobulin M (IgM), and 8244 participants assessed for anti-B19V immunoglobulin G (IgG). The analysis revealed the pooled estimates of the prevalence rates of B19V-DNA, anti-B19V IgM, and anti-B19V IgG among blood donors to be 0.7% (95% confidence interval [CI] 0.2-2.4%), 2.7% (95% CI 1.7-4.3%), and 33.6% (95% CI 28.2-39.4%), respectively. Moreover, phylogenetic analyses indicated that 142 of 169 (84.0%) B19V isolates belonged to Genotype 1. CONCLUSIONS The overall prevalence of B19V among blood donors is not high in mainland China, and most isolates belong to Genotype 1.
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Affiliation(s)
- Xin Li
- Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital
- Department of Blood Transfusion Medicine, School of Medical Technology and Engineering
| | - Zheng Lin
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health
| | - Jiayan Liu
- Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital
| | - Yuanyuan Tang
- Department of Rheumatology, Weifang Yidu Central Hospital, Weifang, Shandong Province
| | - Xiaohong Yuan
- Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital
| | - Nainong Li
- Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital
| | - Zhenxing Lin
- Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital
| | - Yuanzhong Chen
- Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital
| | - Ailin Liu
- Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, China
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19
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Kiss I, Kovács E, Zádori Z, Mészáros I, Cságola A, Bajnóczi P, Mortensen P, Palya V. Vaccine Protection Against Experimental Challenge Infection with a PPV-27a Genotype Virus in Pregnant Gilts. VETERINARY MEDICINE-RESEARCH AND REPORTS 2020; 11:17-24. [PMID: 32158645 PMCID: PMC7048948 DOI: 10.2147/vmrr.s236912] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/20/2020] [Indexed: 01/03/2023]
Abstract
Background/Introduction Porcine parvovirus (PPV), the causative agent of severe reproductive failures in pigs, is present worldwide. The witnessed spread of the virulent 27a type PPV strains since its recognition raised concerns about the efficacy of the available commercial vaccines. Methods To address this question, vaccinated pregnant gilts were challenged with a PPV-27a-like virus strain and parameters related to vaccine efficacy were compared. Results The K22 vaccine strain of Parvoruvax® (PVX) was characterized as “Kresse-like” based on the epitope mapping data. Vaccination of the gilts induced a low level of antibody responses. Based on foetal mortality, the number of sows which had challenge virus-affected foetuses, the percent of PPV positive piglets/litters plus their PPV genome and viral load PVX outscored the other vaccinated groups. Conclusion Stronger protection was provided by the “Kresse-like” K22 PPV strain-based vaccine than by the NADL-2 and NADL-like strain-based commercial vaccines against a PPV-27a cluster strain challenge. Vaccine-induced antibody levels as measured pre-challenge were not found to be an accurate indicator of protection.
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Affiliation(s)
| | | | - Zoltán Zádori
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - István Mészáros
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
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20
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Affiliation(s)
- Hildegard Büning
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Germany.
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21
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Lee Q, Padula MP, Pinello N, Williams SH, O'Rourke MB, Fumagalli MJ, Orkin JD, Song R, Shaban B, Brenner O, Pimanda JE, Weninger W, de Souza WM, Melin AD, Wong JJL, Crim MJ, Monette S, Roediger B, Jolly CJ. Murine and related chapparvoviruses are nephro-tropic and produce novel accessory proteins in infected kidneys. PLoS Pathog 2020; 16:e1008262. [PMID: 31971979 PMCID: PMC6999912 DOI: 10.1371/journal.ppat.1008262] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 02/04/2020] [Accepted: 12/08/2019] [Indexed: 12/21/2022] Open
Abstract
Mouse kidney parvovirus (MKPV) is a member of the provisional genus Chapparvovirus that causes renal disease in immune-compromised mice, with a disease course reminiscent of polyomavirus-associated nephropathy in immune-suppressed kidney transplant patients. Here we map four major MKPV transcripts, created by alternative splicing, to a common initiator region, and use mass spectrometry to identify “p10” and “p15” as novel chapparvovirus accessory proteins produced in MKPV-infected kidneys. p15 and the splicing-dependent putative accessory protein NS2 are conserved in all near-complete amniote chapparvovirus genomes currently available (from mammals, birds and a reptile). In contrast, p10 may be encoded only by viruses with >60% amino acid identity to MKPV. We show that MKPV is kidney-tropic and that the bat chapparvovirus DrPV-1 and a non-human primate chapparvovirus, CKPV, are also found in the kidneys of their hosts. We propose, therefore, that many mammal chapparvoviruses are likely to be nephrotropic. Parvoviruses are small, genetically simple single-strand DNA viruses that remain viable outside their hosts for very long periods of time. They cause disease in several domesticated species and in humans. Mouse kidney parvovirus (MKPV) is a causative agent of kidney failure in immune-compromised mice and is the only member of the provisional Chapparvovirus genus for which the complete genome including telomeres is known. Here, we show that MKPV propagates almost exclusively in the kidneys of mice infected naturally, wherein it produces novel accessory proteins whose coding regions are conserved in amniote-associated chapparvovirus sequences. We assemble a closely related complete viral genome present in DNA extracted from the kidney of a wild Cebus imitator monkey, and show that another related chapparvovirus is preferentially found in kidneys of the vampire bat Desmodus rotundus. We conclude that many mammal-hosted chapparvovirus are adapted to the kidney niche and may therefore cause disease following kidney stress in multiple species.
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Affiliation(s)
- Quintin Lee
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Matthew P. Padula
- Proteomics Core Facility, University of Technology Sydney, Sydney, NSW, Australia
| | - Natalia Pinello
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Simon H. Williams
- Center for Infection & Immunity, Mailman School of Public Health, Columbia University, New York, NY, United States of America
| | - Matthew B. O'Rourke
- Kolling Institute of Medical Research, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Marcilio Jorge Fumagalli
- Virology Research Center, School of Medicine of Ribeirão Preto of the University of São Paulo, Ribeirão Preto, Brazil
| | - Joseph D. Orkin
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
- Department of Anthropology and Archaeology, University of Calgary, Alberta, Canada
| | - Renhua Song
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Babak Shaban
- Melbourne Integrative Genomics, University of Melbourne, Melbourne, Victoria, Australia
| | - Ori Brenner
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - John E. Pimanda
- Lowy Cancer Research Centre, University of New South Wales Sydney, Sydney, NSW, Australia
| | - Wolfgang Weninger
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - William Marciel de Souza
- Virology Research Center, School of Medicine of Ribeirão Preto of the University of São Paulo, Ribeirão Preto, Brazil
| | - Amanda D. Melin
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
- Department of Medical Genetics and Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Justin J.-L. Wong
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Marcus J. Crim
- Microbiology and Aquatic Diagnostics, IDEXX BioAnalytics, Discovery Drive, Columbia, MO, United States of America
| | - Sébastien Monette
- Laboratory of Comparative Pathology, Center of Comparative Medicine and Pathology, Memorial Sloan Kettering Cancer Center, The Rockefeller University, Weill Cornell Medicine, New York, NY, United States of America
| | - Ben Roediger
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Autoimmunity, Transplantation, Inflammation (ATI) Disease Area, Novartis Institutes for Biomedical Research, Basel, Switzerland
- * E-mail: (BR); (CJJ)
| | - Christopher J. Jolly
- Lowy Cancer Research Centre, University of New South Wales Sydney, Sydney, NSW, Australia
- * E-mail: (BR); (CJJ)
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Zeghbib S, Herczeg R, Kemenesi G, Zana B, Kurucz K, Urbán P, Madai M, Földes F, Papp H, Somogyi B, Jakab F. Genetic characterization of a novel picornavirus in Algerian bats: co-evolution analysis of bat-related picornaviruses. Sci Rep 2019; 9:15706. [PMID: 31673141 PMCID: PMC6823487 DOI: 10.1038/s41598-019-52209-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/15/2019] [Indexed: 12/13/2022] Open
Abstract
Bats are reservoirs of numerous zoonotic viruses. The Picornaviridae family comprises important pathogens which may infect both humans and animals. In this study, a bat-related picornavirus was detected from Algerian Minioptreus schreibersii bats for the first time in the country. Molecular analyses revealed the new virus originates to the Mischivirus genus. In the operational use of the acquired sequence and all available data regarding bat picornaviruses, we performed a co-evolutionary analysis of mischiviruses and their hosts, to authentically reveal evolutionary patterns within this genus. Based on this analysis, we enlarged the dataset, and examined the co-evolutionary history of all bat-related picornaviruses including their hosts, to effectively compile all possible species jumping events during their evolution. Furthermore, we explored the phylogeny association with geographical location, host-genus and host-species in both data sets.
