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Tur-Planells V, García-Sastre A, Cuadrado-Castano S, Nistal-Villan E. Engineering Non-Human RNA Viruses for Cancer Therapy. Vaccines (Basel) 2023; 11:1617. [PMID: 37897020 PMCID: PMC10611381 DOI: 10.3390/vaccines11101617] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Alongside the development and progress in cancer immunotherapy, research in oncolytic viruses (OVs) continues advancing novel treatment strategies to the clinic. With almost 50 clinical trials carried out over the last decade, the opportunities for intervention using OVs are expanding beyond the old-fashioned concept of "lytic killers", with promising breakthrough therapeutic strategies focused on leveraging the immunostimulatory potential of different viral platforms. This review presents an overview of non-human-adapted RNA viruses engineered for cancer therapy. Moreover, we describe the diverse strategies employed to manipulate the genomes of these viruses to optimize their therapeutic capabilities. By focusing on different aspects of this particular group of viruses, we describe the insights into the promising advancements in the field of virotherapy and its potential to revolutionize cancer treatment.
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Affiliation(s)
- Vicent Tur-Planells
- Microbiology Section, Department of Pharmaceutical Science and Health, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28668 Boadilla del Monte, Spain;
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sara Cuadrado-Castano
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Genomics Institute (IGI), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Estanislao Nistal-Villan
- Microbiology Section, Department of Pharmaceutical Science and Health, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28668 Boadilla del Monte, Spain;
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, 28668 Boadilla del Monte, Spain
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2
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Rtishchev A, Treshchalina A, Shustova E, Boravleva E, Gambaryan A. An Outbreak of Newcastle Disease Virus in the Moscow Region in the Summer of 2022. Vet Sci 2023; 10:404. [PMID: 37368790 DOI: 10.3390/vetsci10060404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
In August 2022 on a backyard farm in the Moscow region of Russia, mortality was observed among chickens, and all 45 birds of a particular farm died or were slaughtered after the onset of symptoms within a few days. Paramyxovirus was isolated from the diseased birds. Based on the nucleotide sequences of the F and NP gene fragments, it was determined that the virus belonged to subgenotype VII.1 AAvV-1 class II. The cleavage site of the F gene 109SGGRRQKRFIG119 and T in 546 and 555 position of the NP gene were typical for the velogenic type. The genetically closest NDV isolates were found in Iran. The mean time of death of 10-day-old chicken embryos upon infection with the minimal infectious dose was 52 h, which is typical for the velogenic pathotype. The virus caused 100% death of six-week-old chickens during oral infection as well as 100% mortality of all contact chickens, including those located in remote cages, which proves the ability of the virus to spread not only by the fecal-oral route but also by the aerosol route. That demonstrates a high level of pathogenicity and contagiousness of the isolated strain for chicken. However, mice intranasally infected with high doses of the virus did not die.
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Affiliation(s)
- Artyom Rtishchev
- Federal State Budgetary Scientific Institution «I. Mechnikov Research Institute of Vaccines and Sera», 105064 Moscow, Russia
| | - Anastasia Treshchalina
- Chumakov Federal Scientific Center for the Research and Development of Immune-and-Biological Products, Village of Institute of Poliomyelitis, Settlement "Moskovskiy", 108819 Moscow, Russia
| | - Elena Shustova
- Chumakov Federal Scientific Center for the Research and Development of Immune-and-Biological Products, Village of Institute of Poliomyelitis, Settlement "Moskovskiy", 108819 Moscow, Russia
| | - Elizaveta Boravleva
- Chumakov Federal Scientific Center for the Research and Development of Immune-and-Biological Products, Village of Institute of Poliomyelitis, Settlement "Moskovskiy", 108819 Moscow, Russia
| | - Alexandra Gambaryan
- Chumakov Federal Scientific Center for the Research and Development of Immune-and-Biological Products, Village of Institute of Poliomyelitis, Settlement "Moskovskiy", 108819 Moscow, Russia
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3
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Shu B, Wang J, Yu X, Li Z, Li J, Jiang W, Hou G, Peng C, Wang S, Yu J, Chen W, Guo X, Liu H. The genetic and biological characterization of the first avian paramyxovirus serotype 14 isolated from chicken in China. Virus Genes 2023:10.1007/s11262-023-01992-2. [PMID: 37184730 DOI: 10.1007/s11262-023-01992-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 03/30/2023] [Indexed: 05/16/2023]
Abstract
In October 2020, an avian paramyxovirus serotype 14 (APMV-14)-designated chicken/Fujian/2160/2020 (FJ2160) was isolated from tracheal and cloacal swab sample of chicken collected from live bird market in Fujian province in China during the active surveillance program. The complete genome of FJ2160 comprised 15,444 nucleotides (nt) complying with the paramyxovirus "rule of six" and encoded six non-overlapping structural proteins in the order of 3'-NP-P-M-F-HN-L-'5. The complete genome sequence analysis showed that FJ2160 had the highest identity (90.0%) with the APMV-14 isolated from Japan, while the nucleotide sequence identities of FJ2160 and other APMVs ranged from 42.4 to 51.1%. The F protein cleavage site was TREGR↓L, which resembled a lentogenic strain of APMV-1. Phylogenetic analysis revealed that the FJ2160 closest relative was APMV-14. The intracerebral pathogenicity index (ICPI) tests indicated that the virus was lentogenic. This is the first report of APMV-14 in China. These results provide evidence that APMV-14 could infect chickens and reveal the genetic characteristics and biological properties of the virus, which can help to better understand this new emerging APMV-14.
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Affiliation(s)
- Bo Shu
- China Animal Health and Epidemiology Center, Qingdao, 266032, China
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jingjing Wang
- China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Xiaohui Yu
- China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Zheng Li
- China Animal Health and Epidemiology Center, Qingdao, 266032, China
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230000, China
| | - Jinping Li
- China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Wenming Jiang
- China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Guangyu Hou
- China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Cheng Peng
- China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Suchun Wang
- China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Jianmin Yu
- China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Wei Chen
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiaoquan Guo
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Hualei Liu
- China Animal Health and Epidemiology Center, Qingdao, 266032, China.
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4
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Novel avian orthoavulavirus 13 in wild migratory waterfowl: biological and genetic considerations. Vet Res Commun 2021; 46:159-168. [PMID: 34580815 DOI: 10.1007/s11259-021-09839-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 09/18/2021] [Indexed: 10/20/2022]
Abstract
Avian orthoavulavirus 13 (AOAV-13), formerly known as Avian paramyxovirus 13 (APMV-13), is found scatteredly in wild birds around the world. Although four complete genome sequences of AOAV-13 had been identified since the first discovery in Japan in 2003, the information available on the genetic variation and biological characteristics of AOAV-13 is still limited. In the present study, we isolated six AOAV-13 strains from fecal samples of wild migratory waterfowls during annual (2014-2018) viral surveillance of wild bird populations from wetland and domestic poultry of live bird markets (LBMs) in China. The phylogenetic analyses based on the HN and F genes showed that they had very close relationship and the molecular clock estimations showed a low evolutionary rate of AOAV-13. However, Bean goose/Hubei/V97-1/2015 is 1953 nt in size (ORF, 1, 776 nt), which is a unique size and longer than other reported AOAV-13 strains. Additionally, four repeats of conserved sequences "AAAAAT" was presented in the 5'-end trailer region of Swan goose/Hubei/VI49-1/2016, which is unprecedented in the AOAV-13. These findings highlight the importance of continuous monitoring the specific species of APMVs.
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5
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Jin JH, Wang JJ, Ren YC, Liu S, Li JP, Hou GY, Liu HL, Zhuang QY, Wang SC, Jiang WM, Yu XH, Yu JM, Yuan LP, Peng C, Zhang GZ, Chen JM. A set of RT-PCR assays for detection of all known avian paramyxoviruses and application in surveillance of avian paramyxoviruses in China. PeerJ 2021; 9:e10748. [PMID: 33717667 PMCID: PMC7937338 DOI: 10.7717/peerj.10748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/18/2020] [Indexed: 12/13/2022] Open
Abstract
Background Avian paramyxoviruses (APMVs), also termed avian avulaviruses, are of a vast diversity and great significance in poultry. Detection of all known APMVs is challenging, and distribution of APMVs have not been well investigated. Methods A set of reverse transcription polymerase chain reaction (RT-PCR) assays for detection of all known APMVs were established using degenerate primers targeting the viral polymerase L gene. The assays were preliminarily evaluated using in-vitro transcribed double-stranded RNA controls and 24 known viruses, and then they were employed to detect 4,346 avian samples collected from 11 provinces. Results The assays could detect 20-200 copies of the double-stranded RNA controls, and detected correctly the 24 known viruses. Of the 4,346 avian samples detected using the assays, 72 samples were found positive. Of the 72 positives, 70 were confirmed through sequencing, indicating the assays were specific for APMVs. The 4,346 samples were also detected using a reported RT-PCR assay, and the results showed this RT-PCR assay was less sensitive than the assays reported here. Of the 70 confirmed positives, 40 were class I Newcastle disease virus (NDV or APMV-1) and 27 were class II NDV from poultry including chickens, ducks, geese, and pigeons, and three were APMV-2 from parrots. The surveillance identified APMV-2 in parrots for the first time, and revealed that prevalence of NDVs in live poultry markets was higher than that in poultry farms. The surveillance also suggested that class I NDVs in chickens could be as prevalent as in ducks, and class II NDVs in ducks could be more prevalent than in chickens, and class II NDVs could be more prevalent than class I NDVs in ducks. Altogether, we developed a set of specific and sensitive RT-PCR assays for detection of all known APMVs, and conducted a large-scale surveillance using the assays which shed novel insights into APMV epidemiology.
