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de Swart RL, Belov GA. Advantages and challenges of Newcastle disease virus as a vector for respiratory mucosal vaccines. Curr Opin Virol 2023; 62:101348. [PMID: 37591130 DOI: 10.1016/j.coviro.2023.101348] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 07/18/2023] [Indexed: 08/19/2023]
Abstract
Newcastle disease virus (NDV) is an avian pathogen with an unsegmented negative-strand RNA genome. Properties such as the ease of genome modification, respiratory tract tropism, and self-limiting replication in mammals make NDV an attractive vector for vaccine development. Experimental NDV-based vaccines against multiple human and animal pathogens elicited both systemic and mucosal immune responses and were protective in preclinical animal studies, but their real-life efficacy remains to be demonstrated. Only recently, the first results of clinical trials of NDV-based vaccines against SARS-CoV-2 became available, highlighting the challenges that need to be overcome to fully realize the potential of NDV as a platform for the rapid development of economically affordable and effective mucosal vaccines.
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Affiliation(s)
- Rik L de Swart
- Department of Virology, Wageningen Bioveterinary Research, Lelystad, the Netherlands.
| | - George A Belov
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, MD, USA.
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2
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Kumar BA, Panickan S, Bindu S, Kumar V, Ramakrishnan S, Sonal, Shrivastava S, Dandapat S. Immunogenicity and protective efficacy of an inactivated Newcastle disease virus vaccine encapsulated in poly-(lactic-co-glycolic acid) nanoparticles. Poult Sci 2023; 102:102679. [PMID: 37116285 PMCID: PMC10160591 DOI: 10.1016/j.psj.2023.102679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023] Open
Abstract
An immunization experiment was conducted in specific pathogen-free chickens with the inactivated Newcastle disease virus (NDV) vaccine encapsulated in the poly-(lactic-co-glycolic) acid (PLGA) nanoparticles (NP) to evaluate its immunogenicity and protective efficacy. The NDV vaccine was prepared by inactivating one virulent Indian strain of NDV belonging to Genotype VII by using beta-propiolactone. PLGA nanoparticles encapsulating inactivated NDV were prepared by the solvent evaporation method. Scanning electron microscopy and zeta sizer analysis revealed that the (PLGA+NDV) NP were spherical, with an average size of 300 nm, having a zeta potential of -6 mV. The encapsulation efficiency and loading efficiency were 72% and 2.4%, respectively. On immunization trial in chicken, the (PLGA+NDV) NP induced significantly (P < 0.0001) higher levels of HI and IgY antibodies with the peak HI titer of 28 and higher expression of IL-4 mRNA. The consistency of higher antibody levels suggests slow and pulsatile release of the antigens from the (PLGA+NDV) NP. The nano-NDV vaccine also induced cell mediated immunity with higher expression of IFN-γ indicating strong Th1 mediated immune responses in contrast to the commercial oil adjuvanted inactivated NDV vaccine. Further, the (PLGA+NDV) NP afforded 100% protection against the virulent NDV challenge. Our results suggested that PLGA NP have adjuvant potential on induction of humoral as well as Th1 biased cell mediated immune responses and also enhanced protective efficacy of the inactivated NDV vaccine. This study provides an insight for development of PLGA NP based inactivated NDV vaccine using the same genotype circulating in the field as well as for other avian diseases at exigencies.
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Vilela J, Rohaim MA, Munir M. Avian Orthoavulavirus Type-1 as Vaccine Vector against Respiratory Viral Pathogens in Animal and Human. Vaccines (Basel) 2022; 10:259. [PMID: 35214716 PMCID: PMC8876055 DOI: 10.3390/vaccines10020259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/30/2022] [Accepted: 02/04/2022] [Indexed: 11/17/2022] Open
Abstract
Avian orthoavulaviruses type-1 (AOaV-1) have recently transitioned from animal vaccine vector to a bona fide vaccine delivery vehicle in human. Owing to induction of robust innate and adaptive immune responses in mucus membranes in both birds and mammals, AOaVs offer an attractive vaccine against respiratory pathogens. The unique features of AOaVs include over 50 years of safety profile, stable expression of foreign genes, high infectivity rates in avian and mammalian hosts, broad host spectrum, limited possibility of recombination and lack of pre-existing immunity in humans. Additionally, AOaVs vectors allow the production of economical and high quantities of vaccine antigen in chicken embryonated eggs and several GMP-grade mammalian cell lines. In this review, we describe the biology of AOaVs and define protocols to manipulate AOaVs genomes in effectively designing vaccine vectors. We highlighted the potential and established portfolio of AOaV-based vaccines for multiple respiratory and non-respiratory viruses of veterinary and medical importance. We comment on the limitations of AOaV-based vaccines and propose mitigations strategies. The exploitation of AOaVs vectors is expanding at an exciting pace; thus, we have limited the scope to their use as vaccines against viral pathogens in both animals and humans.
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Affiliation(s)
- Julianne Vilela
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster LA1 4YG, UK; (J.V.); (M.A.R.)
| | - Mohammed A. Rohaim
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster LA1 4YG, UK; (J.V.); (M.A.R.)
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster LA1 4YG, UK; (J.V.); (M.A.R.)
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4
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Alatorre-García TA, Fonseca-Coronado S, González-Candelas F. Homologous recombination as a mechanism of genetic changes in bovine parainfluenza-3 virus. Vet Microbiol 2021; 261:109185. [PMID: 34364015 DOI: 10.1016/j.vetmic.2021.109185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/17/2021] [Indexed: 11/19/2022]
Abstract
Bovine parainfluenza-3 virus (BPIV-3) is one of the main viruses associated with bovine respiratory disease complex (BRDC) worldwide. BPIV-3 infect the bovine respiratory tract causing from subclinical infections to severe pneumonia with significant economic losses in the cattle industry. BPIV-3 is a RNA virus with high genetic variability, nevertheless, the contribution of recombination events to its variability has not been assessed so far. In this study the 25 complete genome sequences (CGS) reported so far and 215 partial sequences of different viral genes of BPIV-3 were analyzed to determine their genotypes and subgenotypes, distribution, and the existence of potential recombination events. Based on the analysis of the HN, M, N, and P genes one hypothetical subgenotype was found (subgenotype A4). Four recombination events between sequences of swine and cattle were detected by RDP4 analysis in conjunction with phylogenetic incongruences in the L gene. In addition, 9 sequences reported from Argentina were found to be miss-classified. These results reveal that homologous recombination events have a relevant role in the evolution of BPIV-3 and highlight the importance of implement advanced molecular characterization to better understand the variability and evolution of BPIV-3 as a component of BRDC.
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Affiliation(s)
- Thalia A Alatorre-García
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, Mexico; Unidad de Investigación Multidisciplinaria, Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Estado de México, Mexico.
| | - Salvador Fonseca-Coronado
- Unidad de Investigación Multidisciplinaria, Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Estado de México, Mexico
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5
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Hu Z, Ni J, Cao Y, Liu X. Newcastle Disease Virus as a Vaccine Vector for 20 Years: A Focus on Maternally Derived Antibody Interference. Vaccines (Basel) 2020; 8:vaccines8020222. [PMID: 32422944 PMCID: PMC7349365 DOI: 10.3390/vaccines8020222] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/28/2020] [Accepted: 05/11/2020] [Indexed: 01/08/2023] Open
Abstract
It has been 20 years since Newcastle disease virus (NDV) was first used as a vector. The past two decades have witnessed remarkable progress in vaccine generation based on the NDV vector and optimization of the vector. Protective antigens of a variety of pathogens have been expressed in the NDV vector to generate novel vaccines for animals and humans, highlighting a great potential of NDV as a vaccine vector. More importantly, the research work also unveils a major problem restraining the NDV vector vaccines in poultry, i.e., the interference from maternally derived antibody (MDA). Although many efforts have been taken to overcome MDA interference, a lack of understanding of the mechanism of vaccination inhibition by MDA in poultry still hinders vaccine improvement. In this review, we outline the history of NDV as a vaccine vector by highlighting some milestones. The recent advances in the development of NDV-vectored vaccines or therapeutics for animals and humans are discussed. Particularly, we focus on the mechanisms and hypotheses of vaccination inhibition by MDA and the efforts to circumvent MDA interference with the NDV vector vaccines. Perspectives to fill the gap of understanding concerning the mechanism of MDA interference in poultry and to improve the NDV vector vaccines are also proposed.
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Affiliation(s)
- Zenglei Hu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jie Ni
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Yongzhong Cao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
| | - Xiufan Liu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
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Tran GTH, Sultan S, Osman N, Hassan MI, VAN Dong H, Dao TD, Omatsu T, Katayama Y, Mizutani T, Takeda Y, Ogawa H, Imai K. Molecular characterization of full genome sequences of Newcastle disease viruses circulating among vaccinated chickens in Egypt during 2011-2013. J Vet Med Sci 2020; 82:809-816. [PMID: 32307343 PMCID: PMC7324829 DOI: 10.1292/jvms.19-0623] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Although intensive vaccination programs have been implemented, Newcastle disease (ND)
outbreaks, accompanied by severe economic losses, are still reported in Egypt. The genetic
characterization of ND virus (NDV) strains isolated from ND-vaccinated chicken flocks
provides essential information for improving ND control strategies. Therefore, here, 38
NDV strains were isolated and identified from outbreaks among vaccinated flocks of broiler
chickens located in the provinces of Qena, Luxor, and Aswan of Upper Egypt during
2011–2013. The investigated broiler chicken flocks (aged 28 to 40 days) had high mortality
rates of up to 80%. All NDV isolates were genetically analyzed using next-generation DNA
sequencing. From these isolates, 10 representative NDV strains were selected for further
genetic analyses. Phylogenetic analysis of full-length coding genes revealed that the
Egyptian NDV isolates belonged to a single sub-genotype, VII.1.1. These isolates were
phylogenetically distant from the vaccine strains, including La Sota or Clone 30 (genotype
II), which have been commonly used to vaccinate chicken flocks. Amino acid substitution
K78R was observed in the neutralizing epitopes of the F proteins; whereas several
mutations were found in the neutralizing epitopes of the hemagglutinin-neuraminidase
proteins, notably, E347K. Overall, our results suggested that the occurrence of
neutralizing epitope variants may be one of potential reasons for ND outbreaks. Further
studies are needed to determine the protective effect of current vaccines against
circulating virulent NDV strains.
