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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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Young KT, Stephens JQ, Poulson RL, Stallknecht DE, Dimitrov KM, Butt SL, Stanton JB. Putative Novel Avian Paramyxovirus (AMPV) and Reidentification of APMV-2 and APMV-6 to the Species Level Based on Wild Bird Surveillance (United States, 2016-2018). Appl Environ Microbiol 2022; 88:e0046622. [PMID: 35612300 PMCID: PMC9195946 DOI: 10.1128/aem.00466-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/20/2022] [Indexed: 11/20/2022] Open
Abstract
Avian paramyxoviruses (APMVs) (subfamily Avulavirinae) have been isolated from over 200 species of wild and domestic birds around the world. The International Committee on Taxonomy of Viruses (ICTV) currently defines 22 different APMV species, with Avian orthoavulavirus 1 (whose viruses are designated APMV-1) being the most frequently studied due to its economic burden to the poultry industry. Less is known about other APMV species, including limited knowledge on the genetic diversity in wild birds, and there is a paucity of public whole-genome sequences for APMV-2 to -22. The goal of this study was to use MinION sequencing to genetically characterize APMVs isolated from wild bird swab samples collected during 2016 to 2018 in the United States. Multiplexed MinION libraries were prepared using a random strand-switching approach using 37 egg-cultured, influenza-negative, hemagglutination-positive samples. Forty-one APMVs were detected, with 37 APMVs having complete polymerase coding sequences allowing for species identification using ICTV's current Paramyxoviridae phylogenetic methodology. APMV-1, -4, -6, and -8 viruses were classified, one putative novel species (Avian orthoavulavirus 23) was identified from viruses isolated in this study, two putative new APMV species (Avian metaavulavirus 24 and 27) were identified from viruses isolated in this study and from retrospective GenBank sequences, and two putative new APMV species (Avian metaavulavirus 25 and 26) were identified solely from retrospective GenBank sequences. Furthermore, coinfections of APMVs were identified in four samples. The potential limitations of the branch length being the only species identification criterion and the potential benefit of a group pairwise distance analysis are discussed. IMPORTANCE Most species of APMVs are understudied and/or underreported, and many species were incidentally identified from asymptomatic wild birds; however, the disease significance of APMVs in wild birds is not fully determined. The rapid rise in high-throughput sequencing coupled with avian influenza surveillance programs have identified 12 different APMV species in the last decade and have challenged the resolution of classical serological methods to identify new viral species. Currently, ICTV's only criterion for Paramyxoviridae species classification is the requirement of a branch length of >0.03 using a phylogenetic tree constructed from polymerase (L) amino acid sequences. The results from this study identify one new APMV species, propose four additional new APMV species, and highlight that the criterion may have insufficient resolution for APMV species demarcation and that refinement or expansion of this criterion may need to be established for Paramyxoviridae species identification.
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Affiliation(s)
- Kelsey T. Young
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Jazz Q. Stephens
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Rebecca L. Poulson
- Department of Population Health, Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, Georgia, USA
| | - David E. Stallknecht
- Department of Population Health, Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, Georgia, USA
| | - Kiril M. Dimitrov
- Department of Virology, Texas A&M University, College Station, Texas, USA
| | - Salman L. Butt
- Department of Pathology, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - James B. Stanton
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
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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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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: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [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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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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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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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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Discovery of novel astrovirus and calicivirus identified in ruddy turnstones in Brazil. Sci Rep 2019; 9:5556. [PMID: 30944402 PMCID: PMC6447618 DOI: 10.1038/s41598-019-42110-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 03/25/2019] [Indexed: 01/06/2023] Open
Abstract
Birds are the natural reservoir of viruses with zoonotic potential, as well as contributing to the evolution, emergence, and dissemination of novel viruses. In this study, we applied a high-throughput screening approach to identify the diversity of viruses in 118 samples of birds captured between October 2006 to October 2010 in the North and Northeast regions of Brazil. We found nearly complete genomes of novel species of astrovirus and calicivirus in cloacal swabs of ruddy turnstones (Arenaria interpres) collected in Coroa do Avião islet, Pernambuco State. These viruses are positive-sense single-stranded RNA with a genome of ~7 to 8 kb, and were designated as Ruddy turnstone astrovirus (RtAstV) and Ruddy turnstone calicivirus (RTCV), respectively. Phylogenetic analysis showed that RtAstV and RTCV grouped in a monophyletic clade with viruses identified from poultry samples (i.e., chicken, goose, and turkey), including viruses associated with acute nephritis in chickens. Attempts of viral propagation in monkey and chicken cell lines for both viruses were unsuccessful. Also, we found genomes related with viral families that infect invertebrates and plants, suggesting that they might be ingested in the birds’ diet. In sum, these findings shed new light on the diversity of viruses in migratory birds with the notable characterization of a novel astrovirus and calicivirus.
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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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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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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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12
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Diagnostic and Vaccination Approaches for Newcastle Disease Virus in Poultry: The Current and Emerging Perspectives. BIOMED RESEARCH INTERNATIONAL 2018; 2018:7278459. [PMID: 30175140 PMCID: PMC6098882 DOI: 10.1155/2018/7278459] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/25/2018] [Accepted: 07/16/2018] [Indexed: 01/09/2023]
Abstract
Newcastle disease (ND) is one of the most devastating diseases that considerably cripple the global poultry industry. Because of its enormous socioeconomic importance and potential to rapidly spread to naïve birds in the vicinity, ND is included among the list of avian diseases that must be notified to the OIE immediately upon recognition. Currently, virus isolation followed by its serological or molecular identification is regarded as the gold standard method of ND diagnosis. However, this method is generally slow and requires specialised laboratory with biosafety containment facilities, making it of little relevance under epidemic situations where rapid diagnosis is seriously needed. Thus, molecular based diagnostics have evolved to overcome some of these difficulties, but the extensive genetic diversity of the virus ensures that isolates with mutations at the primer/probe binding sites escape detection using these assays. This diagnostic dilemma leads to the emergence of cutting-edge technologies such as next-generation sequencing (NGS) which have so far proven to be promising in terms of rapid, sensitive, and accurate recognition of virulent Newcastle disease virus (NDV) isolates even in mixed infections. As regards disease control strategies, conventional ND vaccines have stood the test of time by demonstrating track record of protective efficacy in the last 60 years. However, these vaccines are unable to block the replication and shedding of most of the currently circulating phylogenetically divergent virulent NDV isolates. Hence, rationally designed vaccines targeting the prevailing genotypes, the so-called genotype-matched vaccines, are highly needed to overcome these vaccination related challenges. Among the recently evolving technologies for the development of genotype-matched vaccines, reverse genetics-based live attenuated vaccines obviously appeared to be the most promising candidates. In this review, a comprehensive description of the current and emerging trends in the detection, identification, and control of ND in poultry are provided. The strengths and weaknesses of each of those techniques are also emphasised.
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13
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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: 123] [Impact Index Per Article: 20.5] [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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14
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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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15
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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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16
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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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17
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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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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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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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