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Affiliation(s)
- Ji-Hui Jin
- Laboratory for Avian Disease Surveillance (OIE Reference Laboratory for Newcastle Disease), China Animal Health and Epidemiology Center, Qingdao, China
| | - Jing-Jing Wang
- Laboratory for Avian Disease Surveillance (OIE Reference Laboratory for Newcastle Disease), China Animal Health and Epidemiology Center, Qingdao, China
| | - Ying-Chao Ren
- Department for Animal Health Assessment, China Animal Health and Epidemiology Center, Qingdao, China
| | - Shuo Liu
- Laboratory for Avian Disease Surveillance (OIE Reference Laboratory for Newcastle Disease), China Animal Health and Epidemiology Center, Qingdao, China
| | - Jin-Ping Li
- Laboratory for Avian Disease Surveillance (OIE Reference Laboratory for Newcastle Disease), China Animal Health and Epidemiology Center, Qingdao, China
| | - Guang-Yu Hou
- Laboratory for Avian Disease Surveillance (OIE Reference Laboratory for Newcastle Disease), China Animal Health and Epidemiology Center, Qingdao, China
| | - Hua-Lei Liu
- Laboratory for Avian Disease Surveillance (OIE Reference Laboratory for Newcastle Disease), China Animal Health and Epidemiology Center, Qingdao, China
| | - Qing-Ye Zhuang
- Laboratory for Avian Disease Surveillance (OIE Reference Laboratory for Newcastle Disease), China Animal Health and Epidemiology Center, Qingdao, China
| | - Su-Chun Wang
- Laboratory for Avian Disease Surveillance (OIE Reference Laboratory for Newcastle Disease), China Animal Health and Epidemiology Center, Qingdao, China
| | - Wen-Ming Jiang
- Laboratory for Avian Disease Surveillance (OIE Reference Laboratory for Newcastle Disease), China Animal Health and Epidemiology Center, Qingdao, China
| | - Xiao-Hui Yu
- Laboratory for Avian Disease Surveillance (OIE Reference Laboratory for Newcastle Disease), China Animal Health and Epidemiology Center, Qingdao, China
| | - Jian-Min Yu
- Laboratory for Avian Disease Surveillance (OIE Reference Laboratory for Newcastle Disease), China Animal Health and Epidemiology Center, Qingdao, China
| | - Li-Ping Yuan
- Laboratory for Avian Disease Surveillance (OIE Reference Laboratory for Newcastle Disease), China Animal Health and Epidemiology Center, Qingdao, China
| | - Cheng Peng
- Laboratory for Avian Disease Surveillance (OIE Reference Laboratory for Newcastle Disease), China Animal Health and Epidemiology Center, Qingdao, China
| | - Guo-Zhong Zhang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ji-Ming Chen
- Laboratory for Avian Disease Surveillance (OIE Reference Laboratory for Newcastle Disease), China Animal Health and Epidemiology Center, Qingdao, China
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6
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Rao PL, Gandham RK, Subbiah M. Molecular evolution and genetic variations of V and W proteins derived by RNA editing in Avian Paramyxoviruses. Sci Rep 2020; 10:9532. [PMID: 32533018 PMCID: PMC7293227 DOI: 10.1038/s41598-020-66252-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 05/06/2020] [Indexed: 11/12/2022] Open
Abstract
The newly assigned subfamily Avulavirinae in the family Paramyxoviridae includes avian paramyxoviruses (APMVs) isolated from a wide variety of avian species across the globe. Till date, 21 species of APMVs are reported and their complete genome sequences are available in GenBank. The APMV genome comprises of a single stranded, negative sense, non-segmented RNA comprising six transcriptional units (except APMV-6 with seven units) each coding for a structural protein. Additionally, by co-transcriptional RNA editing of phosphoprotein (P) gene, two mRNAs coding for accessory viral proteins, V and W, are generated along with unedited P mRNA. However, in APMV-11, the unedited mRNA codes for V protein while +2 edited mRNA translates to P protein, similar to members of subfamily Rubulavirinae in the same family. Such RNA editing in paramyxoviruses enables maximizing the coding capacity of their smaller genome. The three proteins of P gene: P, V and W, share identical N terminal but varied C terminal sequences that contribute to their unique functions. Here, we analyzed the P gene editing site, V and W sequences of all 21 APMV species known so far (55 viruses) by using bioinformatics and report their genetic variations and molecular evolution. The variations observed in the sequence and hexamer phase positions of the P gene editing sites is likely to influence the levels and relative proportions of P, V and W proteins' expressions which could explain the differences in the pathogenicity of APMVs. The V protein sequences of APMVs had conserved motifs similar to V proteins of other paramyxoviruses including the seven cysteine residues involved in MDA5 interference, STAT1 degradation and interferon antagonism. Conversely, W protein sequences of APMVs were distinct. High sequence homology was observed in both V and W proteins between strains of the same species than between species except in APMV-3 which was the most divergent APMV species. The estimates of synonymous and non-synonymous substitution rates suggested negative selection pressure on the V and W proteins within species indicating their low evolution rate. The molecular clock analysis revealed higher conservation of V protein sequence compared to W protein indicating the important role played by V protein in viral replication, pathogenesis and immune evasion. However, we speculate the genetic diversity of W proteins could impact the degree of pathogenesis, variable interferon antagonistic activity and the wide host range exhibited by APMV species. Phylogenetically, V proteins of APMVs clustered into three groups similar to the recent classification of APMVs into three new genera while no such pattern could be deciphered in the analysis of W proteins except that strains of same species grouped together. This is the first comprehensive study describing in detail the genetic variations and the molecular evolution of P gene edited, accessory viral proteins of Avian paramyxoviruses.
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Affiliation(s)
| | - Ravi Kumar Gandham
- National Institute of Animal Biotechnology, Hyderabad, 500032, Telangana, India
| | - Madhuri Subbiah
- National Institute of Animal Biotechnology, Hyderabad, 500032, Telangana, India.
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7
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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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Liu YP, Kuo ST, Chiou CJ, Terregino C, Tsai HJ. Novel avian metaavulavirus isolated from birds of the family Columbidae in Taiwan. Vet Microbiol 2019; 236:108377. [PMID: 31500723 DOI: 10.1016/j.vetmic.2019.07.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/31/2019] [Accepted: 07/31/2019] [Indexed: 01/06/2023]
Abstract
Avian paramyxoviruses (APMVs) consist of twenty known species and have been isolated from domestic and wild birds around the world. In 2009, the isolate APMV/dove/Taiwan/AHRI33/2009 was isolated from swabs of red turtle doves (Streptopelia tranquebarica) during active surveillance of avian influenza in resident birds in Taiwan, and it was initially identified as paramyxovirus based on electron microscopy. Hemagglutination inhibition assays indicated antigenic heterogeneity of AHRI33 with the known APMV-1, -2, -3, -4, -6, -8, and -9 species, only showing weak but measurable cross-reactivity with APMV-7. Pathogenicity ICPI test revealed that the virus was avirulent for chickens. The AHRI33 virus genome revealed a typical APMV structure consisting of six genes 3'-NP-P-M-F-HN-L-5', and the length of the genome was 16,914 nucleotides, the third longest among the members of the subfamily Avulavirinae. Estimates of the nucleotide sequence identities of the genome between each prototype of APMVs had shown AHRI33 to be more closely related to APMV-7 than to the others, with a sequence identity of 62.8%. Based on topology of the phylogenetic tree of RdRp genes and the branch length between the nearest node and the tip of the branch, AHRI33 met the criteria for designation as distinct species. Together, the data suggest that the isolate APMV/dove/Taiwan/AHRI33/2009 should be considered as the prototype strain of the new species Avian metaavulavirus 21 in the genus Metaavulavirus in the subfamily Avulavirinae.
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Affiliation(s)
- Yu-Pin Liu
- Animal Health Research Institute, 376 Chung-Cheng Road, Tamsui District, New Taipei City, 25158, Taiwan; Graduate Institute of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei, 10617, Taiwan
| | - Shu-Ting Kuo
- Animal Health Research Institute, 376 Chung-Cheng Road, Tamsui District, New Taipei City, 25158, Taiwan
| | - Chwei-Jang Chiou
- Animal Health Research Institute, 376 Chung-Cheng Road, Tamsui District, New Taipei City, 25158, Taiwan
| | - Calogero Terregino
- OIE/FAO and National Reference Laboratory for Newcastle Disease and Avian Influenza, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università, 10-35020, Legnaro, PD, Italy
| | - Hsiang-Jung Tsai
- Graduate Institute of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei, 10617, Taiwan.