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Affiliation(s)
- Giang Thi Huong Tran
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, 2-11 Inada, Obihiro, Hokkaido 080-8555, Japan.,United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan.,Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Trau Quy Town, Gia Lam District, Hanoi, Vietnam
| | - Serageldeen Sultan
- Department of Microbiology, Virology Division, Faculty of Veterinary Medicine, South Valley University, 83523, Qena, Egypt
| | - Nabila Osman
- Department of Poultry Diseases, Faculty of Veterinary Medicine, South Valley University, 83523, Qena, Egypt
| | - Mohamed Ismail Hassan
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, 83911, Luxor, Egypt
| | - Hieu VAN Dong
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, 2-11 Inada, Obihiro, Hokkaido 080-8555, Japan.,United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan.,Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Trau Quy Town, Gia Lam District, Hanoi, Vietnam
| | - Tung Duy Dao
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, 2-11 Inada, Obihiro, Hokkaido 080-8555, Japan.,National Institute of Veterinary Research, 86 Truong Chinh, Dong Da, Hanoi, Vietnam
| | - Tsutomu Omatsu
- Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Yukie Katayama
- Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Tetsuya Mizutani
- Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Yohei Takeda
- Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine, 2-11 Inada, Obihiro, Hokkaido 080-8555, Japan
| | - Haruko Ogawa
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, 2-11 Inada, Obihiro, Hokkaido 080-8555, Japan.,United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Kunitoshi Imai
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, 2-11 Inada, Obihiro, Hokkaido 080-8555, Japan
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7
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A comprehensive global perspective on phylogenomics and evolutionary dynamics of Small ruminant morbillivirus. Sci Rep 2020; 10:17. [PMID: 31913305 PMCID: PMC6949297 DOI: 10.1038/s41598-019-54714-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 11/18/2019] [Indexed: 11/14/2022] Open
Abstract
A string of complete genome sequences of Small ruminant morbillivirus (SRMV) have been reported from different parts of the globe including Asia, Africa and the Middle East. Despite individual genome sequence-based analysis, there is a paucity of comparative genomic and evolutionary analysis to provide overarching and comprehensive evolutionary insights. Therefore, we first enriched the existing database of complete genome sequences of SRMVs with Pakistan-originated strains and then explored overall nucleotide diversity, genomic and residue characteristics, and deduced an evolutionary relationship among strains representing a diverse geographical region worldwide. The average number of pairwise nucleotide differences among the whole genomes was found to be 788.690 with a diversity in nucleotide sequences (0.04889 ± S.D. 0.00468) and haplotype variance (0.00001). The RNA-dependent-RNA polymerase (L) gene revealed phylogenetic relationship among SRMVs in a pattern similar to those of complete genome and the nucleoprotein (N) gene. Therefore, we propose another useful molecular marker that may be employed for future epidemiological investigations. Based on evolutionary analysis, the mean evolution rate for the complete genome, N, P, M, F, H and L genes of SRMV was estimated to be 9.953 × 10–4, 1.1 × 10–3, 1.23 × 10–3, 2.56 × 10–3, 2.01 × 10–3, 1.47 × 10–3 and 9.75 × 10–4 substitutions per site per year, respectively. A recombinant event was observed in a Pakistan-originated strain (KY967608) revealing Indian strains as major (98.1%, KR140086) and minor parents (99.8%, KT860064). Taken together, outcomes of the study augment our knowledge and current understanding towards ongoing phylogenomic and evolutionary dynamics for better comprehensions of SRMVs and effective disease control interventions.
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8
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Dimitrov KM, Abolnik C, Afonso CL, Albina E, Bahl J, Berg M, Briand FX, Brown IH, Choi KS, Chvala I, Diel DG, Durr PA, Ferreira HL, Fusaro A, Gil P, Goujgoulova GV, Grund C, Hicks JT, Joannis TM, Torchetti MK, Kolosov S, Lambrecht B, Lewis NS, Liu H, Liu H, McCullough S, Miller PJ, Monne I, Muller CP, Munir M, Reischak D, Sabra M, Samal SK, Servan de Almeida R, Shittu I, Snoeck CJ, Suarez DL, Van Borm S, Wang Z, Wong FYK. Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus. INFECTION GENETICS AND EVOLUTION 2019; 74:103917. [PMID: 31200111 PMCID: PMC6876278 DOI: 10.1016/j.meegid.2019.103917] [Citation(s) in RCA: 217] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/07/2019] [Accepted: 06/10/2019] [Indexed: 02/07/2023]
Abstract
Several Avian paramyxoviruses 1 (synonymous with Newcastle disease virus or NDV, used hereafter) classification systems have been proposed for strain identification and differentiation. These systems pioneered classification efforts; however, they were based on different approaches and lacked objective criteria for the differentiation of isolates. These differences have created discrepancies among systems, rendering discussions and comparisons across studies difficult. Although a system that used objective classification criteria was proposed by Diel and co-workers in 2012, the ample worldwide circulation and constant evolution of NDV, and utilization of only some of the criteria, led to identical naming and/or incorrect assigning of new sub/genotypes. To address these issues, an international consortium of experts was convened to undertake in-depth analyses of NDV genetic diversity. This consortium generated curated, up-to-date, complete fusion gene class I and class II datasets of all known NDV for public use, performed comprehensive phylogenetic neighbor-Joining, maximum-likelihood, Bayesian and nucleotide distance analyses, and compared these inference methods. An updated NDV classification and nomenclature system that incorporates phylogenetic topology, genetic distances, branch support, and epidemiological independence was developed. This new consensus system maintains two NDV classes and existing genotypes, identifies three new class II genotypes, and reduces the number of sub-genotypes. In order to track the ancestry of viruses, a dichotomous naming system for designating sub-genotypes was introduced. In addition, a pilot dataset and sub-trees rooting guidelines for rapid preliminary genotype identification of new isolates are provided. Guidelines for sequence dataset curation and phylogenetic inference, and a detailed comparison between the updated and previous systems are included. To increase the speed of phylogenetic inference and ensure consistency between laboratories, detailed guidelines for the use of a supercomputer are also provided. The proposed unified classification system will facilitate future studies of NDV evolution and epidemiology, and comparison of results obtained across the world.
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Affiliation(s)
- Kiril M Dimitrov
- Exotic and Emerging Avian Viral Disease Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, ARS, USDA, 934 College Station Road, Athens, GA 30605, USA.
| | - Celia Abolnik
- Department of Production Studies, Faculty of Veterinary Science, University of Pretoria, Old Soutpan Road, Onderstepoort, Pretoria 0110, South Africa
| | - Claudio L Afonso
- Exotic and Emerging Avian Viral Disease Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, ARS, USDA, 934 College Station Road, Athens, GA 30605, USA.