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Affiliation(s)
- Safia Zeghbib
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Róbert Herczeg
- Bioinformatics Research Group, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Gábor Kemenesi
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Brigitta Zana
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Kornélia Kurucz
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Péter Urbán
- Bioinformatics Research Group, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Mónika Madai
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Fanni Földes
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Henrietta Papp
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Balázs Somogyi
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Ferenc Jakab
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary.
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary.
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23
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The relationship of codon usage to the replication strategy of parvoviruses. Arch Virol 2019; 164:2479-2491. [PMID: 31321584 DOI: 10.1007/s00705-019-04343-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 06/03/2019] [Indexed: 01/31/2023]
Abstract
Codon usage is biased in most species, and the pattern of codon usage bias is specific to each species or group of closely related species. Although viruses use the host translational machinery for synthesis of their proteins, their codon usage patterns do not match those of their host. Viral codon usage is determined by a complex interplay of mutational bias, genome composition constraints, translational adaptation to the host, and host cellular innate defense. The codon usage of parvoviruses was previously shown not to be strongly biased and selective pressure was found to be a dominating factor driving codon usage. The family Parvoviridae includes the genus Dependoparvovirus, some of the members of which require a helper virus to complete their replication cycle, whereas the rest of the family can replicate without the need for helper viruses. Here, we show that difference in the replication strategy of these viruses may be an important factor determining viral codon usage. Hierarchical clustering and principal component analysis revealed that the codon usage pattern of adeno-associated viruses (AAVs) of the genus Dependoparvovirus is distinct from that of members of the other genera of vertebrate parvoviruses, and even from that of independent viruses of the genus Dependoparvovirus. Furthermore, the codon usage of human AAVs was found to be similar to that of some human adenoviruses in hierarchical clustering and principal component analysis. This suggests that the codon usage of AAVs is different from that of other parvoviruses because of their distinctive replication strategy and that their codon usage is probably driven by forces similar to those that shaped the codon usage pattern of their helper viruses.
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24
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Linden A, Gilliaux G, Paternostre J, Benzarti E, Rivas JF, Desmecht D, Garigliany M. A novel parvovirus, Roe deer copiparvovirus, identified in Ixodes ricinus ticks. Virus Genes 2019; 55:425-428. [PMID: 30945175 DOI: 10.1007/s11262-019-01661-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 03/26/2019] [Indexed: 12/18/2022]
Abstract
The family Parvoviridae contains diverse viruses that are capable of infecting a wide range of hosts. In this study, metagenomic sequencing of Ixodes ricinus ticks harvested in 2016 on red deer (Cervus elaphus) and European roe deer (Capreolus capreolus) in Belgium detected a new 6296-bp parvoviral genome. Phylogenetic and sequence analyses showed the new virus belongs to a new species within the Copiparvovirus genus. PCR screening of 4 pools of 10 serum samples from both deer species identified the new copiparvovirus DNA only in roe deer sera. Together, these results are the first evidence of a copiparvovirus in a deer species. Besides its potential pathogenicity to roe deers, the detection of this new virus in ticks raises questions about the possible transmission of parvoviruses by ticks. This report further increases the current knowledge on the evolution and diversity of copiparvoviruses.
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Affiliation(s)
- Annick Linden
- Faculty of Veterinary Medicine, FARAH Research Center, University of Liège, Liège, Belgium
| | - Gautier Gilliaux
- Faculty of Veterinary Medicine, FARAH Research Center, University of Liège, Liège, Belgium
| | - Julien Paternostre
- Faculty of Veterinary Medicine, FARAH Research Center, University of Liège, Liège, Belgium
| | - Emna Benzarti
- Faculty of Veterinary Medicine, FARAH Research Center, University of Liège, Liège, Belgium
| | - Jose Felipe Rivas
- Faculty of Veterinary Medicine, FARAH Research Center, University of Liège, Liège, Belgium
| | - Daniel Desmecht
- Faculty of Veterinary Medicine, FARAH Research Center, University of Liège, Liège, Belgium
| | - Mutien Garigliany
- Faculty of Veterinary Medicine, FARAH Research Center, University of Liège, Liège, Belgium.
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25
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Kapgate SS, Kumanan K, Vijayarani K, Barbuddhe SB. Avian parvovirus: classification, phylogeny, pathogenesis and diagnosis. Avian Pathol 2018; 47:536-545. [PMID: 30246559 DOI: 10.1080/03079457.2018.1517938] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Poultry parvoviruses identified during the early 1980s are found worldwide in intestines from young birds with enteric disease syndromes as well as healthy birds. The chicken parvovirus (ChPV) and turkey parvovirus (TuPV) belong to the Aveparvovirus genus within the subfamily Parvovirinae. Poultry parvoviruses are small, non-enveloped, single-stranded DNA viruses consisting of three open reading frames, the first two encoding the non-structural protein (NS) and nuclear phosphoprotein (NP) and the third encoding the viral capsid proteins 1 (VP1 and VP2). In contrast to other parvoviruses, the VP1-unique region does not contain the phospholipase A2 sequence motif. Recent experimental studies suggested the parvoviruses to be the candidate pathogens in cases of enteric disease syndrome. Current diagnostic methods for poultry parvovirus detection include PCR, real-time PCR, enzyme linked immunosorbent assay using recombinant VP2 or VP1 capsid proteins. Moreover, sequence-independent amplification techniques combined with next-generation sequencing platforms have allowed rapid and simultaneous detection of the parvovirus from affected and healthy birds. There is no commercial vaccine; hence, the development of an effective vaccine to control the spread of infection should be of primary importance. This review presents the current knowledge on poultry parvoviruses with emphasis on taxonomy, phylogenetic relationship, genomic analysis, epidemiology, pathogenesis and diagnostic methods.
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Affiliation(s)
- Sunil S Kapgate
- a Department of Animal Biotechnology , Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University , Chennai , India
| | - K Kumanan
- a Department of Animal Biotechnology , Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University , Chennai , India
| | - K Vijayarani
- a Department of Animal Biotechnology , Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University , Chennai , India
| | - Sukhadeo B Barbuddhe
- b Meat Safety Laboratory , ICAR-National Research Centre on Meat , Chengicherla, Hyderabad , India
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26
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Vadivel K, Mageshbabu R, Sankar S, Jain A, Perumal V, Srikanth P, Ranjan GA, Nair A, Simoes EAF, Nandagopal B, Sridharan G. Detection of parvovirus B19 in selected high-risk patient groups & their phylogenetic & selection analysis. Indian J Med Res 2018; 147:391-399. [PMID: 29998875 PMCID: PMC6057248 DOI: 10.4103/ijmr.ijmr_241_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Background & objectives: Human parvovirus B19V (B19V) is known to be associated with erythema infectiosum commonly in children, aplastic crisis, especially in persons with underlying haemolytic disorders, hydrops fetalis in pregnancies and arthritis. This cross-sectional study was aimed to determine the presence of B19V infection in childhood febrile illnesses, association of B19V with arthropathies and in adult patients with end-stage renal disease (ESRD) on dialysis. The genetic diversity among the sequences was also analysed. Methods: A nested polymerase chain reaction (nPCR) assay was used for B19V DNA targeting VP1/VP2 region and used for testing 618 patients and 100 healthy controls. Phylogenetic analysis on nucleotide and amino acid sequences was carried out to compare our sequences with other Indian strains and global strains. Results: Among 618 samples tested, seven (1.13%) were found positive. The phylogenetic analysis revealed that all the seven sequences belonged to genotype 1 and showed low genetic diversity. The clustering pattern of seven sequences was similar both by nucleotide and by predicted amino acid sequences. The fixed effects likelihood analysis showed no positive or negatively selected sites. Interpretation & conclusions: Seven samples (4 from non-traumatic arthropathies, 2 from patients with ESRD and 1 from febrile illness patient) were found positive by nPCR. When our seven sequences were compared with global strains, the closest neighbour was other Indian strains followed by the Tunisian strains.