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9
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The Emergence of Avian Orthoavulavirus 13 in Wild Migratory Waterfowl in China Revealed the Existence of Diversified Trailer Region Sequences and HN Gene Lengths within this Serotype. Viruses 2019; 11:v11070646. [PMID: 31337066 PMCID: PMC6669871 DOI: 10.3390/v11070646] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 01/01/2023] Open
Abstract
Avian orthoavulavirus 13 (AOAV-13), also named avian paramyxovirus 13 (APMV-13), has been found sporadically in wild birds around the world ever since the discovery of AOAV-13 (AOAV-13/wild goose/Shimane/67/2000) in a wild goose from Japan in 2000. However, there are no reports of AOAV-13 in China. In the present study, a novel AOAV-13 virus (AOAV-13/wild goose/China/Hubei/V93-1/2015), isolated from a wild migratory waterfowl in a wetland of Hubei province of China, during active surveillance from 2013 to 2018, was biologically and genetically characterized. Phylogenetic analyses demonstrated a very close genetic relationship among all AOAV-13 strains, as revealed by very few genetic variations. Moreover, pathogenicity tests indicated that the V93-1 strain is a low virulent virus for chickens. However, the genome of the V93-1 virus was found to be 16,158 nucleotides (nt) in length, which is 12 nt or 162 nt longer than the other AOAV-13 strains that have been reported to date. The length difference of 12 nt in strain V93-1 is due to the existence of three repeats of the conserved sequence, “AAAAAT”, in the 5′-end trailer of the genome. Moreover, the HN gene of the V93-1 virus is 2070 nt in size, encoding 610 aa, which is the same size as the AOAV-13 strain from Japan, whereas that of two strains from Ukraine and Kazakhstan are 2080 nt in length, encoding 579 aa. We describe a novel AOAV-13 in migratory waterfowl in China, which suggests that diversified trailer region sequences and HN gene lengths exist within serotype AOAV-13, and highlight the need for its constant surveillance in poultry from live animal markets, and especially migratory birds.
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10
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Yuan X, Meng K, Zhang Y, Yu Z, Wang Y, Ai W. Genetic characterization of one duck-origin paramyxovirus type 4 strain in China. Transbound Emerg Dis 2019; 66:2171-2174. [PMID: 31131964 DOI: 10.1111/tbed.13258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 05/06/2019] [Accepted: 05/20/2019] [Indexed: 11/30/2022]
Abstract
Avian paramyxovirus type 4 (APMV-4) has been frequently reported from wildfowl and waterfowl in recent year. However, few studies have reported on the molecular characteristics and regional transmission of APMV-4, knowledge of which is important for understanding the genetic diversity and epidemiology of avian paramyxovirus. Herein, we report the isolation of one APMV-4 strain, designated as QY17, from the duck in eastern China. The determined complete genome of the isolate with six gene segments 3'-N-P-M-F-HN-L-5' was 15,054 nt in length. Genetic analysis of the whole-fusion gene of this isolate showed that QY17 was derived from a Eurasian lineage. Further phylogenetic analysis showed that the duck-origin strain QY17 had a highly genetic relationship with representative APMV-4 strains from wildfowl in neighbouring regions. These genetic results suggested that APMV-4 viral exchange may occur in wildfowl and poultry via wild bird migration.
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Affiliation(s)
- Xiaoyuan Yuan
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Ji'nan, China
| | - Kai Meng
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Ji'nan, China
| | - Yuxia Zhang
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Ji'nan, China
| | - Zhijun Yu
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Ji'nan, China
| | - Youling Wang
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Ji'nan, China
| | - Wu Ai
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Ji'nan, China
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11
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Antarctic Penguins as Reservoirs of Diversity for Avian Avulaviruses. J Virol 2019; 93:JVI.00271-19. [PMID: 30894472 PMCID: PMC6532105 DOI: 10.1128/jvi.00271-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 03/05/2019] [Indexed: 02/06/2023] Open
Abstract
Approximately 99% of all viruses are still to be described, and in our changing world, any one of these unknown viruses could potentially expand their host range and cause epidemic disease in wildlife, agricultural animals, or humans. Avian avulavirus 1 causes outbreaks in wild birds and poultry and is thus well described. However, for many avulavirus species, only a single specimen has been described, and their viral ecology and epidemiology are unknown. Through the detection of avian avulaviruses in penguins from Antarctica, we have been able to expand upon our understanding of three avian avulavirus species (avian avulaviruses 17 to 19) and report a potentially novel avulavirus species. Importantly, we show that penguins appear to play a key role in the epidemiology of avian avulaviruses, and we encourage additional sampling of this avian group. Wild birds harbor a huge diversity of avian avulaviruses (formerly avian paramyxoviruses). Antarctic penguin species have been screened for avian avulaviruses since the 1980s and, as such, are known hosts of these viruses. In this study, we screened three penguin species from the South Shetland Islands and the Antarctic Peninsula for avian avulaviruses. We show that Adelie penguins (Pygoscelis adeliae) are hosts for four different avian avulavirus species, the recently described avian avulaviruses 17 to 19 and avian avulavirus 10-like, never before isolated in Antarctica. A total of 24 viruses were isolated and sequenced; avian avulavirus 17 was the most common, and phylogenetic analysis demonstrated patterns of occurrence, with different genetic clusters corresponding to penguin age and location. Following infection in specific-pathogen-free (SPF) chickens, all four avian avulavirus species were shed from the oral cavity for up to 7 days postinfection. There was limited shedding from the cloaca in a proportion of infected chickens, and all but one bird seroconverted by day 21. No clinical signs were observed. Taken together, we propose that penguin species, including Antarctic penguins, may be the central reservoir for a diversity of avian avulavirus species and that these viruses have the potential to infect other avian hosts. IMPORTANCE Approximately 99% of all viruses are still to be described, and in our changing world, any one of these unknown viruses could potentially expand their host range and cause epidemic disease in wildlife, agricultural animals, or humans. Avian avulavirus 1 causes outbreaks in wild birds and poultry and is thus well described. However, for many avulavirus species, only a single specimen has been described, and their viral ecology and epidemiology are unknown. Through the detection of avian avulaviruses in penguins from Antarctica, we have been able to expand upon our understanding of three avian avulavirus species (avian avulaviruses 17 to 19) and report a potentially novel avulavirus species. Importantly, we show that penguins appear to play a key role in the epidemiology of avian avulaviruses, and we encourage additional sampling of this avian group.
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12
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Novel avian paramyxovirus-based vaccine vectors expressing the Ebola virus glycoprotein elicit mucosal and humoral immune responses in guinea pigs. Sci Rep 2019; 9:5520. [PMID: 30940854 PMCID: PMC6445115 DOI: 10.1038/s41598-019-42004-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 03/21/2019] [Indexed: 11/24/2022] Open
Abstract
Paramyxovirus vaccine vectors based on human parainfluenza virus type 3 (HPIV-3) and Newcastle disease virus (NDV) have been previously evaluated against Ebola virus (EBOV) challenge. Although both the viral vectored vaccines efficiently induce protective immunity, some concerns remain to be solved. Since HPIV-3 is a common human pathogen, the human population has pre-existing immunity to HPIV-3, which may restrict the replication of the vaccine vector. For NDV, mesogenic (intermediate virulent) strain used in previous studies is currently classified as a Select Agent in the United States, thus making it unsuitable to be used as a vaccine vector. To overcome these concerns, we have developed a modified NDV vector based on a mesogenic NDV strain, in which the ectodomains of envelope glycoproteins were replaced with the corresponding ectodomains from avian paramyxovirus serotype 3 (APMV-3). The modified NDV vector was highly attenuated in chickens and was able to express the EBOV glycoprotein (GP) gene at high level. In addition, the recombinant APMV-3 was also evaluated as a vaccine vector to express the EBOV GP gene. Guinea pigs immunized with these two vector vaccines developed high levels of neutralizing GP-specific IgG and IgA antibodies.
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13
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Karamendin KO, Sayatov MK, Kydyrmanov AI, Kasymbekov ET, Asanova SE, Daulbayeva KD, Khan EY. [Molecular-genetic characterization of Avian avulavirus 20 strains isolated from wild birds.]. Vopr Virusol 2019; 64:185-192. [PMID: 32163685 DOI: 10.36233/0507-4088-2019-64-4-185-192] [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: 09/07/2018] [Accepted: 10/31/2018] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Previously unknown paramyxovirus strains were isolated from wild birds in 2013-2014 in Kazakhstan and subsequently identified as representatives of the novel Avian avulavirus 20 species. The aims and tasks were molecular genetic characterization of novel avulaviruses and investigation of their phylogenetic relationships. MATERIAL AND METHODS Embryonated chicken eggs were inoculated with cloacal and tracheal swabs from wild birds with subsequent virus isolation. The complete nucleotide sequences of viral genomes were obtained by massive parallel sequencing with subsequent bioinformatics processing. RESULTS By initial infection of chicken embryos with samples from 179 wild birds belonging to the Anatidae, Laridae, Scolopacidae and Charadriidae families, 19 hemagglutinating agents were isolated, and five of them were identified as representatives of new viral species. The study of their sequenced genomes revealed their similarity in size, but there was a significant genetic variability within the species. 2,640 nucleotide substitutions were identified and 273 of them were nonsynonymous, influencing the protein structure of viruses. It was shown that isolates Avian avulavirus 20/black-headed gull/Balkhash/5844/2013 and Avian avulavirus 20 /great black-headed gull/Atyrau/5541/2013 were 86% and 95% respectively identical to the previously described reference strain, indicating a significant evolutionary divergence within species. DISCUSSION The authors suggest the existence of two independent lineages - the Caspian, represented by the reference strain Aktau/5976 and Atyrau/5541, as well as the second, geographically significantly distant Balkhash lineage. CONCLUSION The study confirms the role of the birds of the Laridae family as the main reservoir of Avian avulavirus 20 in the avifauna that plays a key role in maintaining viruses of the genus Avulavirus in the biosphere and is a potential natural source for the emergence of new viral variants. Continuous surveillance of them in the wild is one of the most important tasks in ensuring the safety of the poultry industry.
