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Species characterization in the genus Pestivirus according to palindromic nucleotide substitutions in the 5′-untranslated region
https://iwate-u.repo.nii.ac.jp/records/9290
https://iwate-u.repo.nii.ac.jp/records/92905e716874-f7c7-45b2-afe3-604a8ab0b05b
| 名前 / ファイル | ライセンス | アクション |
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jvm-v174i1-2p166-172.pdf (228.4 kB)
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| Item type | 学術雑誌論文 / Journal Article(1) | |||||||||
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| 公開日 | 2011-09-02 | |||||||||
| タイトル | ||||||||||
| タイトル | Species characterization in the genus Pestivirus according to palindromic nucleotide substitutions in the 5′-untranslated region | |||||||||
| キーワード | ||||||||||
| 主題Scheme | Other | |||||||||
| 主題 | Palindromic nucleotide substitutions | |||||||||
| キーワード | ||||||||||
| 主題Scheme | Other | |||||||||
| 主題 | Pestivirus | |||||||||
| キーワード | ||||||||||
| 主題Scheme | Other | |||||||||
| 主題 | Taxonomy | |||||||||
| キーワード | ||||||||||
| 主題Scheme | Other | |||||||||
| 主題 | 5′-UTR | |||||||||
| 資源タイプ | ||||||||||
| 資源タイプ識別子 | http://purl.org/coar/resource_type/c_6501 | |||||||||
| 資源タイプ | journal article | |||||||||
| 著者 |
Giangaspero, Massimo
× Giangaspero, Massimo
× Harasawa, Ryô
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| 著者(機関) | ||||||||||
| 値 | Veterinary Microbiology, School of Veterinary Medicine, Faculty of Agriculture, Iwate University | |||||||||
| 登録日 | ||||||||||
| 日付 | 2011-09-02 | |||||||||
| 書誌情報 |
Journal of Virological Methods 巻 174, 号 1-2, p. 166-172, 発行日 2011-06-01 |
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| ISSN | ||||||||||
| 収録物識別子タイプ | ISSN | |||||||||
| 収録物識別子 | 0166-0934 | |||||||||
| Abstract | ||||||||||
| 内容記述タイプ | Other | |||||||||
| 内容記述 | The palindromic nucleotide substitutions (PNS) at the three variable loci (V1, V2 and V3) in the 5′-untranslated region (UTR) of the Pestivirus genome have been considered for taxonomical segregation of the species, through the evaluation of 534 strains. On the basis of qualitative and quantitative secondary structure characteristics, species have been identified within the genus, determining genetic distances between species isolates, clarifying borderline and multirelated sequences, and characterizing and clustering the Pestivirus strains showing unexpected genomic sequences. Nine genomic groups have been identified: the species Bovine viral diarrhea virus 1 (BVDV-1), Bovine viral diarrhea virus 2 (BVDV-2), Border disease virus (BDV) and Classical swine fever virus (CSFV) and the tentative species Pronghorn, Giraffe, Bovine viral diarrhea virus 3 (BVDV-3) (HoBi group), Border disease virus 2 (BDV-2) (Italian small ruminant isolates) and Bungowannah. Palindromic positions have been characterized according to changes in nucleotide base-pairs identifying low variable positions (LVP) including base-pairs present in less than 80% of the genus. The determination of divergence between single strain sequences or genetic groups was obtained easily by comparing base-pairing combinations from aligned secondary structures. This provided clear information such as the level of heterogeneity within a species, the relatedness between species, or facilitating the characterization and clustering of specific strains. The BVDV-1 and BDV species resulted heterogeneous, showing isolates located on a borderline in the species. Within the BVDV-2 species, two main genogroups were identified, with strains showing common sequence characteristics to both groups (multirelated strains). They could be allocated correctly by quantitative analysis. Similarly, the relation between CSFV and BDV species appeared very clearly. Also in this case, ambiguous strain sequences could be clustered in the species showing the lowest divergence values. In conclusion, the proposed taxonomical procedure is based on the evaluation of only the strategic and highly conserved genome regions in the 5′-UTR. Furthermore, the application of quantitative analytical procedure allowed for a better determination of relation among species. |
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| 出版者 | ||||||||||
| 出版者 | Elsevier B.V. | |||||||||
| 権利 | ||||||||||
| 権利情報 | Copyright © 2011 Elsevier B.V. All rights reserved. | |||||||||
| DOI | ||||||||||
| 関連タイプ | isVersionOf | |||||||||
| 識別子タイプ | DOI | |||||||||
| 関連識別子 | 10.1016/j.jviromet.2011.04.004 | |||||||||
| 著者版フラグ | ||||||||||
| 出版タイプ | AM | |||||||||
| 出版タイプResource | http://purl.org/coar/version/c_ab4af688f83e57aa | |||||||||