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Affiliation(s)
- Kumaran Vadivel
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital & Research Centre, Vellore, India
| | - Ramamurthy Mageshbabu
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital & Research Centre, Vellore, India
| | - Sathish Sankar
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital & Research Centre, Vellore, India
| | - Amita Jain
- Department of Microbiology, King George Medical University, Lucknow, India
| | - Vivekanandan Perumal
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, India
| | - Padma Srikanth
- Department of Microbiology, Sri Ramachandra Medical College & Research Institute, Sri Ramachandra University, Chennai, India
| | | | - Aravindan Nair
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital & Research Centre, Vellore, India
| | - Eric A F Simoes
- School of Medicine & Professor of Pediatrics, University of Colorado, Aurora Colorado, USA
| | - Balaji Nandagopal
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital & Research Centre, Vellore, India
| | - Gopalan Sridharan
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital & Research Centre, Vellore, India
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27
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Mészáros I, Olasz F, Cságola A, Tijssen P, Zádori Z. Biology of Porcine Parvovirus (Ungulate parvovirus 1). Viruses 2017; 9:v9120393. [PMID: 29261104 PMCID: PMC5744167 DOI: 10.3390/v9120393] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 12/17/2017] [Accepted: 12/18/2017] [Indexed: 01/14/2023] Open
Abstract
Porcine parvovirus (PPV) is among the most important infectious agents causing infertility in pigs. Until recently, it was thought that the virus had low genetic variance, and that prevention of its harmful effect on pig fertility could be well-controlled by vaccination. However, at the beginning of the third millennium, field observations raised concerns about the effectiveness of the available vaccines against newly emerging strains. Subsequent investigations radically changed our view on the evolution and immunology of PPV, revealing that the virus is much more diverse than it was earlier anticipated, and that some of the “new” highly virulent isolates cannot be neutralized effectively by antisera raised against “old” PPV vaccine strains. These findings revitalized PPV research that led to significant advancements in the understanding of early and late viral processes during PPV infection. Our review summarizes the recent results of PPV research and aims to give a comprehensive update on the present understanding of PPV biology.
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Affiliation(s)
- István Mészáros
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, 1143 Budapest, Hungary.
| | - Ferenc Olasz
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, 1143 Budapest, Hungary.
| | | | - Peter Tijssen
- INRS-Institut Armand-Frappier, Université du Québec, Québec, QC H7V 1B7, Canada.
| | - Zoltán Zádori
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, 1143 Budapest, Hungary.
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28
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Servant-Delmas A, Morinet F. Update of the human parvovirus B19 biology. Transfus Clin Biol 2016; 23:5-12. [PMID: 26778837 DOI: 10.1016/j.tracli.2015.11.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Indexed: 12/13/2022]
Abstract
Since its discovery, the human parvovirus B19 (B19V) has been associated with many clinical situations in addition to the prototype clinical manifestations, i.e. erythema infectiosum and erythroblastopenia crisis. The clinical significance of the viral B19V DNA persistence in sera after acute infection remains largely unknown. Such data may constitute a new clinical entity and is discussed in this manuscript. In 2002, despite the genetic diversity among B19V viruses has been reported to be very low, the description of markedly distinct sequences showed a new organization into three genotypes. The most recent common ancestor for B19V genotypes was estimated at early 1800s. B19V replication is enhanced by hypoxia and this might to explain the high viral load detected by quantitative PCR in the sera of infected patients. The minimum infectious dose necessary to transmit B19V infection by the transfusion of labile blood products remains unclear. At the opposite, the US Food and Drug Administration proposed a limit of 10(4)IU/mL of viral DNA in plasma pools used for the production of plasma derivatives. Recently, a new human parvovirus (PARV4) has been discovered. The consequences on blood transfusion of this blood-borne agent and its pathogenicity are still unknown.
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Affiliation(s)
- A Servant-Delmas
- Institut national de la transfusion sanguine (INTS), département d'études des agents transmissibles par le sang, Centre national de référence des hépatites virales B et C et du VIH en transfusion, Paris, France
| | - F Morinet
- Pôle biologie-pathologie-physiologie, CHU Saint-Louis, AP-HP, 75010 Paris, France.
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29
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Canuti M, O’Leary KE, Hunter BD, Spearman G, Ojkic D, Whitney HG, Lang AS. Driving forces behind the evolution of the Aleutian mink disease parvovirus in the context of intensive farming. Virus Evol 2016; 2:vew004. [PMID: 27774297 PMCID: PMC4989880 DOI: 10.1093/ve/vew004] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Aleutian mink disease virus (AMDV) causes plasmacytosis, an immune complex-associated syndrome that affects wild and farmed mink. The virus can also infect other small mammals (e.g., ferrets, skunks, ermines, and raccoons), but the disease in these hosts has been studied less. In 2007, a mink plasmacytosis outbreak began on the Island of Newfoundland, and the virus has been endemic in farms since then. In this study, we evaluated the molecular epidemiology of AMDV in farmed and wild animals of Newfoundland since before the beginning of the outbreak and investigated the epidemic in a global context by studying AMDV worldwide, thereby examining its diffusion and phylogeography. Furthermore, AMDV evolution was examined in the context of intensive farming, where host population dynamics strongly influence viral evolution. Partial NS1 sequences and several complete genomes were obtained from Newfoundland viruses and analyzed along with numerous sequences from other locations worldwide that were either obtained as part of this study or from public databases. We observed very high viral diversity within Newfoundland and within single farms, where high rates of co-infection, recombinant viruses and polymorphisms were observed within single infected individuals. Worldwide, we documented a partial geographic distribution of strains, where viruses from different countries co-exist within clades but form country-specific subclades. Finally, we observed the occurrence of recombination and the predominance of negative selection pressure on AMDV proteins. A surprisingly low number of immunoepitopic sites were under diversifying pressure, possibly because AMDV gains no benefit by escaping the immune response as viral entry into target cells is mediated through interactions with antibodies, which therefore contribute to cell infection. In conclusion, the high prevalence of AMDV in farms facilitates the establishment of co-infections that can favor the occurrence of recombination and enhance viral diversity. Viruses are then exchanged between different farms and countries and can be introduced into the wild, with the rapidly evolving viruses producing many parallel lineages.
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Affiliation(s)
- Marta Canuti
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John’s, Newfoundland and Labrador, A1B 3X9, Canada
| | - Kimberly E. O’Leary
- Animal Health Division, Forestry and Agrifoods Agency, P.O. Box 7400, St. John’s, Newfoundland and Labrador, A1E 3Y5, Canada
| | - Bruce D. Hunter
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Grant Spearman
- Department of Agriculture, Animal Health Laboratory, 65 River Rd., Truro, Nova Scotia, B2N 5E3, Canada and
| | - Davor Ojkic
- Animal Health Laboratory, 419 Gordon Street, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Hugh G. Whitney
- Animal Health Division, Forestry and Agrifoods Agency, P.O. Box 7400, St. John’s, Newfoundland and Labrador, A1E 3Y5, Canada
| | - Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John’s, Newfoundland and Labrador, A1B 3X9, Canada
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30
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Cibulski SP, Teixeira TF, Dos Santos HF, de Sales Lima FE, Scheffer CM, Varela APM, de Lima DA, Schmidt C, Silveira F, de Almeida LL, Roehe PM. Ungulate copiparvovirus 1 (bovine parvovirus 2): characterization of a new genotype and associated viremia in different bovine age groups. Virus Genes 2015; 52:134-7. [PMID: 26646894 DOI: 10.1007/s11262-015-1266-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 11/25/2015] [Indexed: 10/22/2022]
Abstract
A novel bovine parvovirus 2 (BPV2) genotype comprising 5394 nt was identified by next generation sequencing from sera of healthy cattle at different age groups farmed in the state of Rio Grande do Sul, Brazil. The genome organization of new BPV2 genotype retains the two ORFs typical of members of the Parvovirinae with 86.4 % of overall nucleotide sequence identities in comparison to other members of the subfamily. Phylogenetic analysis revealed similar clustering with two previously described bovine BPV2 within the genus Copiparvovirus. No significant differences (P ≥ 0.05) were detected in the distribution of BPV2 infection in cattle at different age groups. This is the third complete or near complete genome sequence of BPV2 reported to date and may contribute to a better understanding of the biology of copiparvoviruses and its interactions with the host.
