Complete Genome Sequence of a Novel Avian Paramyxovirus (APMV-13) Isolated from a Wild Bird in Kazakhstan

Karamendin, Kobey; Kydyrmanov, Aidyn; Seidalina, Aigerim; Asanova, Saule; Sayatov, Marat; Kasymbekov, E.; Khan, Elizaveta; Daulbayeva, Klara; Harrison, Sally M.; Carr, Ian; Goodman, Simon J.; Zhumatov, Kainar

doi:10.1128/genomea.00167-16

Cited by 25 publications

(25 citation statements)

References 8 publications

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“…Thus, the results obtained in this study emphasized the possibility that APMV/Shimane67 would be a novel APMV type. Quite recently, Karamendin et al [16] reported the whole genome sequence of a novel APMV isolated from a white fronted goose in northern Kazakhstan (GenBank accession number KU64513). The genome length of APMV/Shimane67 is 150 nt longer than that of Kazakhstan APMV, while genome nt identity of these strains was very high (approximately 96%).…”

Section: Discussionmentioning

confidence: 99%

Completion of full length genome sequence of novel avian paramyxovirus strain APMV/Shimane67 isolated from migratory wild geese in Japan

Yamamoto

Ito

2016

The Journal of Veterinary Medical Science

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The nucleotide sequences of nucleocapsid protein (N); phosphoprotein (P); matrix protein (M); hemagglutinin-neuraminidase (HN); and large polymerase protein (L) genes, 3′-end leader, 5′-end trailer and intergenic regions of the avian paramyxovirus (APMV) strain goose/Shimane/67/2000 (APMV/Shimane67) were determined. Together with previously reported data on fusion protein (F) gene sequence [46], the determination of the genome sequence of APMV/Shimane67 has been completed in this study. The genome of APMV/Shimane67 comprised 16,146 nucleotides in length and contains six genes in the order of 3′-N-P-M-F-HN-L-5′. The features of the APMV/Shimane67 genome (e.g., nucleotide length of whole genome and each of the six genes, and predicted amino acid length of each of the six genes) were distinct from those of other APMV serotypes. Phylogenetic analysis indicated that although APMV/Shimane67 was grouped with APMV-1, -9 and -12, the evolutionary distance between APMV/Shimane67 and these viruses was longer than that observed between intra-serotype viruses. These results show that the genome sequence of APMV/Shimane67 contains specific characteristics and is distinguishable from other types of APMV.

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Section: Discussionmentioning

confidence: 99%

Completion of full length genome sequence of novel avian paramyxovirus strain APMV/Shimane67 isolated from migratory wild geese in Japan

Yamamoto

Ito

2016

The Journal of Veterinary Medical Science

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“…The number of novel viruses discovered needed for a high-profile paper has increased by logarithms (Krishnamurthy et al, 2016;Shi et al, 2016). In the absence of particular phenotypic data or wet-lab viral characterization, many authors have turned to Genome Announcements, biorxiv, or simply uploading to Genbank with extra metadata, figuring that sequencing is the most likely future method of both detection and discovery (Debat, 2017;Greninger and DeRisi, 2015e,f;Karamendin et al, 2016;Sharman et al, 2016;Sparks et al, 2013). Given the glut of new viruses, expansion of sequencing, and the time it takes to publish, scientists may be more likely to align to your novel virus rather than read about it in a journal and decide to screen for it.…”

Section: Experimenting With Functionmentioning

confidence: 99%

A decade of RNA virus metagenomics is (not) enough

2018

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It is hard to overemphasize the role that metagenomics has had on our recent understanding of RNA virus diversity. Metagenomics in the 21st century has brought with it an explosion in the number of RNA virus species, genera, and families far exceeding that following the discovery of the microscope in the 18th century for eukaryotic life or culture media in the 19th century for bacteriology or the 20th century for virology. When the definition of success in organism discovery is measured by sequence diversity and evolutionary distance, RNA viruses win. This review explores the history of RNA virus metagenomics, reasons for the successes so far in RNA virus metagenomics, and methodological concerns. In addition, the review briefly covers clinical metagenomics and environmental metagenomics and highlights some of the critical accomplishments that have defined the fast pace of RNA virus discoveries in recent years. Slightly more than a decade in, the field is exhausted from its discoveries but knows that there is yet even more out there to be found.

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“…The genome sequence showed 97% nucleotide identity to that of goose/Kazakhstan/5751/2013 (accession no. KU646513) that was recently deposited in GenBank and designated APMV-13 ( 18 ). However, the genome of white-fronted goose/Ukraine/Askania-Nova/48-15-02/2011 is 150 nt longer than the one of the virus isolated in Kazakhstan.…”

Section: Genome Announcementmentioning

confidence: 99%

Complete Genome Sequence of an Avian Paramyxovirus Representative of Putative New Serotype 13

et al. 2016

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Complete Genome Sequence of a Novel Avian Paramyxovirus (APMV-13) Isolated from a Wild Bird in Kazakhstan

Cited by 25 publications

References 8 publications

Completion of full length genome sequence of novel avian paramyxovirus strain APMV/Shimane67 isolated from migratory wild geese in Japan

Completion of full length genome sequence of novel avian paramyxovirus strain APMV/Shimane67 isolated from migratory wild geese in Japan

A decade of RNA virus metagenomics is (not) enough

Complete Genome Sequence of an Avian Paramyxovirus Representative of Putative New Serotype 13

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