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Fortin A, Laconi A, Monne I, Zohari S, Andersson K, Grund C, Cecchinato M, Crimaudo M, Valastro V, D'Amico V, Bortolami A, Gastaldelli M, Varotto M, Terregino C, Panzarin V. A novel array of real-time RT-PCR assays for the rapid pathotyping of type I avian paramyxovirus (APMV-1). J Virol Methods 2023; 322:114813. [PMID: 37722509 DOI: 10.1016/j.jviromet.2023.114813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/20/2023]
Abstract
Newcastle disease (ND) caused by virulent avian paramyxovirus type I (APMV-1) is a WOAH and EU listed disease affecting poultry worldwide. ND exhibits different clinical manifestations that may either be neurological, respiratory and/or gastrointestinal, accompanied by high mortality. In contrast, mild or subclinical forms are generally caused by lentogenic APMV-1 and are not subject to notification. The rapid discrimination of virulent and avirulent viruses is paramount to limit the spread of virulent APMV-1. The appropriateness of molecular methods for APMV-1 pathotyping is often hampered by the high genetic variability of these viruses that affects sensitivity and inclusivity. This work presents a new array of real-time RT-PCR (RT-qPCR) assays that enable the identification of virulent and avirulent viruses in dual mode, i.e., through pathotype-specific probes and subsequent Sanger sequencing of the amplification product. Validation was performed according to the WOAH recommendations. Performance indicators on sensitivity, specificity, repeatability and reproducibility yielded favourable results. Reproducibility highlighted the need for assays optimization whenever major changes are made to the procedure. Overall, the new RT-qPCRs showed its ability to detect and pathotype all tested APMV-1 genotypes and its suitability for routine use in clinical samples.
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Affiliation(s)
- Andrea Fortin
- EU/WOAH/National Reference Laboratory for Avian Influenza and Newcastle Disease, FAO Reference Centre for Animal Influenza and Newcastle Disease, Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 35020 Legnaro, Italy; Department of Animal Medicine, Production and Health, University of Padua (Unipd), 35020 Legnaro, Italy
| | - Andrea Laconi
- Department of Comparative Biomedicine and Food Science, University of Padua (Unipd), 35020 Legnaro, Italy
| | - Isabella Monne
- EU/WOAH/National Reference Laboratory for Avian Influenza and Newcastle Disease, FAO Reference Centre for Animal Influenza and Newcastle Disease, Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 35020 Legnaro, Italy
| | - Siamak Zohari
- Department of Microbiology, Swedish National Veterinary Institute (SVA), SE751 89 Uppsala, Sweden
| | - Kristofer Andersson
- Department of Microbiology, Swedish National Veterinary Institute (SVA), SE751 89 Uppsala, Sweden
| | - Christian Grund
- Institute of Diagnostic Virology, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut (FLI), 17493 Greifswald-Insel Riems, Germany
| | - Mattia Cecchinato
- Department of Animal Medicine, Production and Health, University of Padua (Unipd), 35020 Legnaro, Italy
| | - Marika Crimaudo
- EU/WOAH/National Reference Laboratory for Avian Influenza and Newcastle Disease, FAO Reference Centre for Animal Influenza and Newcastle Disease, Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 35020 Legnaro, Italy
| | - Viviana Valastro
- EU/WOAH/National Reference Laboratory for Avian Influenza and Newcastle Disease, FAO Reference Centre for Animal Influenza and Newcastle Disease, Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 35020 Legnaro, Italy
| | - Valeria D'Amico
- EU/WOAH/National Reference Laboratory for Avian Influenza and Newcastle Disease, FAO Reference Centre for Animal Influenza and Newcastle Disease, Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 35020 Legnaro, Italy
| | - Alessio Bortolami
- EU/WOAH/National Reference Laboratory for Avian Influenza and Newcastle Disease, FAO Reference Centre for Animal Influenza and Newcastle Disease, Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 35020 Legnaro, Italy
| | - Michele Gastaldelli
- EU/WOAH/National Reference Laboratory for Avian Influenza and Newcastle Disease, FAO Reference Centre for Animal Influenza and Newcastle Disease, Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 35020 Legnaro, Italy
| | - Maria Varotto
- EU/WOAH/National Reference Laboratory for Avian Influenza and Newcastle Disease, FAO Reference Centre for Animal Influenza and Newcastle Disease, Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 35020 Legnaro, Italy
| | - Calogero Terregino
- EU/WOAH/National Reference Laboratory for Avian Influenza and Newcastle Disease, FAO Reference Centre for Animal Influenza and Newcastle Disease, Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 35020 Legnaro, Italy
| | - Valentina Panzarin
- EU/WOAH/National Reference Laboratory for Avian Influenza and Newcastle Disease, FAO Reference Centre for Animal Influenza and Newcastle Disease, Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 35020 Legnaro, Italy.