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Affiliation(s)
- Samuel Paulo Cibulski
- Virology, FEPAGRO Animal Health - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Estrada do Conde 6000, Eldorado do Sul, RS, 92990-000, Brazil. .,Virology Laboratory, Department of Microbiology, Immunology and Parasitology, Instituto de Ciências Básicas da Saúde, UFRGS. Av. Sarmento Leite 500, sala 208, Porto Alegre, RS, 90050-170, Brazil.
| | - Thais Fumaco Teixeira
- Virology, FEPAGRO Animal Health - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Estrada do Conde 6000, Eldorado do Sul, RS, 92990-000, Brazil.,Virology Laboratory, Department of Microbiology, Immunology and Parasitology, Instituto de Ciências Básicas da Saúde, UFRGS. Av. Sarmento Leite 500, sala 208, Porto Alegre, RS, 90050-170, Brazil
| | - Helton Fernandes Dos Santos
- Virology, FEPAGRO Animal Health - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Estrada do Conde 6000, Eldorado do Sul, RS, 92990-000, Brazil
| | - Francisco Esmaile de Sales Lima
- Virology Laboratory, Department of Microbiology, Immunology and Parasitology, Instituto de Ciências Básicas da Saúde, UFRGS. Av. Sarmento Leite 500, sala 208, Porto Alegre, RS, 90050-170, Brazil
| | - Camila Mengue Scheffer
- Virology, FEPAGRO Animal Health - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Estrada do Conde 6000, Eldorado do Sul, RS, 92990-000, Brazil
| | - Ana Paula Muterle Varela
- Virology, FEPAGRO Animal Health - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Estrada do Conde 6000, Eldorado do Sul, RS, 92990-000, Brazil
| | - Diane Alves de Lima
- Virology, FEPAGRO Animal Health - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Estrada do Conde 6000, Eldorado do Sul, RS, 92990-000, Brazil
| | - Candice Schmidt
- Virology, FEPAGRO Animal Health - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Estrada do Conde 6000, Eldorado do Sul, RS, 92990-000, Brazil
| | - Fernando Silveira
- Departamento de Desarrollo Biotecnológico, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Laura Lopes de Almeida
- Virology, FEPAGRO Animal Health - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Estrada do Conde 6000, Eldorado do Sul, RS, 92990-000, Brazil
| | - Paulo Michel Roehe
- Virology, FEPAGRO Animal Health - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Estrada do Conde 6000, Eldorado do Sul, RS, 92990-000, Brazil.,Virology Laboratory, Department of Microbiology, Immunology and Parasitology, Instituto de Ciências Básicas da Saúde, UFRGS. Av. Sarmento Leite 500, sala 208, Porto Alegre, RS, 90050-170, Brazil
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Streck AF, Canal CW, Truyen U. Molecular epidemiology and evolution of porcine parvoviruses. INFECTION GENETICS AND EVOLUTION 2015; 36:300-306. [DOI: 10.1016/j.meegid.2015.10.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 10/03/2015] [Accepted: 10/06/2015] [Indexed: 11/16/2022]
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Xu F, Pan Y, Wang M, Wu X, Tian L, Baloch AR, Zeng Q. First detection of ungulate tetraparvovirus 1 (bovine hokovirus 1) in domestic yaks in northwestern China. Arch Virol 2015; 161:177-80. [PMID: 26483281 DOI: 10.1007/s00705-015-2638-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 10/04/2015] [Indexed: 01/20/2023]
Abstract
We describe the discovery and phylogenetic analysis of ungulate tetraparvovirus 1 (also referred to as bovine hokovirus 1, B-PARV4, or partetravirus) in domestic yaks (Bos grunniens) in northwestern China. The yak B-PARV4 genome was detected in yak blood samples by PCR, using B-PARV4 primers corresponding to conserved regions. Twenty-two of 370 samples were positive for a B-PARV4-related genome sequence, indicating an overall prevalence of 5.95 %. The prevalence in Qinghai Province (13/195, 6.67 %) and Gansu Province (9/175, 5.14 %) was similar, but it varied significantly between yaks ≤ 1 year old (15/177, 8.47 %) and yaks > 1 year old (7/193, 3.6 %) (p < 0.05). An alignment of the nearly full-length genome sequences of all 22 strains identified six different genomic sequences. A phylogenetic analysis revealed 99.0-99.7 % sequence identity between these six genomes and all known B-PARV4 genomes, excluding JF504698 (only 88.6 % identity), which represents another genotype. This is the first discovery of B-PARV4-related viruses in domestic yaks.
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Affiliation(s)
- Fang Xu
- The College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, People's Republic of China
| | - Yangyang Pan
- The College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, People's Republic of China
| | - Meng Wang
- The College of Veterinary Medicine, Northwest A&F University, Yangling, People's Republic of China
| | - Xin Wu
- The College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, People's Republic of China
| | - Lili Tian
- China Animal Health and Epidemiology Center, Qingdao, People's Republic of China
| | | | - Qiaoying Zeng
- The College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, People's Republic of China.
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Chen H, Dou Y, Tang Y, Zhang Z, Zheng X, Niu X, Yang J, Yu X, Diao Y. Isolation and Genomic Characterization of a Duck-Origin GPV-Related Parvovirus from Cherry Valley Ducklings in China. PLoS One 2015; 10:e0140284. [PMID: 26465143 PMCID: PMC4605506 DOI: 10.1371/journal.pone.0140284] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 09/23/2015] [Indexed: 11/25/2022] Open
Abstract
A newly emerged duck parvovirus, which causes beak atrophy and dwarfism syndrome (BADS) in Cherry Valley ducks, has appeared in Northern China since March 2015. To explore the genetic diversity among waterfowl parvovirus isolates, the complete genome of an identified isolate designated SDLC01 was sequenced and analyzed in the present study. Genomic sequence analysis showed that SDLC01 shared 90.8%–94.6% of nucleotide identity with goose parvovirus (GPV) isolates and 78.6%–81.6% of nucleotide identity with classical Muscovy duck parvovirus (MDPV) isolates. Phylogenetic analysis of 443 nucleotides (nt) of the fragment A showed that SDLC01 was highly similar to a mule duck isolate (strain D146/02) and close to European GPV isolates but separate from Asian GPV isolates. Analysis of the left inverted terminal repeat regions revealed that SDLC01 had two major segments deleted between positions 160–176 and 306–322 nt compared with field GPV and MDPV isolates. Phylogenetic analysis of Rep and VP1 encoded by two major open reading frames of parvoviruses revealed that SDLC01 was distinct from all GPV and MDPV isolates. The viral pathogenicity and genome characterization of SDLC01 suggest that the novel GPV (N-GPV) is the causative agent of BADS and belongs to a distinct GPV-related subgroup. Furthermore, N-GPV sequences were detected in diseased ducks by polymerase chain reaction and viral proliferation was demonstrated in duck embryos and duck embryo fibroblast cells.