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Affiliation(s)
- K O Karamendin
- SPC for Microbiology and Virology, Almaty, 050010, Kazakhstan
| | - M K Sayatov
- SPC for Microbiology and Virology, Almaty, 050010, Kazakhstan
| | - A I Kydyrmanov
- SPC for Microbiology and Virology, Almaty, 050010, Kazakhstan
| | - E T Kasymbekov
- SPC for Microbiology and Virology, Almaty, 050010, Kazakhstan
| | - S E Asanova
- SPC for Microbiology and Virology, Almaty, 050010, Kazakhstan
| | - K D Daulbayeva
- SPC for Microbiology and Virology, Almaty, 050010, Kazakhstan
| | - E Y Khan
- SPC for Microbiology and Virology, Almaty, 050010, Kazakhstan
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14
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Aziz-ul-Rahman, Munir M, Shabbir MZ. Comparative evolutionary and phylogenomic analysis of Avian avulaviruses 1–20. Mol Phylogenet Evol 2018; 127:931-951. [DOI: 10.1016/j.ympev.2018.06.040] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 05/15/2018] [Accepted: 06/25/2018] [Indexed: 12/20/2022]
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15
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Chen Y, Ding Z, Liu X, Chen J, Li J, Fei Y, Liu Z, Stoeger T, Bi Y, Yin R. Biological and phylogenetic characterization of a novel hemagglutination-negative avian avulavirus 6 isolated from wild waterfowl in China. Transbound Emerg Dis 2018; 65:1421-1428. [PMID: 30146734 PMCID: PMC7169737 DOI: 10.1111/tbed.13005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/08/2018] [Accepted: 08/21/2018] [Indexed: 02/05/2023]
Abstract
Up to now only nine whole genome sequences of avian avulavirus 6 (AAvV‐6) had been documented in the world since the first discovery of AAvV‐6 (AAvV‐6/duck/HongKong/18/199/77) at a domestic duck in 1977 from Hong Kong of China. Very limited information is known about the regularities of transmission, genetic and biological characteristics of AAvV‐6 because of the lower isolation rate and mild losses for poultry industry. To better further explore the relationships among above factors, an AAvV‐6 epidemiological surveillance of domestic poultry and wild birds in six provinces of China suspected of sites of inter‐species transmission and being intercontinental flyways during the year 2013–2017 was conducted. Therefore, 9,872 faecal samples from wild birds and 1,642 cloacal and tracheal swab samples from clinically healthy poultry of live bird market (LBM) were collected respectively. However, only one novel hemagglutination‐negative AAvV‐6 isolate (AAvV‐6/mallard/Hubei/2015) was isolated from a fresh faecal sample obtained from mallard at a wetland of Hubei province. Sequencing and phylogenetic analyses of this AAvV‐6 isolate (AAvV‐6/mallard/Hubei/2015) indicated that this isolate grouping to genotype I were epidemiological intercontinentally linked with viruses from the wild birds in Europe and America. Meanwhile, at least two genotypes (I and II) are existed within serotype AAvV‐6. In additional, this novel hemagglutination‐negative AAvV‐6 isolate in chicken embryos restored its hemagglutination when pre‐treated with trypsin. These findings, together with data from other AAvV‐6, suggest potential epidemiological intercontinental spreads among AAvV‐6 transmission by wild migratory birds, and reveal potential threats to wild birds and domestic poultry worldwide.
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Affiliation(s)
- Yanyu Chen
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Zhuang Ding
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xinxin Liu
- College of Food Science and Engineering, Jilin University, Changchun, China
| | - Jianjun Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Hubei, China
| | - Junjiao Li
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yidong Fei
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Zhe Liu
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Tobias Stoeger
- Comprehensive Pneumology Center, Institute of Lung Biology and Disease (iLBD), Helmholtz Zentrum Muenchen, Munich, Germany
| | - Yuhai Bi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Renfu Yin
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Jilin University, Changchun, China
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16
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Aly SE, Hussein HA, Aly¹ AHM, Abdel-Baky MH, El-Sanousi AA. Assessment of in vitro potency of inactivated Newcastle disease oil-adjuvanted vaccines using hemagglutination test and blocking ELISA. Vet World 2018; 11:1222-1228. [PMID: 30410225 PMCID: PMC6200565 DOI: 10.14202/vetworld.2018.1222-1228] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 07/20/2018] [Indexed: 11/20/2022] Open
Abstract
AIM The present study was aimed to establish a protocol for the evaluation of the in vitro potency of commercial inactivated Newcastle disease virus (NDV) oil-adjuvanted vaccines using hemagglutination test (HA) and blocking ELISA (B-ELISA) based on polyclonal antibodies. MATERIALS AND METHODS Aqueous phases from a total of 47 batches of inactivated NDV vaccines manufactured by 20 different companies were extracted with isopropyl myristate. The viral antigen in each sample was detected and quantified by a standard HA test and a B-ELISA assay. To verify the efficiency of the antigen extraction method used in the batches which showed HA and to test the validity of using in vitro antigen quantification by HA and B-ELISA tests, a subset of 13 batches (selected from the total 47 batches) was inoculated in groups of 3-4-week-old specific pathogen-free chickens using the recommended vaccine dose. The immunogenicity of the selected vaccine batches was assessed by the NDV-hemagglutination inhibition antibody titers in individual serum samples collected 4 weeks after vaccination. Further, the efficacy of the vaccines and their protection rates were determined by a challenge test carried out for the vaccinated chickens with the Egyptian 2012 isolate of the virulent NDV genotype VII. RESULTS A strong correlation was observed between HA titers and B-ELISA mean titers in the tested 47 batches (R2=0.817). This indicated the possibility of using the latter in vitro assays for vaccine potency assessment. The recommended protective NDV antigen titer measured by B-ELISA was determined to be 28 ELISA units per dose. The comparison between the HA titers of the aqueous extracts of test vaccines and the corresponding results of in vivo potency assays (i.e., immunogenicity and efficacy), including antibody titers in the serum of vaccinated birds, indicated that the efficiency of the antigen extraction used may interfere with obtaining a strong correlation between the in vitro and in vivo results. CONCLUSION HA or B-ELISA tests can be used as rapid and cost-effective alternatives to traditional in vivo potency tests for vaccine potency assessment by quantifying the NDV antigen present in aqueous phase extracts of the tested vaccines. The latter in vitro protocol, however, requires efficient extraction of the antigen to be able to obtain good correlation with the traditional in vivo potency tests.
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Affiliation(s)
- Saleh E. Aly
- Central Laboratory for Evaluation of Veterinary Biologics, Abbasia 11381, Egypt
| | - Hussein Ali Hussein
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
| | - Abdel-Hakim M. Aly¹
- Central Laboratory for Evaluation of Veterinary Biologics, Abbasia 11381, Egypt
| | | | - Ahmed A. El-Sanousi
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
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17
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Amarasinghe GK, Aréchiga Ceballos NG, Banyard AC, Basler CF, Bavari S, Bennett AJ, Blasdell KR, Briese T, Bukreyev A, Caì Y, Calisher CH, Campos Lawson C, Chandran K, Chapman CA, Chiu CY, Choi KS, Collins PL, Dietzgen RG, Dolja VV, Dolnik O, Domier LL, Dürrwald R, Dye JM, Easton AJ, Ebihara H, Echevarría JE, Fooks AR, Formenty PBH, Fouchier RAM, Freuling CM, Ghedin E, Goldberg TL, Hewson R, Horie M, Hyndman TH, Jiāng D, Kityo R, Kobinger GP, Kondō H, Koonin EV, Krupovic M, Kurath G, Lamb RA, Lee B, Leroy EM, Maes P, Maisner A, Marston DA, Mor SK, Müller T, Mühlberger E, Ramírez VMN, Netesov SV, Ng TFF, Nowotny N, Palacios G, Patterson JL, Pawęska JT, Payne SL, Prieto K, Rima BK, Rota P, Rubbenstroth D, Schwemmle M, Siddell S, Smither SJ, Song Q, Song T, Stenglein MD, Stone DM, Takada A, Tesh RB, Thomazelli LM, Tomonaga K, Tordo N, Towner JS, Vasilakis N, Vázquez-Morón S, Verdugo C, Volchkov VE, Wahl V, Walker PJ, Wang D, Wang LF, Wellehan JFX, Wiley MR, Whitfield AE, Wolf YI, Yè G, Zhāng YZ, Kuhn JH. Taxonomy of the order Mononegavirales: update 2018. Arch Virol 2018; 163:2283-2294. [PMID: 29637429 PMCID: PMC6076851 DOI: 10.1007/s00705-018-3814-x] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 03/12/2018] [Indexed: 11/27/2022]
Abstract
In 2018, the order Mononegavirales was expanded by inclusion of 1 new genus and 12 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV) and summarizes additional taxonomic proposals that may affect the order in the near future.