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Tal S, Ben Izhak M, Wachtel C, Wiseman A, Braun T, Yechezkel E, Golan E, Hadas R, Turjeman A, Banet-Noach C, Bronstein M, Lublin A, Berman E, Raviv Z, Pirak M, Klement E, Louzoun Y. Evaluating methods for Avian avulavirus-1 whole genome sequencing. Gene 2019; 721S:100004. [PMID: 32550541 PMCID: PMC7285907 DOI: 10.1016/j.gene.2019.100004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 01/03/2019] [Indexed: 11/18/2022]
Abstract
Background Avian avulavirus-1 (AAvV-1, previously Newcastle Disease Virus) is responsible for poultry and wild birds' disease outbreaks. Numerous whole genome sequencing methods were reported for this virus. These methods included cloning, specific primers amplification, shotgun PCR approaches, Sequence Independent Single Primer Amplification and next generation sequencing platform kits. Methods Three methods were used to sequence 173 Israeli Avian avulavirus-1 field isolates and one vaccine strain (VH). The sequencing was performed on Proton and Ion Torrent Personal Genome Machine and to a lesser extent, Illumina MiSeq and NextSeq sequencers. Target specific primers (SP) and Sequence Independent Single Primer Amplification (SISPA) products sequenced via the Ion torrent sequencer had a high error rate and truncated genomes. All the next generation sequencing platform sequencing kits generated high sequence accuracy and near-complete genomic size. Results A high level of mutations was observed in the intergenic regions between the avian avulavirus-1 genes. Within genes, multiple regions are more mutated than the Fusion region currently used for typing. Conclusions Our findings suggest that the whole genome sequencing by the Ion torrent sequencing kit is sufficient. However, when higher fidelity is desired, the Illumina NextSeq and Proton torrent sequencing kits were found to be preferable.
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Affiliation(s)
- Saar Tal
- The Poultry Health Laboratories, The Egg and Poultry Board, Israel
| | - Meirav Ben Izhak
- Life Science faculty and Gonda Brain Research Center, Bar Ilan University, Israel
| | | | - Anat Wiseman
- The Poultry Health Laboratories, The Egg and Poultry Board, Israel
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Israel
| | - Tzipi Braun
- Life Science faculty and Gonda Brain Research Center, Bar Ilan University, Israel
| | - Elinor Yechezkel
- The Poultry Health Laboratories, The Egg and Poultry Board, Israel
| | - Einav Golan
- The Poultry Health Laboratories, The Egg and Poultry Board, Israel
| | - Ruth Hadas
- Kimron Veterinary Institute, Division of Avian Diseases, Israel
| | - Adi Turjeman
- The Center for Genomic Technologies, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | | | - Michal Bronstein
- The Center for Genomic Technologies, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Avishai Lublin
- Kimron Veterinary Institute, Division of Avian Diseases, Israel
| | - Elyakum Berman
- The Poultry Health Laboratories, The Egg and Poultry Board, Israel
| | - Ziv Raviv
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Israel
| | - Michael Pirak
- The Poultry Health Laboratories, The Egg and Poultry Board, Israel
| | - Eyal Klement
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Israel
| | - Yoram Louzoun
- Department of Mathematics and Gonda Brain Research Center, Bar Ilan University, Israel
- Corresponding author at: Math Department and Gonda Brain Research Center, Bar Ilan University, Ramat Gan 52900, Israel.