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Affiliation(s)
- Hao Chen
- College of Animal Science and Technology, Shandong Agricultural University, Tai’an, Shandong, 271018, China
| | - Yanguo Dou
- College of Animal Science and Technology, Shandong Agricultural University, Tai’an, Shandong, 271018, China
| | - Yi Tang
- College of Animal Science and Technology, Shandong Agricultural University, Tai’an, Shandong, 271018, China
| | - Zhenjie Zhang
- College of Basic Medicine, Taishan Medical University, Tai’an, Shandong, 271000, China
| | - Xiaoqiang Zheng
- College of Animal Science and Technology, Shandong Agricultural University, Tai’an, Shandong, 271018, China
| | - Xiaoyu Niu
- College of Animal Science and Technology, Shandong Agricultural University, Tai’an, Shandong, 271018, China
| | - Jing Yang
- College of Animal Science and Technology, Shandong Agricultural University, Tai’an, Shandong, 271018, China
| | - Xianglong Yu
- College of Animal Science and Technology, Shandong Agricultural University, Tai’an, Shandong, 271018, China
| | - Youxiang Diao
- College of Animal Science and Technology, Shandong Agricultural University, Tai’an, Shandong, 271018, China
- * E-mail:
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Koo BS, Lee HR, Jeon EO, Han MS, Min KC, Lee SB, Bae YJ, Cho SH, Mo JS, Kwon HM, Sung HW, Kim JN, Mo IP. Genetic characterization of three novel chicken parvovirus strains based on analysis of their coding sequences. Avian Pathol 2015; 44:28-34. [PMID: 25510852 DOI: 10.1080/03079457.2014.991693] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Chicken parvovirus (ChPV) is one of the causative agents of viral enteritis. Recently, the genome of the ABU-P1 strain of ChPV was fully sequenced and determined to have a distinct genomic composition compared with that of vertebrate parvoviruses. However, no comparative sequence analysis of coding regions of ChPVs was possible because of the lack of other sequence information. In this study, we obtained the nucleotide sequences of all genomic coding regions of three ChPVs by polymerase chain reaction using 13 primer sets, and deduced the amino acid sequences from the nucleotide sequences. The non-structural protein 1 (NS1) gene of the three ChPVs showed 95.0 to 95.5% nucleotide sequence identity and 96.5 to 98.1% amino acid sequence identity to those of NS1 from the ABU-P1 strain, respectively, and even higher nucleotide and amino acid similarities to one another. The viral proteins (VP) gene was more divergent between the three ChPV Korean strains and ABU-P1, with 88.1 to 88.3% nucleotide identity and 93.0% amino acid identity. Analysis of the putative tertiary structure of the ChPV VP2 protein showed that variable regions with less than 80% nucleotide similarity between the three Korean strains and ABU-P1 occurred in large loops of the VP2 protein believed to be involved in antigenicity, pathogenicity, and tissue tropism in other parvoviruses. Based on our analysis of full-length coding sequences, we discovered greater variation in ChPV strains than reported previously, especially in partial regions of the VP2 protein.
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Affiliation(s)
- Bon-Sang Koo
- a Avian Disease Laboratory, College of Veterinary Medicine , Chungbuk National University , Cheongju , Republic of Korea
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Principi N, Piralla A, Zampiero A, Bianchini S, Umbrello G, Scala A, Bosis S, Fossali E, Baldanti F, Esposito S. Bocavirus Infection in Otherwise Healthy Children with Respiratory Disease. PLoS One 2015; 10:e0135640. [PMID: 26267139 PMCID: PMC4534143 DOI: 10.1371/journal.pone.0135640] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 07/24/2015] [Indexed: 12/22/2022] Open
Abstract
To evaluate the role of human bocavirus (hBoV) as a causative agent of respiratory disease, the importance of the viral load in respiratory disease type and severity and the pathogenicity of the different hBoV species, we studied all hBoV-positive nasopharyngeal samples collected from children who attended an emergency room for a respiratory tract infection during three winters (2009–2010, 2011–2012, and 2013–2014). Human bocavirus was detected using the respiratory virus panel fast assay and real-time PCR. Of the 1,823 nasopharyngeal samples, 104 (5.7%) were positive for hBoV; a similar prevalence was observed in all three periods studied. Among hBoV-infected children, 53.8% were between 1–2 years old, and hBoV was detected alone in 57/104 (54.8%) cases. All of the detected hBoV strains belonged to genotype 1. The median hBoV load was significantly higher in samples containing strains with both the N546H and T590S mutations compared to other samples (p<0.05). Children with a single hBoV-1 infection more frequently had upper respiratory tract infections (URTIs) than those who were co-infected (37.0% vs 17.8%, respectively, p = 0.04). The duration of hospitalization was longer among children with high viral loads than that observed among children with low viral loads (8.0 ±2.2 days vs 5.0 ±1.5 days, respectively, p = 0.03), and the use of aerosol therapy was more frequent among children with high viral loads than among those with low viral loads (77.1% vs 55.7%, respectively, p = 0.04). This study shows that hBoV is a relatively uncommon but stable infectious agent in children and that hBoV1 seems to be the only strain detected in Italy in respiratory samples. From a clinical point of view, hBoV1 seems to have in the majority of healthy children relatively low clinical relevance. Moreover, the viral load influences only the duration of hospitalization and the use of aerosol therapy without any association with the site of the respiratory disease.
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Affiliation(s)
- Nicola Principi
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Antonio Piralla
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Alberto Zampiero
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Sonia Bianchini
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Giulia Umbrello
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Alessia Scala
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Samantha Bosis
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Emilio Fossali
- Emergency Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Section of Microbiology, Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Susanna Esposito
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- * E-mail:
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Sun J, Huang L, Wei Y, Wang Y, Chen D, Du W, Wu H, Feng L, Liu C. Identification of three PPV1 VP2 protein-specific B cell linear epitopes using monoclonal antibodies against baculovirus-expressed recombinant VP2 protein. Appl Microbiol Biotechnol 2015; 99:9025-36. [PMID: 26153140 DOI: 10.1007/s00253-015-6790-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 06/18/2015] [Accepted: 06/19/2015] [Indexed: 11/25/2022]
Abstract
Porcine parvovirus type 1 (PPV1) is a major causative agent of embryonic and fetal death in swine. The PPV1 VP2 protein is closely associated with viral immunogenicity for eliciting neutralizing antibodies, but its antigenic structures have been largely unknown. We generated three monoclonal antibodies (MAbs) against baculovirus-expressed recombinant PPV1 VP2 protein. A PEPSCAN analysis identified the minimal B cell linear epitopes of PPV1 VP2 based on these MAbs. Three core epitopes, (228)QQITDA(233), (284)RSLGLPPK(291), and (344)FEYSNGGPFLTPI(356), were defined and mapped onto three-dimensional models of the PPV1 virion and VP2 monomer. The epitope (228)QQITDA(233) is exposed on the virion surface, and the other two are located inside the protein. An alignment of the PPV1 VP2 amino acid sequences showed that (284)RSLGLPPK(291) and (344)FEYSNGGPFLTPI(356) are absolutely conserved, whereas (228)QQITDA(233) has a single substitution at residue 233 in some (S → A or T). We developed a VP2 epitope-based indirect enzyme-linked immunosorbent assay (iELISA) to test for anti-PPV1 antibodies. In a comparative analysis with an immunoperoxidase monolayer assay using 135 guinea pig sera, the VP2-epitope-based iELISA had a concordance rate of 85.19 %, sensitivity of 83.33 %, and specificity of 85.47 %. MAb 8H6 was used to monitor VP2 during the PPV1 replication cycle in vitro with an indirect immunofluorescence assay, which indicated that newly encapsulated virions are released from the nucleus at 24 h postinfection and the PPV1 replication cycle takes less than 24 h. This study provides valuable information clarifying the antigenic structure of PPV1 VP2 and lays the foundations for PPV1 serodiagnosis and antigen detection.
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Affiliation(s)
- Jianhui Sun
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), 427 Maduan Street, Nangang District, Harbin, 150001, People's Republic of China.
| | - Liping Huang
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), 427 Maduan Street, Nangang District, Harbin, 150001, People's Republic of China.
| | - Yanwu Wei
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), 427 Maduan Street, Nangang District, Harbin, 150001, People's Republic of China.
| | - Yiping Wang
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), 427 Maduan Street, Nangang District, Harbin, 150001, People's Republic of China.
| | - Dongjie Chen
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), 427 Maduan Street, Nangang District, Harbin, 150001, People's Republic of China.
| | - Wenjuan Du
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), 427 Maduan Street, Nangang District, Harbin, 150001, People's Republic of China.
| | - Hongli Wu
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), 427 Maduan Street, Nangang District, Harbin, 150001, People's Republic of China.
| | - Li Feng
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), 427 Maduan Street, Nangang District, Harbin, 150001, People's Republic of China.
| | - Changming Liu
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), 427 Maduan Street, Nangang District, Harbin, 150001, People's Republic of China.