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Affiliation(s)
- Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | | | | | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Sina Bavari
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Andrew J Bennett
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Kim R Blasdell
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, VIC, Australia
| | - Thomas Briese
- Department of Epidemiology, Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | | | - Yíngyún Caì
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Charles H Calisher
- Arthropod-Borne and Infectious Diseases Laboratory, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Cristine Campos Lawson
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Colin A Chapman
- Department of Anthropology and McGill School of Environment, McGill University, Montreal, QC, Canada
- Wildlife Conservation Society, Bronx, NY, USA
- Section of Social Systems Evolution, Primate Research Institute, Kyoto University, Kyoto, Japan
| | | | - Kang-Seuk Choi
- Avian Disease Research Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Peter L Collins
- Respiratory Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MA, USA
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Valerian V Dolja
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA
| | - Olga Dolnik
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Leslie L Domier
- Department of Crop Sciences, University of Illinois, Chicago, IL, USA
| | | | - John M Dye
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Andrew J Easton
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hideki Ebihara
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Juan E Echevarría
- National Center of Microbiology, Carlos III Institute of Health, Majadahonda, Madrid, Spain
| | | | | | - Ron A M Fouchier
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Conrad M Freuling
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institute, WHO Collaborating Centre for Rabies Surveillance and Research, Greifswald-Insel Riems, Germany
| | - Elodie Ghedin
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Tony L Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Roger Hewson
- Public Health England, Porton Down, Salisbury, Wiltshire, UK
| | - Masayuki Horie
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
| | - Timothy H Hyndman
- College of Veterinary Medicine, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Dàohóng Jiāng
- State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology of Húběi Province, College of Plant Science and Technology, Huázhōng Agricultural University, Wuhan, China
| | - Robert Kityo
- Department of Zoology, Makerere University, Kampala, Uganda
| | - Gary P Kobinger
- Department of Microbiology, Immunology and Infectious Diseases, Université Laval, Quebec City, Canada
| | - Hideki Kondō
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mart Krupovic
- Department of Microbiology, Institut Pasteur, Paris, France
| | - Gael Kurath
- US Geological Survey Western Fisheries Research Center, Seattle, WA, USA
| | - Robert A Lamb
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Howard Hughes Medical Institute, Northwestern University, Evanston, IL, USA
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric M Leroy
- Centre International de Recherches Médicales de Franceville, Institut de Recherche pour le Développement, Franceville, Gabon
| | - Piet Maes
- Zoonotic Infectious Diseases Unit, KU Leuven, Leuven, Belgium
| | - Andrea Maisner
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | | | - Sunil Kumar Mor
- Department of Veterinary Population Medicine and Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Thomas Müller
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institute, WHO Collaborating Centre for Rabies Surveillance and Research, Greifswald-Insel Riems, Germany
| | - Elke Mühlberger
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | | | - Sergey V Netesov
- Novosibirsk State University, Novosibirsk, Novosibirsk Oblast, Russia
| | - Terry Fei Fan Ng
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Norbert Nowotny
- Institute of Virology, University of Veterinary Medicine, Vienna, Austria
- Department of Basic Medical Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Jean L Patterson
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Janusz T Pawęska
- Center for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham, Johannesburg, Gauteng, South Africa
| | - Susan L Payne
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Karla Prieto
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Bertus K Rima
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, Northern Ireland, UK
| | - Paul Rota
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Dennis Rubbenstroth
- Institute of Virology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Martin Schwemmle
- Institute of Virology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stuart Siddell
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | | | - Qisheng Song
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO, USA
| | - Timothy Song
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Mark D Stenglein
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - David M Stone
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | - Ayato Takada
- Division of Global Epidemiology, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Robert B Tesh
- Department of Pathology and Center for Biodefense and Emerging Infectious Diseases, Center for Tropical Diseases and Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, TX, USA
| | | | - Keizō Tomonaga
- Institute for Frontier Life and Medical Sciences (inFront), Kyoto University, Kyoto, Japan
| | - Noël Tordo
- Institut Pasteur, Unité des Stratégies Antivirales, WHO Collaborative Centre for Viral Haemorrhagic Fevers and Arboviruses, OIE Reference Laboratory for RVFV and CCHFV, Paris, France
- Institut Pasteur de Guinée, Conakry, Guinea
| | - Jonathan S Towner
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Nikos Vasilakis
- Department of Pathology and Center for Biodefense and Emerging Infectious Diseases, Center for Tropical Diseases and Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, TX, USA
| | - Sonia Vázquez-Morón
- National Center of Microbiology, Carlos III Institute of Health, Majadahonda, Madrid, Spain
| | - Claudio Verdugo
- Universidad Austral de Chile Facultad de Ciencias Veterinarias, Valdivia, Chile
| | - Viktor E Volchkov
- Molecular Basis of Viral Pathogenicity, CIRI, INSERM U1111-CNRS, UMR5308, Université de Lyon, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Victoria Wahl
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD, USA
| | - Peter J Walker
- School of Biological Sciences, University of Queensland, St. Lucia, QLD, Australia
| | - David Wang
- Departments of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - James F X Wellehan
- College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Michael R Wiley
- The University of Texas Medical Branch, Galveston, TX, USA
- University of Nebraska Medical Center, Omaha, NE, USA
| | - Anna E Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Gōngyín Yè
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yǒng-Zhèn Zhāng
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA.
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Molecular characterization and genetic diversity of avian paramyxovirus type 4 isolated in South Korea from 2013 to 2017. INFECTION GENETICS AND EVOLUTION 2018; 61:127-133. [DOI: 10.1016/j.meegid.2018.03.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 03/17/2018] [Accepted: 03/25/2018] [Indexed: 11/19/2022]
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19
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Neira V, Tapia R, Verdugo C, Barriga G, Mor S, Ng TFF, García V, Del Río J, Rodrigues P, Briceño C, Medina RA, González-Acuña D. Novel Avulaviruses in Penguins, Antarctica. Emerg Infect Dis 2018. [PMID: 28628443 PMCID: PMC5512496 DOI: 10.3201/eid2307.170054] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We identified 3 novel and distinct avulaviruses from Gentoo penguins sampled in Antarctica. We isolated these viruses and sequenced their complete genomes; serologic assays demonstrated that the viruses do not have cross-reactivity between them. Our findings suggest that these 3 new viruses represent members of 3 novel avulavirus species.
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20
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Genetic Diversity of Avian Paramyxovirus Type 6 Isolated from Wild Ducks in the Republic of Korea. J Wildl Dis 2018. [PMID: 29517403 DOI: 10.7589/2017-07-158] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Eleven avian paramyxovirus type 6 (APMV-6) isolates from Eurasian Wigeon ( n=5; Anas penelope), Mallards ( n=2; Anas platyrhynchos), and unknown species of wild ducks ( n=4) from Korea were analyzed based on the nucleotide (nt) and deduced amino acid sequences of the fusion (F) gene. Fecal samples were collected in 2010-14. Genotypes were assigned based on phylogenetic analyses. Our results revealed that APMV-6 could be classified into at least two distinct genotypes, G1 and G2. The open reading frame (ORF) of the G1 genotype was 1,668 nt in length, and the putative F0 cleavage site sequence was 113PAPEPRL119. The G2 genotype viruses included five isolates from Eurasian wigeons and four isolates from unknown waterfowl species, together with two reference APMV-6 strains from the Red-necked Stint ( Calidris ruficollis) from Japan and an unknown duck from Italy. There was an N-truncated ORF (1,638 nt), due to an N-terminal truncation of 30 nt in the signal peptide region of the F gene, and the putative F0 cleavage site sequence was 103SIREPRL109. The genetic diversity and ecology of APMV-6 are discussed.
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21
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Zhao N, Grund C, Beer M, Harder TC. Engineered recombinant protein products of the avian paramyxovirus type-1 nucleocapsid and phosphoprotein genes for serological diagnosis. Virol J 2018; 15:8. [PMID: 29325564 PMCID: PMC5765633 DOI: 10.1186/s12985-018-0924-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 01/08/2018] [Indexed: 11/29/2022] Open
Abstract
Background Virulent Newcastle disease virus (NDV, avian Avulavirus-1, APMV-1) induces a highly contagious and lethal systemic disease in gallinaceous poultry. APMV-1 antibody detection is used for surveillance and to control vaccination, but is hampered by cross-reactivity to other subtypes of avian Avulaviruses. Data are lacking concerning the applicability of NDV V proteins as differential diagnostic marker to distinguish vaccinated from virus-infected birds (DIVA strategy). Methods Full length and C-terminally truncated nucleocapsid (NP) protein, and the unique C-terminal regions of the phospho- (P) and V proteins of the NDV LaSota strain were bacterially expressed as fusion proteins with the multimerization domain of the human C4 binding protein, and used as diagnostic antigens in indirect ELISA. Results When used as diagnostic antigen in indirect ELISAs, recombinant full-length proved to be a sensitive target to detect seroconversion in chickens after APMV-1 vaccination and infection, but revealed some degree of cross reactivity with sera raised against other APMV subtypes. Cross reactivity was abolished but also sensitivity decreased when employing a C-terminal fragment of the NP of NDV as diagnostic antigen. Antibodies to the NDV V protein were mounted in poultry following NDV infection but also, albeit at lower rates and titers, after vaccination with attenuated NDV vaccines. V-specific seroconversion within the flock was incomplete and titers in individual bird transient. Conclusions Indirect ELISA based on bacterially expressed recombinant full-length NP compared favorably with a commercial NDV ELISA based on whole virus antigen, but cross reactivity between the NP proteins of different APMV subtypes could compromise specificity. However, specificity increased when using a less conserved C-terminal fragment of NP instead. Moreover, a serological DIVA strategy built on the NDV V protein was not feasible due to reduced immunogenicity of the V protein and frequent use of live-attenuated NDV vaccines. Electronic supplementary material The online version of this article (10.1186/s12985-018-0924-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Na Zhao
- The Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Suedufer 10, 17493, Greifswald, Germany
| | - Christian Grund
- The Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Suedufer 10, 17493, Greifswald, Germany
| | - Martin Beer
- The Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Suedufer 10, 17493, Greifswald, Germany
| | - Timm C Harder
- The Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Suedufer 10, 17493, Greifswald, Germany.
