Characterization of avian paramyxovirus serotype 14, a novel serotype, isolated from a duck fecal sample in Japan

Thampaisarn, Rapeewan; Bui, Vuong Nghia; Trinh, Dai Quang; Nagai, Makoto; Mizutani, Tetsuya; Omatsu, Tsutomu; Katayama, Yukie; Gronsang, Dulyatad; Le, Duong H.T.; Ogawa, Hideoki; Imai, Kunitoshi

doi:10.1016/j.virusres.2016.11.018

Cited by 36 publications

(29 citation statements)

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“…In recent years, several novel APMVs belonging to APMV serotypes 10–14 were reported in wild birds and penguins around the world (Miller et al, 2010a; Briand et al, 2012; Terregino et al, 2013; Yamamoto et al, 2015; Thampaisarn et al, 2017), implying the presence of additional, as-yet-unreported, novel APMVs in wild birds.…”

Section: Discussionmentioning

confidence: 99%

“…APMVs are divided into 14 different serotypes (APMV-1 to −14) according to cross-hemagglutination inhibition (HI) testing (Alexander, 2003) and/or by phylogenetic analysis (Miller et al, 2010a; Terregino et al, 2013; Yamamoto et al, 2015; Thampaisarn et al, 2017). To date, numerous APMVs have been isolated from domestic and wild birds worldwide.…”

Section: Introductionmentioning

confidence: 99%

“…APMV serotypes −10, −11, and −12 were isolated from Rockhopper penguins ( Eudyptes chrysocome ) in the Falkland Islands in 2007 (Miller et al, 2010a), common snipes ( Gallinago gallinago ) in France in 2010 (Briand et al, 2012), and Eurasian wigeon ( Anas penelope ) in Italy in 2005 (Terregino et al, 2013), respectively. Recently, novel APMVs (putative APMV-13 and -14) were isolated from wild birds around the world during an of avian influenza (AI) surveillance program; species included wild migratory geese in Japan in 2010 (Yamamoto et al, 2015), a white-fronted goose in Ukraine in 2011 (Goraichuk et al, 2016), a white-fronted goose in Kazakhstan in 2013 (Karamendin et al, 2016), and wild ducks in Japan in 2011 (Thampaisarn et al, 2017). …”

Section: Introductionmentioning

confidence: 99%

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A Novel Avian Paramyxovirus (Putative Serotype 15) Isolated from Wild Birds

et al. 2017

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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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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A Novel Avian Paramyxovirus (Putative Serotype 15) Isolated from Wild Birds

et al. 2017

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“…In August 2016, three APMVs isolated from a rockhopper penguin in the Falkland Islands in 2007, a common snipe in France in 2010 and an Eurasian wigeon in Italy 2005 were designated as new serotypes, APMV-10, -11 and -12, respectively [4,1,2,3]. Two unclassified Avulavirus isolated from wild birds in Japan in 2000 and 2011 have been proposed to be additional serotypes, APMV-13 and APMV-14 respectively [5,6,7,8]. Here, based on phylogenetic analysis, serological and biological tests, we propose a new serotype, APMV-15.…”

Section: Introductionmentioning

confidence: 99%

Novel avian paramyxovirus (APMV-15) isolated from a migratory bird in South America

et al. 2017

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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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“…The genus Avulavirus of the family Paramyxoviridae, order Mononegavirales , consists of 14 known avian paramyxovirus serotypes (APMV 1 – 14) [17–19]. Of these, APMV-1, synonymous with Newcastle disease virus, is the most widely characterized and studied due to the economic importance of Newcastle disease (ND) caused by virulent strains of the virus.…”

Section: Introductionmentioning

confidence: 99%

A robust and cost-effective approach to sequence and analyze complete genomes of small RNA viruses

Dimitrov

Sharma

Volkening

et al. 2017

Virol J

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BackgroundNext-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.MethodsIn 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.ResultsTwenty-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.ConclusionsThis 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 materialThe 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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Characterization of avian paramyxovirus serotype 14, a novel serotype, isolated from a duck fecal sample in Japan

Cited by 36 publications

References 43 publications

A Novel Avian Paramyxovirus (Putative Serotype 15) Isolated from Wild Birds

A Novel Avian Paramyxovirus (Putative Serotype 15) Isolated from Wild Birds

Novel avian paramyxovirus (APMV-15) isolated from a migratory bird in South America

A robust and cost-effective approach to sequence and analyze complete genomes of small RNA viruses

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