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Ni J, Qiao C, Han X, Han T, Kang W, Zi Z, Cao Z, Zhai X, Cai X. Identification and genomic characterization of a novel porcine parvovirus (PPV6) in China. Virol J 2014; 11:203. [PMID: 25442288 PMCID: PMC4265361 DOI: 10.1186/s12985-014-0203-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 11/14/2014] [Indexed: 01/01/2023] Open
Abstract
Background Parvoviruses are classified into two subfamilies based on their host range: the Parvovirinae, which infect vertebrates, and the Densovirinae, which mainly infect insects and other arthropods. In recent years, a number of novel parvoviruses belonging to the subfamily Parvovirinae have been identified from various animal species and humans, including human parvovirus 4 (PARV4), porcine hokovirus, ovine partetravirus, porcine parvovirus 4 (PPV4), and porcine parvovirus 5 (PPV5). Methods Using sequence-independent single primer amplification (SISPA), a novel parvovirus within the subfamily Parvovirinae that was distinct from any known parvoviruses was identified and five full-length genome sequences were determined and analyzed. Results A novel porcine parvovirus, provisionally named PPV6, was initially identified from aborted pig fetuses in China. Retrospective studies revealed the prevalence of PPV6 in aborted pig fetuses and piglets(50% and 75%, respectively) was apparently higher than that in finishing pigs and sows (15.6% and 3.8% respectively). Furthermore, the prevalence of PPV6 in finishing pig was similar in affected and unaffected farms (i.e. 16.7% vs. 13.6%-21.7%). This finding indicates that animal age, perhaps due to increased innate immune resistance, strongly influences the level of PPV6 viremia. Complete genome sequencing and multiple alignments have shown that the nearly full-length genome sequences were approximately 6,100 nucleotides in length and shared 20.5%–42.6% DNA sequence identity with other members of the Parvovirinae subfamily. Phylogenetic analysis showed that PPV6 was significantly distinct from other known parvoviruses and was most closely related to PPV4. Conclusion Our findings and review of published parvovirus sequences suggested that a novel porcine parvovirus is currently circulating in China and might be classified into the novel genus Copiparvovirus within the subfamily Parvovirinae. However, the clinical manifestations of PPV6 are still unknown in that the prevalence of PPV6 was similar between healthy pigs and sick pigs in a retrospective epidemiological study. The identification of PPV6 within the subfamily Parvovirinae provides further insight into the viral and genetic diversity of parvoviruses.
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Affiliation(s)
- Jianqiang Ni
- China Animal Disease Control Center Veterinary Diagnostic Center, Tianguidastreet 17, Beijing, 102600, the People's Republic of China.
| | - Caixia Qiao
- Beijing Entry-Exit Inspection and Quarantine Bureau, No.6 Tianshuiyuan Street, Chaoyang District, Beijing, 100026, the People's Republic of China.
| | - Xue Han
- China Animal Disease Control Center Veterinary Diagnostic Center, Tianguidastreet 17, Beijing, 102600, the People's Republic of China.
| | - Tao Han
- China Animal Disease Control Center Veterinary Diagnostic Center, Tianguidastreet 17, Beijing, 102600, the People's Republic of China.
| | - Wenhua Kang
- China Animal Disease Control Center Veterinary Diagnostic Center, Tianguidastreet 17, Beijing, 102600, the People's Republic of China.
| | - Zhanchao Zi
- China Animal Disease Control Center Veterinary Diagnostic Center, Tianguidastreet 17, Beijing, 102600, the People's Republic of China.
| | - Zhen Cao
- China Animal Disease Control Center Veterinary Diagnostic Center, Tianguidastreet 17, Beijing, 102600, the People's Republic of China.
| | - Xinyan Zhai
- China Animal Disease Control Center Veterinary Diagnostic Center, Tianguidastreet 17, Beijing, 102600, the People's Republic of China.
| | - Xuepeng Cai
- China Animal Disease Control Center Veterinary Diagnostic Center, Tianguidastreet 17, Beijing, 102600, the People's Republic of China.
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Wang SF, Su MW, Tseng SP, Li MC, Tsao CH, Huang SW, Chu WC, Liu WT, Chen YMA, Huang JC. Analysis of codon usage preference in hemagglutinin genes of the swine-origin influenza A (H1N1) virus. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2014; 49:477-86. [PMID: 25442859 DOI: 10.1016/j.jmii.2014.08.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 08/14/2014] [Accepted: 08/23/2014] [Indexed: 10/24/2022]
Abstract
BACKGROUND The swine-origin influenza A (H1N1) virus (S-OIV) has come to the forefront since 2009 and was identified as a new reassortant strain. The hemagglutinin (HA) glycoprotein mediates virus binding, contains antigenic regions recognized by neutralizing antibodies, and is associated with viral cross-species infection and adaption. The comparison study of codon usage preferences in influenza viral genomes was less extensive. In this study, we used codon usage pattern analyses to validate the adaption and origins of S-OIV. METHODS Codon usage pattern was used to estimate the host adaption of S-OIVs. Phylogenetic analysis of the HA gene was conducted to understand the phylogeny of H1N1 viruses isolated from different hosts. Amino acid signature pattern on antigenic sites of HA was analyzed to understand the antigenic characteristics. RESULTS Results of phylogenetic analyses of HA gene indicate that S-OIVs group in identical clusters. The synonymous codon usage pattern analyses indicate that the effective number of codons versus GC content at the third codon position in the HA1 gene slightly differ from those in swine H1N1 and gradually adapted to human. Our data indicate that S-OIV evolution occurred according to positive selection within these antigenic regions. A comparison of antigenic site amino acids reveals similar signature patterns between S-OIV and 1918 human influenza strains. CONCLUSION This study proposes a new and effective way to gain a better understanding of the features of the S-OIV genome and evolutionary processes based on the codon usage pattern. It is useful to trace influenza viral origins and cross-species virus transmission.
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Affiliation(s)
- Sheng-Fan Wang
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan; AIDS Prevention and Research Center, National Yang-Ming University, Taipei, Taiwan; Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan; Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ming-Wei Su
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan; Institute of Biomedical Engineering, National Yang-Ming University, Taipei, Taiwan
| | - Sung-Pin Tseng
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ming-Chun Li
- Department of Pediatrics, Taipei City Hospital, Yang-Ming Branch, Taipei, Taiwan
| | - Ching-Han Tsao
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan; Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Szu-Wei Huang
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Woei-Chyn Chu
- Institute of Biomedical Engineering, National Yang-Ming University, Taipei, Taiwan
| | - Wu-Tse Liu
- Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yi-Ming Arthur Chen
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Microbiology, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Jason C Huang
- AIDS Prevention and Research Center, National Yang-Ming University, Taipei, Taiwan; Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei, Taiwan.
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Zinn E, Vandenberghe LH. Adeno-associated virus: fit to serve. Curr Opin Virol 2014; 8:90-7. [PMID: 25128609 PMCID: PMC4195847 DOI: 10.1016/j.coviro.2014.07.008] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 07/21/2014] [Accepted: 07/24/2014] [Indexed: 12/20/2022]
Abstract
Adeno-associated virus (AAV) is a helper-dependent parvovirus which has not been linked with human disease. This aspect, in combination with its broad cell and tissue tropism, and limited viral host response has made it an attractive vector system for gene therapy. The viral protein capsid, the primary interface with the host, is the main determinant for these phenotypes, is highly variable, and is most subject to pressures during replication. Here, we explore the evolutionary path of AAV and other parvoviruses in respect to these phenotypes, as well as directed evolution and engineering strategies that have exploited the lessons learned from natural selection in order to address remaining limitations of AAV as a therapeutic gene transfer platform.
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Affiliation(s)
- Eric Zinn
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, United States
| | - Luk H Vandenberghe
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, United States.
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Joh J, Proctor ML, Ditslear JL, King WW, Sundberg JP, Jenson AB, Ghim SJ. Epidemiological and phylogenetic analysis of institutional mouse parvoviruses. Exp Mol Pathol 2013; 95:32-7. [PMID: 23545399 DOI: 10.1016/j.yexmp.2013.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 03/22/2013] [Indexed: 11/16/2022]
Abstract
Mouse parvoviruses (MPVs) are small, single-stranded, 5 kb DNA viruses that are subclinical and endemic in many laboratory mouse colonies. MPVs cause more distinctive deleterious effects in immune-compromised or genetically-engineered mice than immuno-competent mice. At the University of Louisville (U of L), there was an unexpected increase of MPV sero-positivity for MPV infections in mouse colonies between January 2006 and February 2007, resulting in strategic husbandry changes aimed at controlling MPV spread throughout the animal facility. To investigate these MPVs, VP2 genes of seven MPVs were cloned and sequenced from eight documented incidences by PCR technology. The mutations in these VP2 genes were compared to those found at the Genbank database (NCBI; http://www.ncbi.nlm.nih.gov) and an intra-institutional phylogenetic tree for MPV infections at U of L was constructed. We discovered that the seven MPV isolates were different from those in Genbank and were not identical to each other. These MPVs were designated MPV-UL1 to 7; none of them were minute virus of mice (MVMs). Four isolates could be classified as MPV1, one was classified as MPV2, and two were defined as novel types with less than 96% and 94% homology with existing MPV types. Considering that all seven isolates had mutations in their VP2 genes and no mutations were observed in VP2 genes of MPV during a four-month time period of incubation, we concluded that all seven MPVs isolated at U of L between 2006 and 2007 probably originated from different sources. Serological survey for MPV infections verified that each MPV outbreak was controlled without further contamination within the institution.