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22
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Karamendin K, Kydyrmanov A, Kasymbekov Y, Asanova S, Daulbayeva K, Seidalina A, Khan E, Harrison SM, Carr IM, Goodman SJ, Moldakozhayev A, Sayatov M. Novel avian paramyxovirus isolated from gulls in Caspian seashore in Kazakhstan. PLoS One 2017; 12:e0190339. [PMID: 29284037 PMCID: PMC5746266 DOI: 10.1371/journal.pone.0190339] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 12/07/2017] [Indexed: 01/30/2023] Open
Abstract
Three isolates APMV/gull/Kazakhstan/5976/2014, APMV/gull/Kazakhstan/ 5977/2014 and APMV/gull/Kazakhstan/5979/2014, were obtained from independent samples during annual surveillance for avian influenza and paramyxoviruses in wild birds from the Caspian Sea coast in Western Kazakhstan, and were initially identified as putative paramyxoviruses on the basis of electron microscopy. Hemagglutination Inhibition Assays with antisera to nine known APMV serotypes (APMV1-9) indicated no relation to any of them. Next generation sequencing of whole genome sequences indicated the three isolates were genetically identical, and had a nucleotide structure typical for all APMVs, consisting of six genes 3'-NP-P-M-F-HN-L-5'. Phylogenetic analyses, and assessment of amino acid identities, suggested the most closely related lineages to be APMV-2, 8, 10 and 15, but the novel isolate had less than 64% identity to them and all other known avian paramyxoviruses. This value was above levels considered to generally define other APMV serotypes. Estimates of the evolutionary divergence of the nucleotide sequences of the genomes of APMVs have shown that novel Kazakhstan APMV strain was closest to APMV-2, APMV-8, APMV-10 and APMV-15, with calculated distance values of 2.057, 2.058, 2.026 and 2.286 respectively, which is above values considered to differentiate other serotypes (observed minimum was 1.108 between APMV-1 and recently isolated APMV/UPO216/Korea). Together, the data suggest that isolate APMV/gull/Kazakhstan/5976/2014 and other two should be considered as the first representative of a novel APMV-20 group, and is the first time that avian paramyxoviruses have been found infecting members of the gull family, extending the known taxonomic host range.
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Affiliation(s)
- Kobey Karamendin
- Laboratory of Viral Ecology, Institute of Microbiology and Virology, Almaty, Kazakhstan
- * E-mail:
| | - Aidyn Kydyrmanov
- Laboratory of Viral Ecology, Institute of Microbiology and Virology, Almaty, Kazakhstan
| | | | - Saule Asanova
- Laboratory of Viral Ecology, Institute of Microbiology and Virology, Almaty, Kazakhstan
| | - Klara Daulbayeva
- Laboratory of Viral Ecology, Institute of Microbiology and Virology, Almaty, Kazakhstan
| | - Aigerim Seidalina
- Laboratory of Viral Ecology, Institute of Microbiology and Virology, Almaty, Kazakhstan
| | - Elizaveta Khan
- Laboratory of Viral Ecology, Institute of Microbiology and Virology, Almaty, Kazakhstan
| | - Sally M. Harrison
- School of Medicine, Faculty of Medicine and Health, University of Leeds, St. James’s University Hospital, Leeds, United Kingdom
| | - Ian M. Carr
- School of Medicine, Faculty of Medicine and Health, University of Leeds, St. James’s University Hospital, Leeds, United Kingdom
| | - Simon J. Goodman
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Alibek Moldakozhayev
- Laboratory of Viral Ecology, Institute of Microbiology and Virology, Almaty, Kazakhstan
| | - Marat Sayatov
- Laboratory of Viral Ecology, Institute of Microbiology and Virology, Almaty, Kazakhstan
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23
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Next-generation sequencing of five new avian paramyxoviruses 8 isolates from Kazakhstan indicates a low genetic evolution rate over four decades. Arch Virol 2017; 163:331-336. [PMID: 29058150 PMCID: PMC5799330 DOI: 10.1007/s00705-017-3593-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 08/22/2017] [Indexed: 11/06/2022]
Abstract
Five avian paramyxoviruses of serotype 8 (APMV-8) were isolated during a study monitoring wild birds in Kazakhstan in 2013 and each was further characterized. The viruses were isolated from three White-fronted geese (Anser albifrons), one Whooper swan (Cygnus cygnus), and one Little stint (Calidris minuta). Before our study, only two complete APMV-8 sequences had been reported worldwide since their discovery in the USA and Japan in the 1970s. We report the complete genome sequences of the newly detected viruses and analyze the genetic evolution of the APMV-8 viruses over four decades.
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24
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Jeong J, Kim Y, An I, Wang SJ, Kim Y, Lee HJ, Choi KS, Im SP, Min W, Oem JK, Jheong W. Complete genome sequence of a novel avian paramyxovirus isolated from wild birds in South Korea. Arch Virol 2017; 163:223-227. [PMID: 29038866 PMCID: PMC5756290 DOI: 10.1007/s00705-017-3588-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 09/23/2017] [Indexed: 11/03/2022]
Abstract
A novel avian paramyxovirus (APMV), Cheonsu1510, was isolated from wild bird feces in South Korea and serologically and genetically characterized. In hemagglutination inhibition tests, antiserum against Cheonsu1510 showed low reactivity with other APMVs and vice versa. The complete genome of Cheonsu1510 comprised 15,408 nucleotides, contained six open reading frames (3'-N-P-M-F-HN-L-5'), and showed low sequence identity to other APMVs (< 63%) and a unique genomic composition. Phylogenetic analysis revealed that Cheonsu1510 was related to but distinct from APMV-1, -9, and -15. These results suggest that Cheonsu1510 represents a new APMV serotype, APMV-17.
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Affiliation(s)
- Jipseol Jeong
- Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro42, Seo-gu, Incheon, 22689, Republic of Korea.