| | - Emmanuel Albina
- CIRAD, UMR ASTRE, F-97170 Petit-Bourg, Guadeloupe, France; ASTRE CIRAD, INRA, Université de Montpellier, Montpellier, France
| | - Justin Bahl
- Center for Ecology of Infectious Disease, Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Mikael Berg
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07 Uppsala, Sweden
| | - Francois-Xavier Briand
- ANSES, Avian and Rabbit Virology Immunology and Parasitology Unit, National reference laboratory for avian Influenza and Newcastle disease, BP 53, 22440 Ploufragan, France
| | - Ian H Brown
- OIE/FAO International Reference Laboratory for Newcastle Disease, Animal and Plant Health Agency (APHA -Weybridge), Addlestone KT15 3NB, UK
| | - Kang-Seuk Choi
- Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs (MAFRA), 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do 39660, Republic of Korea
| | - Ilya Chvala
- Federal Governmental Budgetary Institution, Federal Centre for Animal Health, FGI ARRIAH, Vladimir 600901, Russia
| | - Diego G Diel
- Department of Veterinary and Biomedical Sciences, Animal Disease, Research and Diagnostic Laboratory, South Dakota State University, Brookings, SD, USA
| | - Peter A Durr
- CSIRO Australian Animal Health Laboratory, Portarlington Road, East Geelong, Victoria 3219, Australia
| | - Helena L Ferreira
- Exotic and Emerging Avian Viral Disease Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, ARS, USDA, 934 College Station Road, Athens, GA 30605, USA; University of Sao Paulo, ZMV, FZEA, Pirassununga 13635900, Brazil
| | - Alice Fusaro
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Viale dell'Università 10, Legnaro 35020, Italy
| | - Patricia Gil
- ASTRE CIRAD, INRA, Université de Montpellier, Montpellier, France; CIRAD, UMR ASTRE, F-34398 Montpellier, France
| | - Gabriela V Goujgoulova
- National Diagnostic and Research Veterinary Medical Institute, 15 Pencho Slaveikov blvd., Sofia 1606, Bulgaria
| | - Christian Grund
- Friedrich-Loeffler-Institut, 17493 Greifswald, Insel Riems, Germany
| | - Joseph T Hicks
- Center for Ecology of Infectious Disease, Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Tony M Joannis
- Regional Laboratory for Animal Influenzas and Transboundary Animal Diseases, National Veterinary Research Institute, Vom, Nigeria
| | - Mia Kim Torchetti
- National Veterinary Services Laboratories, Diagnostics and Biologics, Veterinary Services, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, 1920 Dayton Ave, Ames, IA 50010, USA
| | - Sergey Kolosov
- Federal Governmental Budgetary Institution, Federal Centre for Animal Health, FGI ARRIAH, Vladimir 600901, Russia
| | - Bénédicte Lambrecht
- Infectious Diseases in Animals, SCIENSANO, Groeselenberg 99, 1180, Ukkel, Brussels, Belgium
| | - Nicola S Lewis
- OIE/FAO International Reference Laboratory for Newcastle Disease, Animal and Plant Health Agency (APHA -Weybridge), Addlestone KT15 3NB, UK; Royal Veterinary College, University of London, 4 Royal College Street, London NW1 0TU, UK
| | - Haijin Liu
- College of Veterinary Medicine, Northwest A & F University, Yangling, Shaanxi 712100, PR China
| | - Hualei Liu
- China Animal Health and Epidemiology Center (CAHEC), 369 Nanjing Road, Qingdao 266032, China
| | - Sam McCullough
- CSIRO Australian Animal Health Laboratory, Portarlington Road, East Geelong, Victoria 3219, Australia
| | - Patti J Miller
- Department of Population Health, College of Veterinary Medicine, University of Georgia, 953 College Station Road, Athens, GA 30602, USA
| | - Isabella Monne
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Viale dell'Università 10, Legnaro 35020, Italy
| | - Claude P Muller
- Infectious Diseases Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom
| | - Dilmara Reischak
- Ministério da Agricultura, Pecuária e Abastecimento, Laboratório Federal de Defesa Agropecuário, Campinas, SP 13100-105, Brazil
| | - Mahmoud Sabra
- Department of Poultry Diseases, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt
| | - Siba K Samal
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, MD, USA
| | - Renata Servan de Almeida
- ASTRE CIRAD, INRA, Université de Montpellier, Montpellier, France; CIRAD, UMR ASTRE, F-34398 Montpellier, France
| | - Ismaila Shittu
- Regional Laboratory for Animal Influenzas and Transboundary Animal Diseases, National Veterinary Research Institute, Vom, Nigeria
| | - Chantal J Snoeck
- Infectious Diseases Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg
| | - David L Suarez
- Exotic and Emerging Avian Viral Disease Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, ARS, USDA, 934 College Station Road, Athens, GA 30605, USA
| | - Steven Van Borm
- Infectious Diseases in Animals, SCIENSANO, Groeselenberg 99, 1180, Ukkel, Brussels, Belgium
| | - Zhiliang Wang
- China Animal Health and Epidemiology Center (CAHEC), 369 Nanjing Road, Qingdao 266032, China
| | - Frank Y K Wong
- CSIRO Australian Animal Health Laboratory, Portarlington Road, East Geelong, Victoria 3219, Australia
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9
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A comparative genomic and evolutionary analysis of circulating strains of Avian avulavirus 1 in Pakistan. Mol Genet Genomics 2019; 294:1289-1309. [PMID: 31147843 DOI: 10.1007/s00438-019-01580-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 05/20/2019] [Indexed: 01/10/2023]
Abstract
Newcastle disease, caused by Avian avulavirus 1 (AAvV 1), is endemic to many developing countries around the globe including Pakistan. Frequent epidemics are not uncommon even in vaccinated populations and are largely attributed to the genetic divergence of prevailing isolates and their transmission in the environment. With the strengthening of laboratory capabilities in Pakistan, a number of genetically diverse AAvV 1 strains have recently been isolated and individually characterized in comparison with isolates reported elsewhere in the world. However, there lacks sufficient comparative genomic and phylogenomic analyses of field circulating strains that can elucidate the evolutionary dynamics over a period of time. Herein, we enriched the whole genome sequences of AAvV reported so far (n = 35) from Pakistan and performed comparative genomic, phylogenetic and evolutionary analyses. Based on these analyses, we found only isolates belonging to genotypes VI, VII and XIII of AAvV 1 in a wide range of avian and human hosts. Comparative phylogeny revealed the concurrent circulation of avulaviruses representing different sub-genotypes such as VIg, VIm, VIIa, VIIb, VIIe, VIIf, VIIi, XIIIb and XIIId. We found that the isolates of genotype VII were more closely associated with viruses of genotype XIII than genotype VI. An inter-genotype comparative residue analysis revealed a few substitutions in structurally and functionally important motifs. Putative recombination events were reported for only one of the captive-wild bird (pheasant)-origin isolates. The viruses of genotype VII had a high genetic diversity as compared to isolates from genotypes VI and XIII and, therefore, have more potential to evolve over a period of time. Taken together, the current study provides an insight into the genetic diversity and evolutionary dynamics of AAvV 1 strains circulating in Pakistan. Such findings are expected to facilitate better intervention strategies for the prevention and control of ND in disease-endemic countries across the globe particularly Pakistan.
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10
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Absalón AE, Cortés-Espinosa DV, Lucio E, Miller PJ, Afonso CL. Epidemiology, control, and prevention of Newcastle disease in endemic regions: Latin America. Trop Anim Health Prod 2019; 51:1033-1048. [PMID: 30877525 PMCID: PMC6520322 DOI: 10.1007/s11250-019-01843-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/07/2019] [Indexed: 12/17/2022]
Abstract
Newcastle disease (ND) infects wild birds and poultry species worldwide, severely impacting the economics of the poultry industry. ND is especially problematic in Latin America (Mexico, Colombia, Venezuela, and Peru) where it is either endemic or re-emerging. The disease is caused by infections with one of the different strains of virulent avian Newcastle disease virus (NDV), recently renamed Avian avulavirus 1. Here, we describe the molecular epidemiology of Latin American NDVs, current control and prevention methods, including vaccines and vaccination protocols, as well as future strategies for control of ND. Because the productive, cultural, economic, social, and ecological conditions that facilitate poultry endemicity in South America are similar to those in the developing world, most of the problems and control strategies described here are applicable to other continents.
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Affiliation(s)
- A E Absalón
- Vaxbiotek, S.C. San Lorenzo 122-7, 72700, Cuautlancingo, Puebla, Mexico.
- Instituto Politécnico Nacional, CIBA-Tlaxcala, Carr. Est. Santa Ines Tecuexcomac-Tepetitla Km. 1.5, 90700, Tepetitla, Tlaxcala, Mexico.
| | | | - E Lucio
- Boehringer Ingelheim Animal Health, PO Drawer 2497, Gainesville, GA, 30503-2497, USA
| | - P J Miller
- Department of Population Health, College of Veterinary Medicine, The University of Georgia, 953 College Station Road, Athens, GA, 30602, USA
| | - C L Afonso
- Exotic and Emerging Avian Viral Disease Research Unit, Southeast Poultry Research Laboratory, United States National Poultry Research Center, USDA/ARS, Athens, GA, 30605, USA.
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11
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Esmaelizad M, Mayahi V. Analysis of natural recombination and host-related evolutionary dynamics of avian avulavirus 1 isolates based on positive and negative selection from 1948 to 2017. Arch Virol 2019; 164:717-724. [DOI: 10.1007/s00705-018-04130-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/08/2018] [Indexed: 12/26/2022]
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12
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Takada M, Matsuura R, Kokuho T, Tsuboi T, Kameyama KI, Takeuchi K. Reciprocal complementation of bovine parainfluenza virus type 3 lacking either the membrane or fusion gene. J Virol Methods 2017; 249:25-30. [DOI: 10.1016/j.jviromet.2017.08.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 08/16/2017] [Accepted: 08/16/2017] [Indexed: 10/19/2022]
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13
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Fan W, Xu Y, Zhang P, Chen P, Zhu Y, Cheng Z, Zhao X, Liu Y, Liu J. Analysis of molecular evolution of nucleocapsid protein in Newcastle disease virus. Oncotarget 2017; 8:97127-97136. [PMID: 29228598 PMCID: PMC5722550 DOI: 10.18632/oncotarget.21373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/30/2017] [Indexed: 11/25/2022] Open
Abstract
The present study investigated the molecular evolution of nucleocapsid protein (NP) in different Newcastle disease virus (NDV) genotypes. The evolutionary timescale and rate were estimated using the Bayesian Markov chain Monte Carlo (MCMC) method. The p-distance, Bayesian skyline plot (BSP), and positively selected sites were also analyzed. The MCMC tree indicated that NDV diverged about 250 years ago with a rapid evolution rate (1.059 × 10-2 substitutions/site/year) and that different NDV genotypes formed three lineages. The p-distance results reflected the great genetic diversity of NDV. BSP analysis suggested that the effective population size of NDV has been increasing since 2000 and that the basic reproductive number (R0) of NDV ranged from 1.003 to 1.006. The abundance of negatively selected sites in the NP and the mean dN/dS value of 0.07 indicated that the NP of NDV may have undergone purifying selection. However, the predicted positively selected site at position 370 was located in the known effective epitopic region of the NP. In conclusion, although NDV evolved at a high rate and showed great genetic diversity, the structure and function of the NP had been well conserved. However, R0>1 suggests that NDV might have been causing an epidemic since the time of radiation.