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Chong YL, Lam TTY, Kim O, Lu H, Dunn P, Poss M. Successful establishment and global dispersal of genotype VI avian paramyxovirus serotype 1 after cross species transmission. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2013; 17:260-8. [PMID: 23628639 PMCID: PMC7106292 DOI: 10.1016/j.meegid.2013.04.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 04/08/2013] [Accepted: 04/22/2013] [Indexed: 02/02/2023]
Abstract
The evolutionary history of avian paramyxovirus serotype 1 (PMV1), which includes the agents of Newcastle disease (ND), is characterized by a series of strain emergence events since viruses in this family were first recognized in the 1920s. Despite the importance of ND to the poultry industry, little is known about PMV1 strain emergence events and the subsequent dispersal and evolution of new strains. The genotype VI-PMV1 was first identified in the 1980s and has been named pigeon paramyxovirus-1 (PPMV1) because of unusual host specificity with Columbiformes (Collins et al., 1996); it has been responsible for panzootics in both chickens and pigeons during that time. Here, we used evolutionary analyses to characterize the emergence of this contemporary PMV1 lineage. We demonstrate that GVI-PMV1 arose through cross-species transmission events from Galliformes (i.e. chicken) to Columbiformes, and quickly established in pigeon populations. Our studies revealed a close association between the time of viral emergence and panzootic events of this virus. The virus appeared first in Southeastern Europe and quickly spread across the European continent, which became the epicenter for global virus dissemination. With new viral gene sequences, we show that GVI-PMV1 viruses currently circulating in North America resulted from multiple invasion events from Europe, one associated with an exotic European Columbiformes species, and that extant lineages have diversified locally. This study extends our understanding of successful viral emergence subsequent to cross-species transmission and dispersal patterns of newly emerged avian viruses, which may improve surveillance awareness and disease control of this and other important avian pathogens.
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Affiliation(s)
- Yee Ling Chong
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
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Virtue ER, Marsh GA, Wang LF. Paramyxoviruses infecting humans: the old, the new and the unknown. Future Microbiol 2009; 4:537-54. [DOI: 10.2217/fmb.09.26] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Prior to the emergence of Hendra virus in Australia in 1994, paramyxoviruses were considered to be a taxonomic group of ubiquitous pathogens, consisting primarily of Biosafety Level 2 agents, which possessed narrow host ranges and often caused only mild or preventable diseases in humans and animals. In recent years, a number of Paramyxoviridae members have emerged, including previously unrecognized human pathogens and highly pathogenic zoonoses. The recent emergence of paramyxoviruses in humans suggests that there is an increased incidence of zoonotic transmission between wildlife, livestock and human hosts. This article explores the current body of scientific knowledge, disease burden and knowledge of reservoirs of these emerging paramyxoviruses and provides a comparative review of both older and emerging viruses that have been shown to infect humans.