| | - Youngsik Kim
- Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro42, Seo-gu, Incheon, 22689, Republic of Korea
| | - Injung An
- Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro42, Seo-gu, Incheon, 22689, Republic of Korea
| | - Seung-Jun Wang
- Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro42, Seo-gu, Incheon, 22689, Republic of Korea
| | - Yongkwan Kim
- Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro42, Seo-gu, Incheon, 22689, Republic of Korea
| | - Hyun-Jeong Lee
- Avian Disease Research Division, Animal and Plant Quarantine Agency, 177 Hyeokshin 8-ro, Gimcheon, Republic of Korea
| | - Kang-Seuk Choi
- Avian Disease Research Division, Animal and Plant Quarantine Agency, 177 Hyeokshin 8-ro, Gimcheon, Republic of Korea
| | - Se-Pyeong Im
- College of Veterinary Medicine & Institute of Animal Medicine, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Wongi Min
- College of Veterinary Medicine & Institute of Animal Medicine, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Jae-Ku Oem
- Department of Veterinary Infectious Diseases, College of Veterinary Medicine, Chonbuk National University, Iksan, Republic of Korea
| | - Weonhwa Jheong
- Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro42, Seo-gu, Incheon, 22689, Republic of Korea
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25
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Sabra M, Dimitrov KM, Goraichuk IV, Wajid A, Sharma P, Williams-Coplin D, Basharat A, Rehmani SF, Muzyka DV, Miller PJ, Afonso CL. Phylogenetic assessment reveals continuous evolution and circulation of pigeon-derived virulent avian avulaviruses 1 in Eastern Europe, Asia, and Africa. BMC Vet Res 2017; 13:291. [PMID: 28950869 PMCID: PMC5615457 DOI: 10.1186/s12917-017-1211-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 09/22/2017] [Indexed: 01/24/2023] Open
Abstract
Background The remarkable diversity and mobility of Newcastle disease viruses (NDV) includes virulent viruses of genotype VI. These viruses are often referred to as pigeon paramyxoviruses 1 because they are normally isolated and cause clinical disease in birds from the Columbidae family. Genotype VI viruses occasionally infect, and may also cause clinical disease in poultry. Thus, the evolution, current spread and detection of these viruses are relevant to avian health. Results Here, we describe the isolation and genomic characterization of six Egyptian (2015), four Pakistani (2015), and two Ukrainian (2007, 2013) recent pigeon-derived NDV isolates of sub-genotype VIg. These viruses are closely related to isolates from Kazakhstan, Nigeria and Russia. In addition, eight genetically related NDV isolates from Pakistan (2014–2016) that define a new sub-genotype (VIm) are described. All of these viruses, and the ancestral Bulgarian (n = 2) and South Korean (n = 2) viruses described here, have predicted virulent cleavage sites of the fusion protein, and those selected for further characterization have intracerebral pathogenicity index assay values characteristic of NDV of genotype VI (1.31 to 1.48). A validated matrix gene real-time RT-PCR (rRT-PCR) NDV test detect all tested isolates. However, the validated rRT-PCR test that is normally used to identify the virulent fusion gene fails to detect the Egyptian and Ukrainian viruses due to mismatches in primers and probe. A new rapid rRT-PCR test to determine the presence of virulent cleavage sites for viruses from sub-genotypes VIg was developed and evaluated on these and other viruses. Conclusions We describe the almost simultaneous circulation and continuous evolution of genotype VI Newcastle disease viruses in distant locations, suggesting epidemiological connections among three continents. As pigeons are not migratory, this study suggests the need to understand the possible role of human activity in the dispersal of these viruses. Complete genomic characterization identified previously unrecognized genetic diversity that contributes to diagnostic failure and will facilitate future evolutionary studies. These results highlight the importance of conducting active surveillance on pigeons worldwide and the need to update existent rapid diagnostic protocols to detect emerging viral variants and help manage the disease in affected regions. Electronic supplementary material The online version of this article (10.1186/s12917-017-1211-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mahmoud Sabra
- Department of Poultry Diseases, Faculty of Veterinary Medicine, South Valley University, Qena, 83523, Egypt.,Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, USA
| | - Kiril M Dimitrov
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, USA
| | - Iryna V Goraichuk
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, USA.,National Scientific Center Institute of Experimental and Clinical Veterinary Medicine, 83 Pushkinskaya Street, Kharkiv, 61023, Ukraine
| | - Abdul Wajid
- Quality Operations Laboratory (QOL), University of Veterinary and Animal Sciences, Syed Abdul Qadir Jilani Road, Lahore, 54000, Pakistan.,Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Syed Abdul Qadir Jilani Road, Lahore, 54000, Pakistan
| | - Poonam Sharma
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, USA
| | - Dawn Williams-Coplin
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, USA
| | - Asma Basharat
- Quality Operations Laboratory (QOL), University of Veterinary and Animal Sciences, Syed Abdul Qadir Jilani Road, Lahore, 54000, Pakistan
| | - Shafqat F Rehmani
- Quality Operations Laboratory (QOL), University of Veterinary and Animal Sciences, Syed Abdul Qadir Jilani Road, Lahore, 54000, Pakistan
| | - Denys V Muzyka
- National Scientific Center Institute of Experimental and Clinical Veterinary Medicine, 83 Pushkinskaya Street, Kharkiv, 61023, Ukraine
| | - Patti J Miller
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, USA
| | - Claudio L Afonso
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, USA.
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26
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Bui VN, Trinh DQ, Abao LNB, Ozeki Y, Runstadler J, Nakamura K, Ogawa H, Imai K. Evaluation of the replication and pathogenicity of a variant avian paramyxovirus serotype 6 in mice. Arch Virol 2017; 162:3035-3043. [PMID: 28685285 DOI: 10.1007/s00705-017-3459-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 04/26/2017] [Indexed: 01/30/2023]
Abstract
Avian paramyxoviruses (APMVs) have been evaluated for their potential use as vaccine vectors, sparking research efforts leading to a better understanding of APMVs' replication and pathogenicity. However, within APMV serotypes, significant genetic diversity exists, and the infectivity of variant strains in mammals has not been studied. We utilized a mouse model to evaluate the pathogenicity of a variant strain of APMV-6 (APMV-6/red-necked stint/Japan/8KS0813/2008) in comparison with the prototype APMV-6 strain (APMV-6/duck/Hong Kong/18/199/1977). Although the two viruses differ substantially, both genetically and antigenically, we found that the variant and prototype strains could similarly replicate in respiratory tissues of infected mice and induce respiratory disease, sometimes resulting in death of the mice. Both viruses induced a humoral immune response that could be clearly detected by ELISA but which was poorly recognized by the hemagglutination inhibition test.
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Affiliation(s)
- Vuong Nghia Bui
- Diagnostic Center for Animal Health and Food Safety, 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
| | - Dai Quang Trinh
- Diagnostic Center for Animal Health and Food Safety, 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
| | - Lary N B Abao
- Diagnostic Center for Animal Health and Food Safety, Obihiro University of Agriculture and Veterinary Medicine, 2-11 Inada, Obihiro, Hokkaido, 080-8555, Japan.,Department of Agriculture-Agribusiness and Marketing Assistance Service, 1101, Quezon City, Philippines
| | - Yuki Ozeki
- Diagnostic Center for Animal Health and Food Safety, Obihiro University of Agriculture and Veterinary Medicine, 2-11 Inada, Obihiro, Hokkaido, 080-8555, Japan
| | | | - Kikuyasu Nakamura
- National Institute of Animal Health, Tsukuba, Ibaraki, 305-0856, Japan
| | - Haruko Ogawa
- Diagnostic Center for Animal Health and Food Safety, Obihiro University of Agriculture and Veterinary Medicine, 2-11 Inada, Obihiro, Hokkaido, 080-8555, Japan.
| | - Kunitoshi Imai
- Diagnostic Center for Animal Health and Food Safety, Obihiro University of Agriculture and Veterinary Medicine, 2-11 Inada, Obihiro, Hokkaido, 080-8555, Japan
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27
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Complete Genome Sequences of Four Avian Paramyxoviruses of Serotype 10 Isolated from Rockhopper Penguins on the Falkland Islands. GENOME ANNOUNCEMENTS 2017; 5:5/22/e00472-17. [PMID: 28572332 PMCID: PMC5454215 DOI: 10.1128/genomea.00472-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The first complete genome sequences of four avian paramyxovirus serotype 10 (APMV-10) isolates are described here. The viruses were isolated from rockhopper penguins on the Falkland Islands, sampled in 2007. All four genomes are 15,456 nucleotides in length, and phylogenetic analyses show them to be closely related.
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28
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Yin R, Zhang P, Liu X, Chen Y, Tao Z, Ai L, Li J, Yang Y, Li M, Xue C, Qian J, Wang X, Chen J, Li Y, Xiong Y, Zhang J, Stoeger T, Bi Y, Chen J, Ding Z. Dispersal and Transmission of Avian Paramyxovirus Serotype 4 among Wild Birds and Domestic Poultry. Front Cell Infect Microbiol 2017; 7:212. [PMID: 28603697 PMCID: PMC5445105 DOI: 10.3389/fcimb.2017.00212] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 05/10/2017] [Indexed: 11/13/2022] Open
Abstract
Avian paramyxovirus serotype 4 (APMV-4) is found sporadically in wild birds worldwide, and it is an economically important poultry pathogen. Despite the existence of several published strains, very little is known about the distribution, host species, and transmission of APMV-4 strains. To better understand the relationships among these factors, we conducted an APMV-4 surveillance of wild birds and domestic poultry in six provinces of China suspected of being intercontinental flyways and sites of interspecies transmission. APMV-4 surveillance was conducted in 9,160 wild birds representing seven species, and 1,461 domestic poultry in live bird markets (LMBs) from December 2013 to June 2016. The rate of APMV-4 isolation was 0.10% (11/10,621), and viruses were isolated from swan geese, bean geese, cormorants, mallards, and chickens. Sequencing and phylogenetic analyses of the 11 isolated viruses indicated that all the isolates belonging to genotype I were epidemiologically connected with wild bird-origin viruses from the Ukraine and Italy. Moreover, chicken-origin APMV-4 strains isolated from the LBMs were highly similar to wild bird-origin viruses from nearby lakes with free-living wild birds. In additional, a hemagglutination-negative APMV-4 virus was identified. These findings, together with recent APMV-4 studies, suggest potential virus interspecies transmission between wild birds and domestic poultry, and reveal possible epidemiological intercontinental connections between APMV-4 transmission by wild birds.