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Affiliation(s)
- Wentao Fan
- College of Animal Medicine and Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, PR China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, Tai'an 271018, China
| | - Yuliang Xu
- Research Center for Animal Disease Control Engineering Shandong Province, Shandong Agricultural University, Tai'an 271018, PR China
| | - Pu Zhang
- Central Hospital of Tai'an City, Tai'an 271018, China
| | - Peng Chen
- Research Center for Animal Disease Control Engineering Shandong Province, Shandong Agricultural University, Tai'an 271018, PR China
| | - Yiran Zhu
- College of Animal Medicine and Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, PR China
| | - Ziqiang Cheng
- College of Animal Medicine and Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, PR China
| | - Xiaona Zhao
- College of Animal Medicine and Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, PR China
| | - Yongxia Liu
- College of Animal Medicine and Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, PR China
| | - Jianzhu Liu
- College of Animal Medicine and Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, PR China.,Research Center for Animal Disease Control Engineering Shandong Province, Shandong Agricultural University, Tai'an 271018, PR China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, Tai'an 271018, China
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14
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Samanta I, Bandyopadhyay S. Infectious Diseases. PET BIRD DISEASES AND CARE 2017. [PMCID: PMC7121861 DOI: 10.1007/978-981-10-3674-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The chapter describes bacerial, viral, parasitic and fungal infections commonly detected in pet birds. The chapter includes history, etiology, susceptible hosts, transmission, pathogenesis, clinical symptoms, lesion, diagnosis, zoonosis, Treatment and control strategy of Tuberculosis, Salmonellosis, Chlamydiosis, Campylobacteriosis, Lyme disease, other bacterial infection, Newcastle disease, Avian Influenza infection, West Nile Virus infection, Usutu virus infection, Avian Borna Virus infection, Beak and feather disease, other viral infection, Toxoplasmosis, Giardiasis, Cryptosporidiosis, other parasitic infection, Cryptococcosis, Aspergillosis, Other fungal infections.
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15
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Satharasinghe DA, Murulitharan K, Tan SW, Yeap SK, Munir M, Ideris A, Omar AR. Detection of Inter-Lineage Natural Recombination in Avian Paramyxovirus Serotype 1 Using Simplified Deep Sequencing Platform. Front Microbiol 2016; 7:1907. [PMID: 27965642 PMCID: PMC5127838 DOI: 10.3389/fmicb.2016.01907] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 11/15/2016] [Indexed: 12/18/2022] Open
Abstract
Newcastle disease virus (NDV) is a prototype member of avian paramyxovirus serotype 1 (APMV-1), which causes severe and contagious disease in the commercial poultry and wild birds. Despite extensive vaccination programs and other control measures, the disease remains endemic around the globe especially in Asia, Africa, and the Middle East. Being a single serotype, genotype II based vaccines remained most acceptable means of immunization. However, the evidence is emerging on failures of vaccines mainly due to evolving nature of the virus and higher genetic gaps between vaccine and field strains of APMV-1. Most of the epidemiological and genetic characterizations of APMVs are based on conventional methods, which are prone to mask the diverse population of viruses in complex samples. In this study, we report the application of a simple, robust, and less resource-demanding methodology for the whole genome sequencing of NDV, using next-generation sequencing (NGS) on the Illumina MiSeq platform. Using this platform, we sequenced full genomes of five virulent Malaysian NDV strains collected during 2004–2013. All isolates clustered within highly prevalent lineage 5 (specifically in lineage 5a); however, a significantly greater genetic divergence was observed in isolates collected from 2004 to 2011. Interestingly, genetic characterization of one isolate collected in 2013 (IBS025/13) shown natural recombination between lineage 2 and lineage 5. In the event of recombination, the isolate (IBS025/13) carried nucleocapsid protein consist of 55–1801 nucleotides (nts) and near-complete phosphoprotein (1804–3254 nts) genes of lineage 2 whereas surface glycoproteins (fusion, hemagglutinin-neuraminidase) and large polymerase of lineage 5. Additionally, the recombinant virus has a genome size of 15,186 nts which is characteristics for the old genotypes I–IV isolated from 1930 to 1960. Taken together, we report the occurrence of a natural recombination in circulating strains of NDV in commercial poultry using NGS methodology. These findings will not only highlight the potential of RNA viruses to evolve but also to consider the application of NGS in revealing the genetic diversity of these viruses in clinical materials. Factors that drive these evolutionary events and subsequent impact of these divergences on clinical outcome of the disease warrant future investigations.
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Affiliation(s)
- Dilan A Satharasinghe
- Laboratory of Vaccine and Immunotherapeutic, Institute of Bioscience, Universiti Putra MalaysiaSerdang, Malaysia; Faculty of Veterinary Medicine and Animal Science, University of PeradeniyaPeradeniya, Sri Lanka
| | - Kavitha Murulitharan
- Laboratory of Vaccine and Immunotherapeutic, Institute of Bioscience, Universiti Putra Malaysia Serdang, Malaysia
| | - Sheau W Tan
- Laboratory of Vaccine and Immunotherapeutic, Institute of Bioscience, Universiti Putra Malaysia Serdang, Malaysia
| | - Swee K Yeap
- Laboratory of Vaccine and Immunotherapeutic, Institute of Bioscience, Universiti Putra Malaysia Serdang, Malaysia
| | - Muhammad Munir
- Infection and Innate Immunity Research Group, Avian Viral Diseases, The Pirbright Institute Surrey, UK
| | - Aini Ideris
- Laboratory of Vaccine and Immunotherapeutic, Institute of Bioscience, Universiti Putra MalaysiaSerdang, Malaysia; Faculty of Veterinary Medicine, Universiti Putra MalaysiaSerdang, Malaysia
| | - Abdul R Omar
- Laboratory of Vaccine and Immunotherapeutic, Institute of Bioscience, Universiti Putra MalaysiaSerdang, Malaysia; Faculty of Veterinary Medicine, Universiti Putra MalaysiaSerdang, Malaysia
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16
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Unique safety issues associated with virus-vectored vaccines: Potential for and theoretical consequences of recombination with wild type virus strains. Vaccine 2016; 34:6610-6616. [PMID: 27346303 PMCID: PMC5204448 DOI: 10.1016/j.vaccine.2016.04.060] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 04/20/2016] [Indexed: 12/26/2022]
Abstract
In 2003 and 2013, the World Health Organization convened informal consultations on characterization and quality aspects of vaccines based on live virus vectors. In the resulting reports, one of several issues raised for future study was the potential for recombination of virus-vectored vaccines with wild type pathogenic virus strains. This paper presents an assessment of this issue formulated by the Brighton Collaboration. To provide an appropriate context for understanding the potential for recombination of virus-vectored vaccines, we review briefly the current status of virus-vectored vaccines, mechanisms of recombination between viruses, experience with recombination involving live attenuated vaccines in the field, and concerns raised previously in the literature regarding recombination of virus-vectored vaccines with wild type virus strains. We then present a discussion of the major variables that could influence recombination between a virus-vectored vaccine and circulating wild type virus and the consequences of such recombination, including intrinsic recombination properties of the parent virus used as a vector; sequence relatedness of vector and wild virus; virus host range, pathogenesis and transmission; replication competency of vector in target host; mechanism of vector attenuation; additional factors potentially affecting virulence; and circulation of multiple recombinant vectors in the same target population. Finally, we present some guiding principles for vector design and testing intended to anticipate and mitigate the potential for and consequences of recombination of virus-vectored vaccines with wild type pathogenic virus strains.
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17
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Rouxel RN, Mérour E, Biacchesi S, Brémont M. Efficient Co-Replication of Defective Novirhabdovirus. Viruses 2016; 8:69. [PMID: 26959049 PMCID: PMC4810259 DOI: 10.3390/v8030069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/25/2016] [Accepted: 03/02/2016] [Indexed: 11/16/2022] Open
Abstract
We have generated defective Viral Hemorrhagic Septicemia Viruses (VHSV) which express either the green fluorescent protein (GFP) or a far-red fluorescent protein (mKate) by replacing the genes encoding the nucleoprotein N or the polymerase-associated P protein. To recover viable defective viruses, rVHSV-ΔN-Red and rVHSV-ΔP-Green, fish cells were co-transfected with both deleted cDNA VHSV genomes, together with plasmids expressing N, P and L of the RNA-dependent RNA polymerase. After one passage of the transfected cell supernatant, red and green cell foci were observed. Viral titer reached 10⁷ PFU/mL after three passages. Infected cells were always red and green with the very rare event of single red or green cell foci appearing. To clarify our understanding of how such defective viruses could be so efficiently propagated, we investigated whether (i) a recombination event between both defective genomes had occurred, (ii) whether both genomes were co-encapsidated in a single viral particle, and (iii) whether both defective viruses were always replicated together through a complementation phenomenon or even as conglomerate. To address these hypotheses, genome and viral particles have been fully characterized and, thus, allowing us to conclude that rVHSV-ΔN-Red and rVHSV-ΔP-Green are independent viral particles which could propagate only by simultaneously infecting the same cells.
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Affiliation(s)
- Ronan N Rouxel
- VIM, INRA, Université Paris-Saclay, Jouy-en-Josas 78350, France.
| | - Emilie Mérour
- VIM, INRA, Université Paris-Saclay, Jouy-en-Josas 78350, France.
| | | | - Michel Brémont
- VIM, INRA, Université Paris-Saclay, Jouy-en-Josas 78350, France.
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18
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High Genetic Diversity of Newcastle Disease Virus in Wild and Domestic Birds in Northeastern China from 2013 to 2015 Reveals Potential Epidemic Trends. Appl Environ Microbiol 2015; 82:1530-1536. [PMID: 26712543 DOI: 10.1128/aem.03402-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 12/16/2015] [Indexed: 11/20/2022] Open
Abstract
Newcastle disease (ND), caused by the virulent Newcastle disease virus (NDV), is one of the most important viral diseases of birds globally, but little is currently known regarding enzootic trends of NDV in northeastern China, especially for class I viruses. Thus, we performed a surveillance study for NDV in northeastern China from 2013 to 2015. A total 755 samples from wild and domestic birds in wetlands and live bird markets (LBMs) were collected, and 10 isolates of NDV were identified. Genetic and phylogenetic analyses showed that five isolates from LBMs belong to class I subgenotype 1b, two (one from wild birds and one from LBMs) belong to the vaccine-like class II genotype II, and three (all from wild birds) belong to class II subgenotype Ib. Interestingly, the five class I isolates had epidemiological connections with viruses from southern, eastern, and southeastern China. Our findings, together with recent prevalence trends of class I and virulent class II NDV in China, suggest possible virus transmission between wild and domestic birds and the potential for an NDV epidemic in the future.