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Affiliation(s)
- Elena R Virtue
- CSIRO Livestock Industries, Australian Animal Health Laboratory (AAHL), Geelong, VIC, Australia and, Australian Biosecurity Cooperative Research Centre for Emerging Infectious Disease and, Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, Australia
| | - Glenn A Marsh
- CSIRO Livestock Industries, Australian Animal Health Laboratory (AAHL), Geelong, VIC, Australia
| | - Lin-Fa Wang
- CSIRO Livestock Industries, Australian Animal Health Laboratory, PO Bag 24, Geelong, VIC 3220, Australia, and, Australian Biosecurity Cooperative Research Centre for Emerging Infectious Disease and, Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, Australia
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Goebel SJ, Taylor J, Barr BC, Kiehn TE, Castro-Malaspina HR, Hedvat CV, Rush-Wilson KA, Kelly CD, Davis SW, Samsonoff WA, Hurst KR, Behr MJ, Masters PS. Isolation of avian paramyxovirus 1 from a patient with a lethal case of pneumonia. J Virol 2007; 81:12709-14. [PMID: 17855523 PMCID: PMC2168997 DOI: 10.1128/jvi.01406-07] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An unknown virus was isolated from a lung biopsy sample and multiple other samples from a patient who developed a lethal case of pneumonia following a peripheral blood stem cell transplant. A random PCR-based molecular screening method was used to identify the infectious agent as avian paramyxovirus 1 (APMV-1; a group encompassing Newcastle disease virus), which is a highly contagious poultry pathogen that has only rarely been found in human infections. Immunohistochemical analysis confirmed the presence of APMV-1 antigen in sloughed alveolar cells in lung tissue from autopsy. Sequence from the human isolate showed that it was most closely related to virulent pigeon strains of APMV-1. This is the most completely documented case of a systemic human infection caused by APMV-1 and is the first report of an association between this virus and a fatal disease in a human.
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Affiliation(s)
- Scott J Goebel
- Divisions of Infectious Disease and Molecular Medicine, David Axelrod Institute, Wadsworth Center, NYSDOH, Albany, NY 12201-2002, USA
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Barbezange C, Jestin V. Quasispecies nature of an unusual avian paramyxovirus type-1 isolated from pigeons. Virus Genes 2005; 30:363-70. [PMID: 15830155 DOI: 10.1007/s11262-004-6780-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Revised: 09/17/2004] [Accepted: 11/16/2004] [Indexed: 11/28/2022]
Abstract
An avian paramyxovirus type-1 (APMV-1) was classified as virulent according to its Intra Cerebral Pathogenicity Index (ICPI), but as avirulent according to the motif of its F protein cleavage site. Although this atypical APMV-1 was isolated from sick, unvaccinated pigeons, it was not grouped with pigeon variants regarding its antigenic and genetic characterisation. We analysed its quasispecies nature by cloning and sequencing parts of the genome in three different genes to evaluate if heterogeneity might explain the difference observed between the ICPI and the F protein cleavage site motif. Two distinct sub-populations were detected in the phosphoprotein gene. In the fusion protein gene, two clones were found to be related to typical pigeon variants in the hypervariable domain.
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Affiliation(s)
- Cyril Barbezange
- AFSSA (French Agency for Food Safety), BP 53 22440, Ploufragan cedex, France
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Barbezange C, Jestin V. Molecular study of the quasispecies evolution of a typical pigeon paramyxovirus type 1 after serial passages in pigeons by contact. Avian Pathol 2005; 34:111-22. [PMID: 16191691 DOI: 10.1080/03079450500059321] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The quasispecies nature of a typical pigeon paramyxovirus type 1 (pPMV-1) was, for the first time, studied under conditions close to the natural infectious environment. The virus was serially passaged in pigeons by successive contacts. Viral heterogeneity was analysed in the kidneys and brain of five pigeons from the last contact, by reverse transcriptase-polymerase chain reactions performed on RNA directly extracted from the organ and targeting the P and HN genes of the virus. The viral diversity following in vivo passage was found to be different from that in the inoculum, but demonstrated the reality of the quasispecies concept for pPMV-1 strains. Moreover, some aberrant genomic RNAs comprising insertions in the P gene editing site or deletions in the HN gene were also detected, with possible consequences for the pathogenicity and infectivity of the virus.
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Affiliation(s)
- C Barbezange
- AFSSA (French Agency for Food Safety), Avian and Rabbit Virology Immunology and Parasitology Unit, BP53, 22440 Ploufragan, Ploufragan, France
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