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Affiliation(s)
- Renfu Yin
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Jilin UniversityChangchun, China
| | - Pingze Zhang
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Jilin UniversityChangchun, China
| | - Xinxin Liu
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin UniversityChangchun, China
| | - Yanyu Chen
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Jilin UniversityChangchun, China
| | - Zhi Tao
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Jilin UniversityChangchun, China
| | - Lili Ai
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Jilin UniversityChangchun, China
| | - Junjiao Li
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Jilin UniversityChangchun, China
| | - Yingying Yang
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Jilin UniversityChangchun, China
| | - Mingxin Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of SciencesHubei, China
| | - Cong Xue
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Jilin UniversityChangchun, China
| | - Jing Qian
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Jilin UniversityChangchun, China
| | - Xueli Wang
- Department of Veterinary Basic Medicine, College of Animal Science and Technology, Inner Mongolia University for NationalitiesTongliao, China
| | - Jing Chen
- Hubei Wildlife Rescue, Research and Development CenterWuhan, China
| | - Yong Li
- Hubei Wildlife Rescue, Research and Development CenterWuhan, China
| | - Yanping Xiong
- Hubei Wildlife Rescue, Research and Development CenterWuhan, China
| | - Jun Zhang
- Hubei Wildlife Rescue, Research and Development CenterWuhan, China
| | - Tobias Stoeger
- Comprehensive Pneumology Center, Institute of Lung Biology and Disease (iLBD), Helmholtz Zentrum MuenchenMunich, Germany
| | - Yuhai Bi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of SciencesBeijing, China
| | - Jianjun Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of SciencesHubei, China
| | - Zhuang Ding
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Jilin UniversityChangchun, China
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Novel avian paramyxovirus (APMV-15) isolated from a migratory bird in South America. PLoS One 2017; 12:e0177214. [PMID: 28486490 PMCID: PMC5423646 DOI: 10.1371/journal.pone.0177214] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 04/24/2017] [Indexed: 11/19/2022] Open
Abstract
A novel avian paramyxovirus (APMV) isolated from a migratory bird cloacal swab obtained during active surveillance in April 2012 in the Lagoa do Peixe National Park, Rio Grande do Sul state, South of Brazil was biologically and genetically characterized. The nucleotide sequence of the full viral genome was completed using a next-generation sequencing approach. The genome was 14,952 nucleotides (nt) long, with six genes (3'-NP-P-M-F-HN-L-5') encoding 7 different proteins, typical of APMV. The fusion (F) protein gene of isolate RS-1177 contained 1,707 nucleotides in a single open reading frame encoding a protein of 569 amino acids. The F protein cleavage site contained two basic amino acids (VPKER↓L), typical of avirulent strains. Phylogenetic analysis of the whole genome indicated that the virus is related to APMV-10, -2 and -8, with 60.1% nucleotide sequence identity to the closest APMV-10 virus, 58.7% and 58.5% identity to the closest APMV-8 and APMV-2 genome, respectively, and less than 52% identity to representatives of the other APMVs groups. Such distances are comparable to the distances observed among other previously identified APMVs serotypes. These results suggest that unclassified/calidris_fuscicollis/Brazil/RS-1177/2012 is the prototype strain of a new APMV serotype, APMV-15.
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Lee HJ, Kim JY, Lee YJ, Lee EK, Song BM, Lee HS, Choi KS. A Novel Avian Paramyxovirus (Putative Serotype 15) Isolated from Wild Birds. Front Microbiol 2017; 8:786. [PMID: 28529504 PMCID: PMC5418332 DOI: 10.3389/fmicb.2017.00786] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/18/2017] [Indexed: 11/24/2022] Open
Abstract
In January 2014, a viral hemagglutinating agent named UPO216 was isolated from fecal droppings of wild birds at the UPO wetland in South Korea during an avian influenza surveillance program. Electron microscopy identified the UPO216 virus as an avian paramyxovirus (APMV). Pathogenicity tests and molecular pathotyping revealed that the virus was avirulent in chickens. The UPO216 virus was assigned to a serological group antigenically distinct from known serotypes of APMV (−1, −2, −3, −4, −6, −7, −8, and −9) by hemagglutination inhibition test, despite showing weak cross-reactivity with APMV-1 and APMV-9. The UPO216 virus RNA genome is 15,180 nucleotides (nts) in length, encodes 3′-N-P(V/W)-M-F-HN-L-5′ in that order, and shows unique genetic characteristics in terms of genomic composition and evolutionary divergence (0.43 or greater from known serotypes of APMV). Phylogenetic analysis revealed that the UPO216 occupies a branch separate from APMV-1, -9, -12, and -13. Serologic surveillance of wild birds (n = 880; 15 species, five Orders) detected UPO216-reactive antibodies in 4% (20/494) of serum samples taken from five species of wild duck belonging to the Order Anseriformes. In particular, UPO216-specific antibodies showing no cross-reaction with other serotypes of APMV were detected in four species: Eurasian teal (1/36), European wigeon (1/73), mallard (4/139), and Spot-Billed duck (1/137). These results indicate that the UPO216 virus has antigenically and genetically unique characteristics distinct from known serotypes of APMV and likely has been circulating widely in wild duck species of the Order Anseriformes. Thus, we propose the UPO216 isolate as a prototype strain of a novel APMV serotype (putative APMV-15).
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Affiliation(s)
- Hyun-Jeong Lee
- Avian Disease Division, Animal and Plant Quarantine AgencyGimcheon-si, South Korea
| | - Ji-Ye Kim
- Animal Veterinary Drugs and Biologics Division, Animal and Plant Quarantine AgencyGimcheon-si, South Korea
| | - Youn-Jeong Lee
- Avian Disease Division, Animal and Plant Quarantine AgencyGimcheon-si, South Korea
| | - Eun-Kyung Lee
- Avian Disease Division, Animal and Plant Quarantine AgencyGimcheon-si, South Korea
| | - Byoung-Min Song
- Avian Disease Division, Animal and Plant Quarantine AgencyGimcheon-si, South Korea
| | - Hee-Soo Lee
- Avian Disease Division, Animal and Plant Quarantine AgencyGimcheon-si, South Korea
| | - Kang-Seuk Choi
- Avian Disease Division, Animal and Plant Quarantine AgencyGimcheon-si, South Korea
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Dimitrov KM, Sharma P, Volkening JD, Goraichuk IV, Wajid A, Rehmani SF, Basharat A, Shittu I, Joannis TM, Miller PJ, Afonso CL. A robust and cost-effective approach to sequence and analyze complete genomes of small RNA viruses. Virol J 2017; 14:72. [PMID: 28388925 PMCID: PMC5384157 DOI: 10.1186/s12985-017-0741-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 03/29/2017] [Indexed: 01/26/2023] Open
Abstract
Background Next-generation sequencing (NGS) allows ultra-deep sequencing of nucleic acids. The use of sequence-independent amplification of viral nucleic acids without utilization of target-specific primers provides advantages over traditional sequencing methods and allows detection of unsuspected variants and co-infecting agents. However, NGS is not widely used for small RNA viruses because of incorrectly perceived cost estimates and inefficient utilization of freely available bioinformatics tools. Methods In this study, we have utilized NGS-based random sequencing of total RNA combined with barcode multiplexing of libraries to quickly, effectively and simultaneously characterize the genomic sequences of multiple avian paramyxoviruses. Thirty libraries were prepared from diagnostic samples amplified in allantoic fluids and their total RNAs were sequenced in a single flow cell on an Illumina MiSeq instrument. After digital normalization, data were assembled using the MIRA assembler within a customized workflow on the Galaxy platform. Results Twenty-eight avian paramyxovirus 1 (APMV-1), one APMV-13, four avian influenza and two infectious bronchitis virus complete or nearly complete genome sequences were obtained from the single run. The 29 avian paramyxovirus genomes displayed 99.6% mean coverage based on bases with Phred quality scores of 30 or more. The lower and upper quartiles of sample median depth per position for those 29 samples were 2984 and 6894, respectively, indicating coverage across samples sufficient for deep variant analysis. Sample processing and library preparation took approximately 25–30 h, the sequencing run took 39 h, and processing through the Galaxy workflow took approximately 2–3 h. The cost of all steps, excluding labor, was estimated to be 106 USD per sample. Conclusions This work describes an efficient multiplexing NGS approach, a detailed analysis workflow, and customized tools for the characterization of the genomes of RNA viruses. The combination of multiplexing NGS technology with the Galaxy workflow platform resulted in a fast, user-friendly, and cost-efficient protocol for the simultaneous characterization of multiple full-length viral genomes. Twenty-nine full-length or near-full-length APMV genomes with a high median depth were successfully sequenced out of 30 samples. The applied de novo assembly approach also allowed identification of mixed viral populations in some of the samples. Electronic supplementary material The online version of this article (doi:10.1186/s12985-017-0741-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kiril M Dimitrov
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, USA
| | - Poonam Sharma
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, USA
| | | | - Iryna V Goraichuk
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, USA.,National Scientific Center Institute of Experimental and Clinical Veterinary Medicine, 83 Pushkinskaya Street, Kharkiv, 61023, Ukraine
| | - Abdul Wajid
- Quality Operations Laboratory (QOL), University of Veterinary and Animal Sciences, Syed Abdul Qadir Jilani Road, Lahore, 54000, Pakistan.,Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Syed Abdul Qadir Jilani Road, Lahore, 54000, Pakistan
| | - Shafqat Fatima Rehmani
- Quality Operations Laboratory (QOL), University of Veterinary and Animal Sciences, Syed Abdul Qadir Jilani Road, Lahore, 54000, Pakistan
| | - Asma Basharat
- Quality Operations Laboratory (QOL), University of Veterinary and Animal Sciences, Syed Abdul Qadir Jilani Road, Lahore, 54000, Pakistan
| | - Ismaila Shittu
- Regional Laboratory for Animal Influenza and other Transboundary Animal Diseases, National Veterinary Research Institute, PMB01, Vom, 930010, Plateau State, Nigeria
| | - Tony M Joannis
- Regional Laboratory for Animal Influenza and other Transboundary Animal Diseases, National Veterinary Research Institute, PMB01, Vom, 930010, Plateau State, Nigeria
| | - Patti J Miller
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, USA
| | - Claudio L Afonso
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, USA.
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