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19
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Baron J, Baron MD. Development of a helper cell-dependent form of peste des petits ruminants virus: a system for making biosafe antigen. Vet Res 2015; 46:101. [PMID: 26396073 PMCID: PMC4579661 DOI: 10.1186/s13567-015-0231-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 07/29/2015] [Indexed: 11/10/2022] Open
Abstract
Peste des petits ruminants (PPR) is a viral disease of sheep and goats that is spreading through many countries in the developing world. Work on the virus is often restricted to studies of attenuated vaccine strains or to work in laboratories that have high containment facilities. We have created a helper cell dependent form of PPR virus by removing the entire RNA polymerase gene and complementing it with polymerase made constitutively in a cell line. The resultant L-deleted virus grows efficiently in the L-expressing cell line but not in other cells. Virus made with this system is indistinguishable from normal virus when used in diagnostic assays, and can be grown in normal facilities without the need for high level biocontainment. The L-deleted virus will thus make a positive contribution to the control and study of this important disease.
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Affiliation(s)
- Jana Baron
- The Pirbright Institute, Ash Road, Pirbright, Surrey, GU24 0NF, UK.
| | - Michael D Baron
- The Pirbright Institute, Ash Road, Pirbright, Surrey, GU24 0NF, UK.
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20
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Genomic Characterizations of Six Pigeon Paramyxovirus Type 1 Viruses Isolated from Live Bird Markets in China during 2011 to 2013. PLoS One 2015; 10:e0124261. [PMID: 25928057 PMCID: PMC4415766 DOI: 10.1371/journal.pone.0124261] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 03/12/2015] [Indexed: 11/19/2022] Open
Abstract
The genomes of six pigeon paramyxovirus type 1 (PPMV-1) isolated from symptomless pigeons in live poultry markets during the national active surveillance from 2011 to 2013 were sequenced and analyzed in this study. The complete genome lengths of all isolates were 15,192 nucleotides with the gene order of 3’-NP-P-M-F-HN-L-5’. All isolates had the same motif of 112RRQKRF117 at the cleavage site of the fusion protein, which was typical of velogenic Newcastle disease virus (NDV). Several mutations were identified in the functional domains of F and HN proteins, including fusion peptide, heptad repeat region, transmembrane domains and neutralizing epitopes. Phylogenetic analysis based on sequences of complete genomes and six genes revealed that all isolates belonged to genotype VI in class II, but at least 2 sub-genotypes were identified. Most isolates were placed into sub-genotype VIb with the exception of pi/GX/1015/13, which was classified in sub-genotype VIa. The obvious antigenic difference between PPMV-1 isolates and La Sota strain was found based on the R-value calculated by cross hemagglutination inhibition (HI) assay. These results provided the evidence that PPMV-1 could be detected from healthy pigeons, and our study may be useful in designing vaccines used in pigeon, and developing molecular diagnostic tools to monitor and prevent future PPMV-1 outbreaks.
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21
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Antiviral effect of sulfated Chuanmingshen violaceum polysaccharide in chickens infected with virulent Newcastle disease virus. Virology 2015; 476:316-322. [PMID: 25577148 DOI: 10.1016/j.virol.2014.12.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 12/08/2014] [Accepted: 12/19/2014] [Indexed: 11/20/2022]
Abstract
Newcastle disease virus (NDV) belonging to the Paramyxovirinae subfamily is one of the most devastating pathogens in poultry. Although vaccines are widely applied to control the infection, outbreaks of Newcastle disease (ND) repeatedly happen. Currently, there are no alternative control measures available for ND. In the present study, we found that sulfated Chuanmingshen violaceum polysaccharide (sCVPS) were potent inhibitors of NDV in specific pathogen free chickens infected with a virulent strain. With sCVPS treatment, the survival rate increased by almost 20% and virus titers in test organs, including brain, lung, spleen and thymus, were significantly decreased. The sCVPS also exhibited the ability to prevent viral transmission by reducing the amount of virus shed in saliva and feces. Higher concentrations of interferon α and γ in serum were detected in chickens treated with sCVPS, indicating that one of the antiviral mechanisms may be attributed to the property of immunoenhancement. Histopathological examination showed that sCVPS could alleviate the tissue lesions caused by NDV infection. These results suggest that sCVPS are expected to be a new alternative control measure for NDV infection and further studies could be carried out to evaluate the antiviral activity of sCVPS against other paramyxoviruses.
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22
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Park ES, Suzuki M, Kimura M, Maruyama K, Mizutani H, Saito R, Kubota N, Furuya T, Mizutani T, Imaoka K, Morikawa S. Identification of a natural recombination in the F and H genes of feline morbillivirus. Virology 2014; 468-470:524-531. [PMID: 25262470 DOI: 10.1016/j.virol.2014.09.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 07/31/2014] [Accepted: 09/04/2014] [Indexed: 01/11/2023]
Abstract
Feline morbillivirus (FmoPV) has recently been identified in Hong Kong and Japan. FmoPV is considered to belong to the genus Morbillivirus, in the family Paramyxoviridae. In this study, the complete nucleotide sequences of three strains of FmoPV detected in cats in Japan were determined. Among the six genes in FmoPV; N, P/V/C, M, F, H and L, the P gene showed the highest polymorphism in the nucleotide and putative amino acid sequences among the FmoPV strains. There was no geographical association in terms of the FmoPV phylogeny; however, from extensive phylogenetic and recombination analyses, we found that one Japanese FmoPV strain, MiJP003, was a probable recombinant between two virus strains in the independent lineages found in Japan and Hong Kong, respectively. The recombination was considered to have occurred within the F and H genes. Such recombination is thought to be involved in the evolution of FmoPV.
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Affiliation(s)
- Eun-Sil Park
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Michio Suzuki
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Masanobu Kimura
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Keiji Maruyama
- Tokyo Metropolitan Animal Care and Consultation Center Jounanjima Branch Office, Tokyo 143-0002, Japan
| | - Hiroshi Mizutani
- Tokyo Metropolitan Animal Care and Consultation Center Jounanjima Branch Office, Tokyo 143-0002, Japan
| | - Ryuichi Saito
- Tokyo Metropolitan Animal Care and Consultation Center Jounanjima Branch Office, Tokyo 143-0002, Japan
| | - Nami Kubota
- Tokyo Metropolitan Animal Care and Consultation Center Jounanjima Branch Office, Tokyo 143-0002, Japan
| | - Tetsuya Furuya
- Research and education center for prevention of global infectious diseases of animals, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Tetsuya Mizutani
- Research and education center for prevention of global infectious diseases of animals, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Koichi Imaoka
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Shigeru Morikawa
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo 162-8640, Japan.
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23
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Umali DV, Ito H, Shirota K, Katoh H, Ito T. Characterization of complete genome sequence of genotype VI and VII velogenic Newcastle disease virus from Japan. Virus Genes 2014; 49:89-99. [PMID: 24788358 DOI: 10.1007/s11262-014-1075-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Accepted: 04/10/2014] [Indexed: 10/25/2022]
Abstract
The complete genome sequences of three strains of Newcastle disease virus (NDV) isolated from vaccinated commercial layer flocks in Japan in the span of three decades were characterized. All strains had genome lengths of 15,192 nucleotides consisting of six genes in the order of 3'-NP-P/V/W-M-F-HN-L-5'. The general genomic characteristics of the Japanese field strains were consistent with previously characterized class II NDV, except for those belonging to early genotypes (genotype I-IV), which lack the six nucleotide insertion at nucleotide positions 1,648-1,653 of the nucleoprotein (NP) gene. Phylogenetic analysis showed that the Japanese strains could be classified into genotypes VIc and VIIe using the complete genome sequence and the complete coding sequence of the fusion (F) gene according to the unified NDV classification system. Characterization of functional domains and neutralizing epitopes of the F and hemagglutinin-neuraminidase (HN) proteins of Japanese field strains revealed a total of 31 amino acid substitutions, as compared to vaccine strains Ishii and B1, which were widely used in Japan. Although virus neutralization (VN) test showed that poor flock immunity due to vaccination failure or partial and non-uniform immunization maybe the major factors involved in the mechanism of breakthrough infection of the Japanese field strains, approximately two to threefold decrease in the VN titers of the field NDV strains possessing a point mutation (E347K or E347G) at the linear epitope of the HN protein was observed, as compared to vaccine strain B1 and field strain 2440/69, which lack the point mutation. This study may be a useful reference in characterizing future ND outbreaks in vaccinated chickens and as a genetic map for future investigations regarding vaccine designs, reverse genetics systems, and development of molecular diagnostic tools to prevent future ND outbreaks in vaccinated poultry flocks.
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Affiliation(s)
- Dennis V Umali
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of the Philippines Los Baños, Laguna, 4031, Philippines
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24
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He CQ, Meng SL, Yan HY, Ding NZ, He HB, Yan JX, Xu GL. Isolation and identification of a novel rabies virus lineage in China with natural recombinant nucleoprotein gene. PLoS One 2012; 7:e49992. [PMID: 23226506 PMCID: PMC3514186 DOI: 10.1371/journal.pone.0049992] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Accepted: 10/19/2012] [Indexed: 12/25/2022] Open
Abstract
Rabies virus (RABV) causes severe neurological disease and death. As an important mechanism for generating genetic diversity in viruses, homologous recombination can lead to the emergence of novel virus strains with increased virulence and changed host tropism. However, it is still unclear whether recombination plays a role in the evolution of RABV. In this study, we isolated and sequenced four circulating RABV strains in China. Phylogenetic analyses identified a novel lineage of hybrid origin that comprises two different strains, J and CQ92. Analyses revealed that the virus 3′ untranslated region (UTR) and part of the N gene (approximate 500 nt in length) were likely derived from Chinese lineage I while the other part of the genomic sequence was homologous to Chinese lineage II. Our findings reveal that homologous recombination can occur naturally in the field and shape the genetic structure of RABV populations.