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Affiliation(s)
- Joongho Joh
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, United States
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Farid AH. Aleutian mink disease virus in furbearing mammals in Nova Scotia, Canada. Acta Vet Scand 2013; 55:10. [PMID: 23394546 PMCID: PMC3602201 DOI: 10.1186/1751-0147-55-10] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Accepted: 02/03/2013] [Indexed: 11/13/2022] Open
Abstract
Background Aleutian mink disease virus (AMDV) is widespread among ranched and free-ranging American mink in Canada, but there is no information on its prevalence in other wild animal species. This paper describes the prevalence of AMDV of 12 furbearing species in Nova Scotia (NS), Canada. Methods Samples were collected from carcasses of 462 wild animals of 12 furbearing species, trapped in 10 NS counties between November 2009 and February 2011. Viral DNA was tested by PCR using two primer pairs, and anti-viral antibodies were tested by counterimmunoelectrophoresis (CIEP) on spleen homogenates. Results Positive PCR or CIEP samples were detected in 56 of 60 (93.3%) American mink, 43 of 61 (70.5%) short-tailed weasels, 2 of 8 (25.0%) striped skunks, 2 of 11 (18.2%) North American river otters, 9 of 85 (10.6%) raccoons, and 2 of 20 (10.0%) bobcats. Samples from six fishers, 24 coyotes, 25 red foxes, 58 beavers, 45 red-squirrels and 59 muskrats were negative. Antibodies to AMDV were detected by CIEP in 16 of 56 (28.6%) mink and one of the 8 skunks (12.5%). Thirteen of the mink were positive for PCR and CIEP, but three mink and one skunk were CIEP positive and PCR negative. Positive CIEP or PCR animals were present in all nine counties from which mink or weasel samples were collected. Conclusions The presence of AMDV in so many species across the province has important epidemiological ramifications and could pose a serious health problem for the captive mink, as well as for susceptible wildlife. The mechanism of virus transmission between wildlife and captive mink and the effects of AMDV exposure on the viability of the susceptible species deserve further investigation.
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Cadar D, Cságola A, Kiss T, Tuboly T. Capsid protein evolution and comparative phylogeny of novel porcine parvoviruses. Mol Phylogenet Evol 2013; 66:243-53. [DOI: 10.1016/j.ympev.2012.09.030] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 09/24/2012] [Accepted: 09/25/2012] [Indexed: 12/17/2022]
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Leal É, Villanova FE, Lin W, Hu F, Liu Q, Liu Y, Cui S. Interclade recombination in porcine parvovirus strains. J Gen Virol 2012; 93:2692-2704. [DOI: 10.1099/vir.0.045765-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
Abstract
A detailed analysis of the Ns1/Vp1Vp2 genome region of the porcine parvovirus (PPV) strains isolated from vaccinated animals was performed. We found many inconsistencies in the phylogenetic trees of these viral isolates, such as low statistical support and strains with long branches in the phylogenetic trees. Thus, we used distance-based and phylogenetic methods to distinguish de facto recombinants from spurious recombination signals. We found a mosaic virus in which the Ns1 gene was acquired from one PPV clade and the Vp1Vp2 gene was acquired from a distinct phylogenetic clade. We also described the interclade mosaic structure of the Vp1Vp2 gene of a reference strain. If recombination is an adaptive mechanism over the course of PPV evolution, we would likely observe increasing numbers of chimeric strains over time. However, when the PPV sequences isolated from 1964 to 2011 were analysed, only two chimeric strains were detected. Thus, PPV recombination is an independent event, resulting from close contact between animals housed in high-density conditions.
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Affiliation(s)
- Élcio Leal
- Federal University of Pará, Belém, Brazil
| | | | - Wencheng Lin
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of CAAS, Heilongjiang, PR China
| | - Feng Hu
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of CAAS, Heilongjiang, PR China
| | - Qinfang Liu
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of CAAS, Heilongjiang, PR China
| | - Yebing Liu
- China Institute of Veterinary Drug Control, Beijing 100081, PR China
| | - Shangjin Cui
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of CAAS, Heilongjiang, PR China
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Capsid protein expression and adeno-associated virus like particles assembly in Saccharomyces cerevisiae. Microb Cell Fact 2012; 11:124. [PMID: 22966759 PMCID: PMC3539887 DOI: 10.1186/1475-2859-11-124] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 08/06/2012] [Indexed: 11/25/2022] Open
Abstract
Background The budding yeast Saccharomyces cerevisiae supports replication of many different RNA or DNA viruses (e.g. Tombusviruses or Papillomaviruses) and has provided means for up-scalable, cost- and time-effective production of various virus-like particles (e.g. Human Parvovirus B19 or Rotavirus). We have recently demonstrated that S. cerevisiae can form single stranded DNA AAV2 genomes starting from a circular plasmid. In this work, we have investigated the possibility to assemble AAV capsids in yeast. Results To do this, at least two out of three AAV structural proteins, VP1 and VP3, have to be simultaneously expressed in yeast cells and their intracellular stoichiometry has to resemble the one found in the particles derived from mammalian or insect cells. This was achieved by stable co-transformation of yeast cells with two plasmids, one expressing VP3 from its natural p40 promoter and the other one primarily expressing VP1 from a modified AAV2 Cap gene under the control of the inducible yeast promoter Gal1. Among various induction strategies we tested, the best one to yield the appropriate VP1:VP3 ratio was 4.5 hour induction in the medium containing 0.5% glucose and 5% galactose. Following such induction, AAV virus like particles (VLPs) were isolated from yeast by two step ultracentrifugation procedure. The transmission electron microscopy analysis revealed that their morphology is similar to the empty capsids produced in human cells. Conclusions Taken together, the results show for the first time that yeast can be used to assemble AAV capsid and, therefore, as a genetic system to identify novel cellular factors involved in AAV biology.
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Molenaar-de Backer MWA, Lukashov VV, van Binnendijk RS, Boot HJ, Zaaijer HL. Global co-existence of two evolutionary lineages of parvovirus B19 1a, different in genome-wide synonymous positions. PLoS One 2012; 7:e43206. [PMID: 22912828 PMCID: PMC3418230 DOI: 10.1371/journal.pone.0043206] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 07/18/2012] [Indexed: 11/18/2022] Open
Abstract
Parvovirus B19 (B19V) can cause infection in humans. To date, three genotypes of B19V, with subtypes, are known, of which genotype 1a is the most prevalent genotype in the Western world. We sequenced the genome of B19V strains of 65 asymptomatic, recently infected Dutch blood donors, to investigate the spatio-temporal distribution of B19V strains, in the years 2003-2009. The sequences were compared to B19V sequences from Dutch patients with fifth disease, and to global B19V sequences as available from GenBank. All Dutch B19V strains belonged to genotype 1a. Phylogenetic analysis of the strains from Dutch blood donors showed that two groups of genotype 1a co-exist. A clear-cut division into the two groups was also found among the B19V strains from Dutch patients, and among the B19V sequences in GenBank. The two groups of genotype 1a co-exist around the world and do not appear to differ in their ability to cause disease. Strikingly, the two groups of B19V predominantly differ in synonymous mutations, distributed throughout the entire genome of B19V. We propose to call the two groups of B19V genotype 1a respectively subtype 1a1 and 1a2.