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Affiliation(s)
- Cheng-Qiang He
- Key Laboratory of Systems Biology in Universities of Shandong, College of Life Science, Shandong Normal University, Jinan, China
- * E-mail: (CQH); (HBH)
| | - Sheng-Li Meng
- Wuhan Institute of Biological Products, Wuhan, China
| | - Hong-Yan Yan
- Key Laboratory of Systems Biology in Universities of Shandong, College of Life Science, Shandong Normal University, Jinan, China
| | - Nai-Zheng Ding
- Key Laboratory of Systems Biology in Universities of Shandong, College of Life Science, Shandong Normal University, Jinan, China
| | - Hong-Bin He
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- * E-mail: (CQH); (HBH)
| | - Jia-Xin Yan
- Wuhan Institute of Biological Products, Wuhan, China
| | - Ge-Lin Xu
- Wuhan Institute of Biological Products, Wuhan, China
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Li J, Hu H, Yu Q, Diel DG, Li DS, Miller PJ. Generation and characterization of a recombinant Newcastle disease virus expressing the red fluorescent protein for use in co-infection studies. Virol J 2012; 9:227. [PMID: 23034005 PMCID: PMC3502164 DOI: 10.1186/1743-422x-9-227] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 09/26/2012] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Many viruses have evolved multiple strategies to prevent super infection of host cells by more than one virion. This phenomenon, known as super infection exclusion, may play an important role on virus evolution because it can affect the frequency of reassortment and/or recombination. Newcastle disease virus (NDV), a negative sense single-stranded RNA virus, is characterized by its continuous evolutionary dynamics and by a low frequency of recombination events. However, the mechanisms that contribute to the low recombination rates on NDV are still not completely understood. METHODS In this study we assessed the ability of two NDV strains (LaSota and B1) to super infect host cells in vitro. We generated a recombinant NDV strain LaSota expressing the red fluorescent protein (RFP) and used it in co-infection assays with a related NDV strain B1 expressing the green fluorescent protein (GFP). DF-1 cells were inoculated with both viruses at the same time or at different intervals between primary infection and super infection. RESULTS When both viruses were inoculated at the same time point, a 27% co-infection rate was observed, whereas when they were inoculated at different time points the super infection rates decreased to levels as low as 1.4%. CONCLUSIONS These results indicate that although different NDV strains can co-infect host cells in vitro, the super infection rates are low, specially as the time between the primary infection and super infection increases. These results confirm the occurrence of super infection exclusion between different strains of NDV.
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Affiliation(s)
- Jinnan Li
- USDA-ARS, Southeast Poultry Research Laboratory, 934 College Station Road, Athens, GA 30605, USA
- Heilongjiang Fisheries Research Institute, Harbin, 150070, China
| | - Haixia Hu
- USDA-ARS, Southeast Poultry Research Laboratory, 934 College Station Road, Athens, GA 30605, USA
- College of Animal Science and Technology, Southwest University, 2 Tiansheng Road, Chongqing, BeiBei District, 400715, China
| | - Qingzhong Yu
- USDA-ARS, Southeast Poultry Research Laboratory, 934 College Station Road, Athens, GA 30605, USA
| | - Diego G Diel
- USDA-ARS, Southeast Poultry Research Laboratory, 934 College Station Road, Athens, GA 30605, USA
| | - De-shan Li
- College of Life Sciences, Northeast Agriculture University, Harbin, 150030, China
| | - Patti J Miller
- USDA-ARS, Southeast Poultry Research Laboratory, 934 College Station Road, Athens, GA 30605, USA
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26
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Beck ET, He J, Nelson MI, Bose ME, Fan J, Kumar S, Henrickson KJ. Genome sequencing and phylogenetic analysis of 39 human parainfluenza virus type 1 strains isolated from 1997-2010. PLoS One 2012; 7:e46048. [PMID: 23029382 PMCID: PMC3459887 DOI: 10.1371/journal.pone.0046048] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 08/28/2012] [Indexed: 12/14/2022] Open
Abstract
Thirty-nine human parainfluenza type 1 (HPIV-1) genomes were sequenced from samples collected in Milwaukee, Wisconsin from 1997–2010. Following sequencing, phylogenetic analyses of these sequences plus any publicly available HPIV-1 sequences (from GenBank) were performed. Phylogenetic analysis of the whole genomes, as well as individual genes, revealed that the current HPIV-1 viruses group into three different clades. Previous evolutionary studies of HPIV-1 in Milwaukee revealed that there were two genotypes of HPIV-1 co-circulating in 1991 (previously described as HPIV-1 genotypes C and D). The current study reveals that there are still two different HPIV-1 viruses co-circulating in Milwaukee; however, both groups of HPIV-1 viruses are derived from genotype C indicating that genotype D may no longer be in circulation in Milwaukee. Analyses of genetic diversity indicate that while most of the genome is under purifying selection some regions of the genome are more tolerant of mutation. In the 40 HPIV-1 genomes sequenced in this study, the nucleotide sequence of the L gene is the most conserved while the sequence of the P gene is the most variable. Over the entire protein coding region of the genome, 81 variable amino acid residues were observed and as with nucleotide diversity, the P protein seemed to be the most tolerant of mutation (and contains the greatest proportion of non-synonymous to synonymous substitutions) while the M protein appears to be the least tolerant of amino acid substitution.
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Affiliation(s)
- Eric T. Beck
- Midwest Respiratory Virus Program, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Children's Research Institute, Children's Hospital of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Jie He
- Midwest Respiratory Virus Program, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Children's Research Institute, Children's Hospital of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Martha I. Nelson
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Michael E. Bose
- Midwest Respiratory Virus Program, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Children's Research Institute, Children's Hospital of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Jiang Fan
- Midwest Respiratory Virus Program, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Children's Research Institute, Children's Hospital of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Swati Kumar
- Midwest Respiratory Virus Program, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Children's Research Institute, Children's Hospital of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Kelly J. Henrickson
- Midwest Respiratory Virus Program, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Children's Research Institute, Children's Hospital of Wisconsin, Milwaukee, Wisconsin, United States of America
- * E-mail:
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Diel DG, da Silva LHA, Liu H, Wang Z, Miller PJ, Afonso CL. Genetic diversity of avian paramyxovirus type 1: proposal for a unified nomenclature and classification system of Newcastle disease virus genotypes. INFECTION GENETICS AND EVOLUTION 2012; 12:1770-9. [PMID: 22892200 DOI: 10.1016/j.meegid.2012.07.012] [Citation(s) in RCA: 243] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 07/11/2012] [Accepted: 07/12/2012] [Indexed: 10/28/2022]
Abstract
The avian paramyxovirus type 1 (APMV-1), or Newcastle disease virus (NDV), comprise a diverse group of viruses with a single-stranded, negative-sense RNA genome. Historically, two systems have been simultaneously used to classify NDV isolates into lineages or genotypes, generating confusion in the nomenclature and discrepancies in the assignment of genetic groups. In the present study we assessed the genetic diversity of the avian paramyxovirus type-1 (APMV-1) and propose a unified nomenclature and a classification system based on objective criteria to separate NDV into genotypes. Complete F gene sequences of class I (n = 110) and class II (n = 602) viruses were used for the phylogenetic reconstruction and to identify distinct taxonomic groups. The mean interpopulational evolutionary distance was estimated (10%) and set as the cutoff value to assign new genotypes. Results of our study revealed that class I viruses comprise a single genotype, while class II contains 15 genetic groups including 10 previously established (I-IX, and XI) and five new genotypes (X, XII, XIII, XIV and XV). Sub-genotypes were identified among class I and class II genotypes. Adoption of a unified nomenclature and of objective criteria to classify NDV isolates will facilitate studies on NDV epidemiology, evolution, disease control and diagnostics.
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Affiliation(s)
- Diego G Diel
- Southeast Poultry Research Laboratory, United States Department of Agriculture, Agricultural Research Services, 934 College Station Rd, Athens, GA 30605, United States
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28
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Walker PJ, Dietzgen RG, Joubert DA, Blasdell KR. Rhabdovirus accessory genes. Virus Res 2011; 162:110-25. [PMID: 21933691 PMCID: PMC7114375 DOI: 10.1016/j.virusres.2011.09.004] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 09/02/2011] [Accepted: 09/04/2011] [Indexed: 12/16/2022]
Abstract
The Rhabdoviridae is one of the most ecologically diverse families of RNA viruses with members infecting a wide range of organisms including placental mammals, marsupials, birds, reptiles, fish, insects and plants. The availability of complete nucleotide sequences for an increasing number of rhabdoviruses has revealed that their ecological diversity is reflected in the diversity and complexity of their genomes. The five canonical rhabdovirus structural protein genes (N, P, M, G and L) that are shared by all rhabdoviruses are overprinted, overlapped and interspersed with a multitude of novel and diverse accessory genes. Although not essential for replication in cell culture, several of these genes have been shown to have roles associated with pathogenesis and apoptosis in animals, and cell-to-cell movement in plants. Others appear to be secreted or have the characteristics of membrane-anchored glycoproteins or viroporins. However, most encode proteins of unknown function that are unrelated to any other known proteins. Understanding the roles of these accessory genes and the strategies by which rhabdoviruses use them to engage, divert and re-direct cellular processes will not only present opportunities to develop new anti-viral therapies but may also reveal aspects of cellar function that have broader significance in biology, agriculture and medicine.
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Affiliation(s)
- Peter J Walker
- CSIRO Livestock Industries, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC 3220, Australia.
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29
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Homologous recombination in negative sense RNA viruses. Viruses 2011; 3:1358-73. [PMID: 21994784 PMCID: PMC3185808 DOI: 10.3390/v3081358] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 07/12/2011] [Accepted: 07/22/2011] [Indexed: 01/05/2023] Open
Abstract
Recombination is an important process that influences biological evolution at many different levels. More and more homologous recombination events have been reported among negative sense RNA viruses recently. While sporadic authentic examples indicate that homologous recombination does occur, recombination seems to be generally rare or even absent in most negative sense RNA viruses, and most of the homologous recombination events reported in the literature were likely generated artificially due to lab contamination or inappropriate bioinformatics methods. Homologous recombination in negative sense RNA viruses should be reported with caution in the future, and only after stringent quality control efforts. Moreover, co-infection experiments should be performed to confirm whether recombination can occur.
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30
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Artificial recombination may influence the evolutionary analysis of Newcastle disease virus. J Virol 2011; 85:10409-14. [PMID: 21775447 DOI: 10.1128/jvi.00544-11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The recombination rate in Newcastle disease virus (NDV) was as high as 10% in RDP analysis with full-length NDV genome sequences available in GenBank. We found that two NDV strains, China/Guangxi09/2003 and NDV/03/018, previously reported as recombinants, failed to show any evidence of recombination upon complete genome resequencing. Furthermore, we were able to reproduce artificial recombination by amplification of the M gene in a mixed sample of strains LaSota and ZJ1. It appears that the recombination of NDV is not as common as has been reported. NDV sequences in GenBank should be analyzed with caution during bioinformatic analyses for natural recombination events.
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31
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Yang HT, Jiang Q, Zhou X, Bai MQ, Si HL, Wang XJ, Lu Y, Zhao H, He HB, He CQ. Identification of a natural human serotype 3 parainfluenza virus. Virol J 2011; 8:58. [PMID: 21306605 PMCID: PMC3045893 DOI: 10.1186/1743-422x-8-58] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 02/09/2011] [Indexed: 12/21/2022] Open
Abstract
Parainfluenza virus is an important pathogen threatening the health of animals and human, which brings human many kinds of disease, especially lower respiratory tract infection involving infants and young children. In order to control the virus, it is necessary to fully understand the molecular basis resulting in the genetic diversity of the virus. Homologous recombination is one of mechanisms for the rapid change of genetic diversity. However, as a negative-strand virus, it is unknown whether the recombination can naturally take place in human PIV. In this study, we isolated and identified a mosaic serotype 3 human PIV (HPIV3) from in China, and also provided several putative PIV mosaics from previous reports to reveal that the recombination can naturally occur in the virus. In addition, two swine PIV3 isolates transferred from cattle to pigs were found to have mosaic genomes. These results suggest that homologous recombination can promote the genetic diversity and potentially bring some novel biologic characteristics of HPIV.
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Affiliation(s)
- Hui-Ting Yang
- College of Life Science, Shandong Normal University, Jinan 250014, China
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32
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Maminiaina OF, Gil P, Briand FX, Albina E, Keita D, Andriamanivo HR, Chevalier V, Lancelot R, Martinez D, Rakotondravao R, Rajaonarison JJ, Koko M, Andriantsimahavandy AA, Jestin V, Servan de Almeida R. Newcastle disease virus in Madagascar: identification of an original genotype possibly deriving from a died out ancestor of genotype IV. PLoS One 2010; 5:e13987. [PMID: 21085573 PMCID: PMC2981552 DOI: 10.1371/journal.pone.0013987] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 10/17/2010] [Indexed: 11/25/2022] Open
Abstract
In Madagascar, Newcastle disease (ND) has become enzootic after the first documented epizootics in 1946, with recurrent annual outbreaks causing mortality up to 40%. Four ND viruses recently isolated in Madagascar were genotypically and pathotypically characterised. By phylogenetic inference based on the F and HN genes, and also full-genome sequence analyses, the NDV Malagasy isolates form a cluster distant enough to constitute a new genotype hereby proposed as genotype XI. This new genotype is presumably deriving from an ancestor close to genotype IV introduced in the island probably more than 50 years ago. Our data show also that all the previously described neutralising epitopes are conserved between Malagasy and vaccine strains. However, the potential implication in vaccination failures of specific amino acid substitutions predominantly found on surface-exposed epitopes of F and HN proteins is discussed.
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Affiliation(s)
| | - Patricia Gil
- CIRAD, BIOS Department, UMR CMAEE, Montpellier, France
| | | | | | - Djénéba Keita
- CIRAD, BIOS Department, UMR CMAEE, Montpellier, France
| | | | | | | | | | | | | | - M. Koko
- Antananarivo University Madagascar, Antananarivo, Madagascar
| | | | - Véronique Jestin
- Anses-Ploufragan Plouzané Laboratory, VIPAC Unit, Ploufragan, France
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33
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Han GZ, Boni MF, Li SS. No observed effect of homologous recombination on influenza C virus evolution. Virol J 2010; 7:227. [PMID: 20840780 PMCID: PMC2949832 DOI: 10.1186/1743-422x-7-227] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Accepted: 09/14/2010] [Indexed: 11/10/2022] Open
Abstract
The occurrence of homologous recombination in influenza viruses has been under some debate recently. To determine the extent of homologous recombination in influenza C virus, recombination analyses of all available gene sequences of influenza C virus were carried out. No recombination signal was found. With the previous evidence in influenza A and B viruses, it seems that homologous recombination has minimal or no effect on influenza virus evolution.
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Affiliation(s)
- Guan-Zhu Han
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, China
- Current Address: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Maciej F Boni
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- MRC Centre for Genomics and Global Health, University of Oxford, Oxford, UK
| | - Si-Shen Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, China
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34
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The effect of vaccination on the evolution and population dynamics of avian paramyxovirus-1. PLoS Pathog 2010; 6:e1000872. [PMID: 20421950 PMCID: PMC2858710 DOI: 10.1371/journal.ppat.1000872] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 03/23/2010] [Indexed: 12/12/2022] Open
Abstract
Newcastle Disease Virus (NDV) is a pathogenic strain of avian paramyxovirus (aPMV-1) that is among the most serious of disease threats to the poultry industry worldwide. Viral diversity is high in aPMV-1; eight genotypes are recognized based on phylogenetic reconstruction of gene sequences. Modified live vaccines have been developed to decrease the economic losses caused by this virus. Vaccines derived from avirulent genotype II strains were developed in the 1950s and are in use globally, whereas Australian strains belonging to genotype I were developed as vaccines in the 1970s and are used mainly in Asia. In this study, we evaluated the consequences of attenuated live virus vaccination on the evolution of aPMV-1 genotypes. There was phylogenetic incongruence among trees based on individual genes and complete coding region of 54 full length aPMV-1 genomes, suggesting that recombinant sequences were present in the data set. Subsequently, five recombinant genomes were identified, four of which contained sequences from either genotype I or II. The population history of vaccine-related genotype II strains was distinct from other aPMV-1 genotypes; genotype II emerged in the late 19th century and is evolving more slowly than other genotypes, which emerged in the 1960s. Despite vaccination efforts, genotype II viruses have experienced constant population growth to the present. In contrast, other contemporary genotypes showed population declines in the late 1990s. Additionally, genotype I and II viruses, which are circulating in the presence of homotypic vaccine pressure, have unique selection profiles compared to nonvaccine-related strains. Collectively, these data show that vaccination with live attenuated viruses has changed the evolution of aPMV-1 by maintaining a large effective population size of a vaccine-related genotype, allowing for coinfection and recombination of vaccine and wild type strains, and by applying unique selective pressures on viral glycoproteins. Modified live virus (MLV) vaccines have been effective in reducing disease burden and economic loss caused by Newcastle Disease (ND) in domestic poultry. Because the vaccine is a live virus, it is transmissible among birds. Thus, vaccination strategies have the potential to impact the evolutionary genetics of wild type strains of aPMV-1 including those that cause ND. In this report, we provided evidence that viruses isolated from wild and domestic birds have recombined with vaccine strains, because vaccinated birds are protected from disease but not infection with other strains of aPMV-1. Despite the use of vaccines since the 1950s, the population size of the strain from which the most widely used vaccine was derived has steadily increased. In contrast, other contemporary genotypes, which emerged in the 1960s, experienced a decline in population size in 1998, which may reflect a change in poultry farming practices or disease. Vaccination imposed a unique selection profile on the genotypes derived from the vaccine-related strains when compared with nonvaccine-related strains. Although modified live viruses are important for controlling Newcastle Disease, the potential of vaccination strategies to change viral diversity and population dynamics should be considered.
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35
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Zhang R, Wang X, Su J, Zhao J, Zhang G. Isolation and analysis of two naturally-occurring multi-recombination Newcastle disease viruses in China. Virus Res 2010; 151:45-53. [PMID: 20363269 DOI: 10.1016/j.virusres.2010.03.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2010] [Revised: 03/25/2010] [Accepted: 03/26/2010] [Indexed: 10/19/2022]
Abstract
Two Newcastle disease viruses (NDV), designated QG/Hebei/07 and XD/Shandong/08, were isolated from infected chicken flocks in China in 2007 and 2008, respectively. The results of phylogenetic and recombination analyses on complete NDV genome sequences (excluding terminal segments) show that the QG/Hebei/07 isolate had evidence of recombination in the M and F genes, and recombination in the XD/Shandong/08 isolate in the F, L genes and the non-coding region between the HN and L genes. These two naturally-occurring recombinants we found to be descended from at least three putative parents from vaccine and circulating virus lineages. Moreover, we found that evidence that homologous recombination also occurred between NDV viruses of chicken and swine lineages, while the major putative parent is likely to have been derived from the chicken avirulent vaccine lineage. This study suggests that homologous recombination can occur in all coding and non-coding regions of the NDV genome and a live vaccine strain is capable of recombination with circulating viruses resulting in significant genetic change. The potential role of swine-origin viruses in the evolution of virulent NDV warrants further investigation.