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Canuti M, Eis-Huebinger AM, Deijs M, de Vries M, Drexler JF, Oppong SK, Müller MA, Klose SM, Wellinghausen N, Cottontail VM, Kalko EKV, Drosten C, van der Hoek L. Two novel parvoviruses in frugivorous New and Old World bats. PLoS One 2011; 6:e29140. [PMID: 22216187 PMCID: PMC3246463 DOI: 10.1371/journal.pone.0029140] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 11/21/2011] [Indexed: 02/07/2023] Open
Abstract
Bats, a globally distributed group of mammals with high ecological importance, are increasingly recognized as natural reservoir hosts for viral agents of significance to human and animal health. In the present study, we evaluated pools of blood samples obtained from two phylogenetically distant bat families, in particular from flying foxes (Pteropodidae), Eidolon helvum in West Africa, and from two species of New World leaf-nosed fruit bats (Phyllostomidae), Artibeus jamaicensis and Artibeus lituratus in Central America. A sequence-independent virus discovery technique (VIDISCA) was used in combination with high throughput sequencing to detect two novel parvoviruses: a PARV4-like virus named Eh-BtPV-1 in Eidolon helvum from Ghana and the first member of a putative new genus in Artibeus jamaicensis from Panama (Aj-BtPV-1). Those viruses were circulating in the corresponding bat colony at rates of 7–8%. Aj-BtPV-1 was also found in Artibeus lituratus (5.5%). Both viruses were detected in the blood of infected animals at high concentrations: up to 10E8 and to 10E10 copies/ml for Aj-BtPV-1 and Eh-BtPV-1 respectively. Eh-BtPV-1 was additionally detected in all organs collected from bats (brain, lungs, liver, spleen, kidneys and intestine) and spleen and kidneys were identified as the most likely sites where viral replication takes place. Our study shows that bat parvoviruses share common ancestors with known parvoviruses of humans and livestock. We also provide evidence that a variety of Parvovirinae are able to cause active infection in bats and that they are widely distributed in these animals with different geographic origin, ecologies and climatic ranges.
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Affiliation(s)
- Marta Canuti
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity (CINIMA), Academic Medical Centre (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | | | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity (CINIMA), Academic Medical Centre (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Michel de Vries
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity (CINIMA), Academic Medical Centre (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Jan Felix Drexler
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Samuel K. Oppong
- Department of Wildlife and Range Management, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Marcel A. Müller
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Stefan M. Klose
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
- Institute of Experimental Ecology, University of Ulm, Ulm, Germany
| | | | - Veronika M. Cottontail
- Institute of Experimental Ecology, University of Ulm, Ulm, Germany
- Institute of Medical Microbiology and Hygiene, University of Ulm, Ulm, Germany
| | - Elisabeth K. V. Kalko
- Institute of Experimental Ecology, University of Ulm, Ulm, Germany
- Smithsonian Tropical Research Institute, Balboa, Panama
| | - Christian Drosten
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity (CINIMA), Academic Medical Centre (AMC), University of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
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Biđin M, Lojkić I, Biđin Z, Tišljar M, Majnarić D. Identification and Phylogenetic Diversity of Parvovirus Circulating in Commercial Chicken and Turkey Flocks in Croatia. Avian Dis 2011; 55:693-6. [DOI: 10.1637/9746-032811-reg.1] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Gao Y, Luo L. Genome-based phylogeny of dsDNA viruses by a novel alignment-free method. Gene 2011; 492:309-14. [PMID: 22100880 DOI: 10.1016/j.gene.2011.11.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2011] [Revised: 09/19/2011] [Accepted: 11/01/2011] [Indexed: 12/25/2022]
Abstract
Sequence alignment is not directly applicable to whole genome phylogeny since several events such as rearrangements make full length alignments impossible. Here, a novel alignment-free method derived from the standpoint of information theory is proposed and used to construct the whole-genome phylogeny for a population of viruses from 13 viral families comprising 218 dsDNA viruses. The method is based on information correlation (IC) and partial information correlation (PIC). We observe that (i) the IC-PIC tree segregates the population into clades, the membership of each is remarkably consistent with biologist's systematics only with little exceptions; (ii) the IC-PIC tree reveals potential evolutionary relationships among some viral families; and (iii) the IC-PIC tree predicts the taxonomic positions of certain "unclassified" viruses. Our approach provides a new way for recovering the phylogeny of viruses, and has practical applications in developing alignment-free methods for sequence classification.
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Affiliation(s)
- Yang Gao
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
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Streck AF, Bonatto SL, Homeier T, Souza CK, Gonçalves KR, Gava D, Canal CW, Truyen U. High rate of viral evolution in the capsid protein of porcine parvovirus. J Gen Virol 2011; 92:2628-2636. [DOI: 10.1099/vir.0.033662-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In recent years, it has been shown that some parvoviruses exhibit high substitution rates, close to those of RNA viruses. In order to monitor and determine new mutations in porcine parvovirus (PPV), recent PPV field isolates from Austria, Brazil, Germany and Switzerland were sequenced and analysed. These samples, together with sequences retrieved from GenBank, were included in three datasets, consisting of the complete NS1 and VP1 genes and a partial VP1 gene. For each dataset, the nucleotide substitution rate and the molecular clock were determined. Analysis of the PPV field isolates revealed that a recently described amino acid substitution, S436T, appeared to be common in the VP2 protein in the Austrian, Brazilian and German virus populations. Furthermore, new amino acid substitutions were identified, located mainly in the viral capsid loops. By inferring the evolutionary dynamics of the PPV sequences, nucleotide substitution rates of approximately 10−5 substitutions per site per year for the non-structural protein gene and 10−4 substitutions per site per year for the capsid protein gene (for both viral protein datasets) were found. The latter rate is similar to those commonly found in RNA viruses. An association of the phylogenetic tree with the molecular clock analysis revealed that the mutations on which the divergence for both capsid proteins was based occurred in the past 30 years. Based on these findings, it was concluded that PPV variants are continuously evolving and that vaccines, which are based mainly on strains isolated about 30 years ago, should perhaps be updated.
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Affiliation(s)
- André Felipe Streck
- Institute for Animal Hygiene and Veterinary Public Health, Faculty of Veterinary Medicine, University of Leipzig, An den Tierkliniken 1, 04103 Leipzig, Germany
| | - Sandro Luis Bonatto
- Laboratório de Biologia Genômica e Molecular, Pontifícia Universidade Católica, Av. Ipiranga 6681, Prédio12, bloco C, sala 172, 90619-900 Porto Alegre, Brazil
| | - Timo Homeier
- Institute for Animal Hygiene and Veterinary Public Health, Faculty of Veterinary Medicine, University of Leipzig, An den Tierkliniken 1, 04103 Leipzig, Germany
| | - Carine Kunzler Souza
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9090, Prédio 42.602, CEP 91540-000, Porto Alegre, Brazil
| | - Karla Rathje Gonçalves
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9090, Prédio 42.602, CEP 91540-000, Porto Alegre, Brazil
| | - Danielle Gava
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9090, Prédio 42.602, CEP 91540-000, Porto Alegre, Brazil
| | - Cláudio Wageck Canal
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9090, Prédio 42.602, CEP 91540-000, Porto Alegre, Brazil
| | - Uwe Truyen
- Institute for Animal Hygiene and Veterinary Public Health, Faculty of Veterinary Medicine, University of Leipzig, An den Tierkliniken 1, 04103 Leipzig, Germany
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Discovery and genomic characterization of a novel ovine partetravirus and a new genotype of bovine partetravirus. PLoS One 2011; 6:e25619. [PMID: 21980506 PMCID: PMC3181347 DOI: 10.1371/journal.pone.0025619] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 09/08/2011] [Indexed: 01/19/2023] Open
Abstract
Partetravirus is a recently described group of animal parvoviruses which include the human partetravirus, bovine partetravirus and porcine partetravirus (previously known as human parvovirus 4, bovine hokovirus and porcine hokovirus respectively). In this report, we describe the discovery and genomic characterization of partetraviruses in bovine and ovine samples from China. These partetraviruses were detected by PCR in 1.8% of bovine liver samples, 66.7% of ovine liver samples and 71.4% of ovine spleen samples. One of the bovine partetraviruses detected in the present samples is phylogenetically distinct from previously reported bovine partetraviruses and likely represents a novel genotype. The ovine partetravirus is a novel partetravirus and phylogenetically most related to the bovine partetraviruses. The genome organization is conserved amongst these viruses, including the presence of a putative transmembrane protein encoded by an overlapping reading frame in ORF2. Results from the present study provide further support to the classification of partetraviruses as a separate genus in Parvovirinae.
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