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Affiliation(s)
- Rui Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
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36
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Abstract
RNA genomes are vulnerable to corruption by a range of activities, including inaccurate replication by the error-prone replicase, damage from environmental factors, and attack by nucleases and other RNA-modifying enzymes that comprise the cellular intrinsic or innate immune response. Damage to coding regions and loss of critical cis-acting signals inevitably impair genome fitness; as a consequence, RNA viruses have evolved a variety of mechanisms to protect their genome integrity. These include mechanisms to promote replicase fidelity, recombination activities that allow exchange of sequences between different RNA templates, and mechanisms to repair the genome termini. In this article, we review examples of these processes from a range of RNA viruses to showcase the diverse approaches that viruses have evolved to maintain their genome sequence integrity, focusing first on mechanisms that viruses use to protect their entire genome, and then concentrating on mechanisms that allow protection of the genome termini, which are especially vulnerable. In addition, we discuss examples in which it might be beneficial for a virus to 'lose' its genomic termini and reduce its replication efficiency.
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Affiliation(s)
- John N Barr
- Institute of Molecular and Cellular Biology, University of Leeds, Leeds, UK
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37
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Rui Z, Juan P, Jingliang S, Jixun Z, Xiaoting W, Shouping Z, Xiaojiao L, Guozhong Z. Phylogenetic characterization of Newcastle disease virus isolated in the mainland of China during 2001–2009. Vet Microbiol 2010; 141:246-57. [DOI: 10.1016/j.vetmic.2009.09.020] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2009] [Revised: 09/10/2009] [Accepted: 09/22/2009] [Indexed: 12/14/2022]
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38
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Miller PJ, Kim LM, Ip HS, Afonso CL. Evolutionary dynamics of Newcastle disease virus. Virology 2009; 391:64-72. [PMID: 19564032 DOI: 10.1016/j.virol.2009.05.033] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2009] [Revised: 03/27/2009] [Accepted: 05/22/2009] [Indexed: 12/26/2022]
Abstract
A comprehensive dataset of NDV genome sequences was evaluated using bioinformatics to characterize the evolutionary forces affecting NDV genomes. Despite evidence of recombination in most genes, only one event in the fusion gene of genotype V viruses produced evolutionarily viable progenies. The codon-associated rate of change for the six NDV proteins revealed that the highest rate of change occurred at the fusion protein. All proteins were under strong purifying (negative) selection; the fusion protein displayed the highest number of amino acids under positive selection. Regardless of the phylogenetic grouping or the level of virulence, the cleavage site motif was highly conserved implying that mutations at this site that result in changes of virulence may not be favored. The coding sequence of the fusion gene and the genomes of viruses from wild birds displayed higher yearly rates of change in virulent viruses than in viruses of low virulence, suggesting that an increase in virulence may accelerate the rate of NDV evolution.
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Affiliation(s)
- Patti J Miller
- Southeast Poultry Research Laboratories, USDA ARS, Southeast Poultry Research Laboratory, Athens, GA 30605, USA
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39
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Hughes AL. Relaxation of purifying selection on live attenuated vaccine strains of the family Paramyxoviridae. Vaccine 2009; 27:1685-90. [PMID: 19195493 DOI: 10.1016/j.vaccine.2009.01.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Revised: 01/12/2009] [Accepted: 01/14/2009] [Indexed: 11/25/2022]
Abstract
In wild-type sequences of three paramyxoviruses (measles virus, mumps virus, and Newcastle disease virus), nucleotide diversity at both non-coding sites and at nonsynonymous sites in coding regions was significantly reduced in comparison to that at synonymous sites. Likewise, both the mean and variance of gene diversity at nonsynonymous polymorphic sites were reduced in comparison to non-coding and synonymous sites. Neither of these patterns, which reflect the action of purifying selection against deleterious mutations at nonsynonymous and non-coding sites, were seen in the case of live attenuated vaccine strains, implying that purifying selection has been substantially relaxed on the latter, potentially affecting their biological properties, including antigenicity and vaccine effectiveness. Since the accumulation of mutations increases as a function of the number of generations of replication, these findings highlight the utility of minimizing the number of generations between the original vaccine master seed and the strains used in vaccination, along with periodic monitoring of the extent of sequence evolution.
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Affiliation(s)
- Austin L Hughes
- Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg., 700 Sumter St., Columbia, SC 29208, USA.
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40
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He CQ, Ma LY, Wang D, Li GR, Ding NZ. Homologous recombination is apparent in infectious bursal disease virus. Virology 2008; 384:51-8. [PMID: 19064275 DOI: 10.1016/j.virol.2008.11.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Revised: 10/31/2008] [Accepted: 11/04/2008] [Indexed: 11/16/2022]
Abstract
Infectious bursal disease virus (IBDV) is a non-enveloped double-stranded RNA virus belonging to the Birnaviridae family. It shows substantial variation in the major antigen region of the viral capsid protein VP2, where a hypervariable region plays a key role in the virulence of IBDV and its epitope. This study identifies several putative recombinants from previously published data to suggest that homologous recombination may naturally occur between different IBDV strains. In addition, a novel very virulence sublineage emerges in the VP2 phylogenic tree, comprising three putative recombination strains isolated in Korea and China, KSH, KK1 and SH-h. The major putative parents of the three mosaics are descended from the vaccine lineage while their hypervariable regions from vvIBDV. These findings also suggest that vaccine coverage may have influence on the evolution and genetic diversity of IBDV, resulting in a novel group with vvIBDV phenotype through recombination with wild IBDV.
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Affiliation(s)
- Cheng-Qiang He
- College of Life Science, Shandong Normal University, Jinan, China.
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41
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He CQ, Xie ZX, Han GZ, Dong JB, Wang D, Liu JB, Ma LY, Tang XF, Liu XP, Pang YS, Li GR. Homologous recombination as an evolutionary force in the avian influenza A virus. Mol Biol Evol 2008; 26:177-87. [PMID: 18931384 DOI: 10.1093/molbev/msn238] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Avian influenza A viruses (AIVs), including the H5N1, H9N2, and H7N7 subtypes, have been directly transmitted to humans, raising concerns over the possibility of a new influenza pandemic. To prevent a future avian influenza pandemic, it is very important to fully understand the molecular basis driving the change in AIV virulence and host tropism. Although virulent variants of other viruses have been generated by homologous recombination, the occurrence of homologous recombination within AIV segments is controversial and far from proven. This study reports three circulating H9N2 AIVs with similar mosaic PA genes descended from H9N2 and H5N1. Additionally, many homologous recombinants are also found deposited in GenBank. Recombination events can occur in PB2, PB1, PA, HA, and NP segments and between lineages of the same/different serotype. These results collectively demonstrate that intragenic recombination plays a role in driving the evolution of AIVs, potentially resulting in effects on AIV virulence and host tropism changes.
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Affiliation(s)
- Cheng-Qiang He
- Department of Biotechnology College of Life Science, Shandong Normal University, Shandong Province, Jinan, China.
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What are the risks--hypothetical and observed--of recombination involving live vaccines and vaccine vectors based on nonsegmented negative-strain RNA viruses? J Virol 2008; 82:9805-6. [PMID: 18796655 DOI: 10.1128/jvi.01336-08] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Han GZ, Liu XP, Li SS. Cross-species recombination in the haemagglutinin gene of canine distemper virus. Virus Res 2008; 136:198-201. [PMID: 18550189 DOI: 10.1016/j.virusres.2008.04.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Revised: 04/18/2008] [Accepted: 04/23/2008] [Indexed: 12/18/2022]
Abstract
Canine distemper virus (CDV) has high prevalence in the world dog population and poses an important conservation threat to many carnivore species. In this study, extensive phylogenetic and recombination analyses were performed on all available complete haemagglutinin gene sequences and a strain (AF178038) isolated from giant panda was identified as putative recombinant. Interestingly, the mosaic was produced by recombination between genotypes European wildlife and Asia-1 and the recombination event involves viruses infecting different host species. This finding may have important implications for the evolution of CDV.
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Affiliation(s)
- Guan-Zhu Han
- College of Life Science, Shandong Normal University, Jinan, Shandong 250014, China.
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Rapid discrimination of H5 and H9 subtypes of avian influenza viruses and Newcastle disease virus by multiplex RT-PCR. Vet Res Commun 2008; 32:491-8. [PMID: 18481190 DOI: 10.1007/s11259-008-9052-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Accepted: 04/02/2008] [Indexed: 10/22/2022]
Abstract
Avian influenza and Newcastle disease are the highly contagious and most economically important diseases in poultry industry throughout the world. A multiplex reverse transcription polymerase chain reaction (mRT-PCR) assay was developed for the rapid and specific discrimination of H5 and H9 subtypes of avian influenza viruses (AIV) and Newcastle disease virus (NDV). Three sets of specific primers were applied in the assay based on the sequences of the hemagglutinin gene of H5-AIV, H9-AIV and fusion protein gene of NDV. 59 clinical samples including the throat washes, oral swabs, and cloacal scrapings were detected by mRT-PCR and single RT-PCR (sRT-PCR), respectively. The results indicated that the sensitivity and specificity of mRT-PCR were in accordance with sRT-PCR. The mRT-PCR developed in this study may therefore provide a new avenue to rapid detection of these important pathogens in one reaction.
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