Analysis of the ORF2 of human astroviruses reveals lineage diversification, recombination and rearrangement and provides the basis for a novel sub-classification system

Vito Martella, Pierfrancesco Pinto, Fabio Tummolo, Simona De Grazia, Giovanni M. Giammanco, Maria C. Medici, Balasubramanian Ganesh, Yvan L’Homme, Tibor Farkas, F. Jakab, K. Bányai

Research output: Contribution to journalArticle

21 Citations (Scopus)

Abstract

Canonical human astroviruses (HAstVs) are important enteric pathogens that can be classified genetically and antigenically into eight types. Sequence analysis of small diagnostic regions at either the 5′ or 3′ end of ORF2 (capsid precursor) is a good proxy for prediction of HAstV types and for distinction of intratypic genetic lineages (subtypes), although lineage diversification/classification has not been investigated systematically. Upon sequence and phylogenetic analysis of the full-length ORF2 of 86 HAstV strains selected from the databases, a detailed classification of HAstVs into lineages was established. Three main lineages could be defined in HAstV-1, four in HAstV-2, two in HAstV-3, three in HAstV-4, three in HAstV-5 and two in HAstV-6. Intratypic (inter-lineages) ORF2 recombinant strains were identified in type 1 (1b/1d) and type 2 (2c/2b) with distinct crossover points. Other potential intratypic recombinant strains were identified in type 3, type 5 and type 6. In addition, a type-1b strain with a large insertion (~600 bp) of heterologous RNA in the N-terminal region and a type-6 strain with a large RNA rearrangement in the hypervariable region were identified. The classification scheme was integrated in a novel nomenclature system suitable for designation of HAstV strains.

Original languageEnglish
Pages (from-to)3185-3196
Number of pages12
JournalArchives of Virology
Volume159
Issue number12
DOIs
Publication statusPublished - 2014

Fingerprint

Mamastrovirus
Genetic Recombination
Sequence Analysis
RNA
Capsid
Proxy
Terminology
Databases

ASJC Scopus subject areas

  • Virology
  • Medicine(all)

Cite this

Analysis of the ORF2 of human astroviruses reveals lineage diversification, recombination and rearrangement and provides the basis for a novel sub-classification system. / Martella, Vito; Pinto, Pierfrancesco; Tummolo, Fabio; De Grazia, Simona; Giammanco, Giovanni M.; Medici, Maria C.; Ganesh, Balasubramanian; L’Homme, Yvan; Farkas, Tibor; Jakab, F.; Bányai, K.

In: Archives of Virology, Vol. 159, No. 12, 2014, p. 3185-3196.

Research output: Contribution to journalArticle

Martella, Vito ; Pinto, Pierfrancesco ; Tummolo, Fabio ; De Grazia, Simona ; Giammanco, Giovanni M. ; Medici, Maria C. ; Ganesh, Balasubramanian ; L’Homme, Yvan ; Farkas, Tibor ; Jakab, F. ; Bányai, K. / Analysis of the ORF2 of human astroviruses reveals lineage diversification, recombination and rearrangement and provides the basis for a novel sub-classification system. In: Archives of Virology. 2014 ; Vol. 159, No. 12. pp. 3185-3196.
@article{8afe9c6d769f4ef49dcbccb1ecc865ba,
title = "Analysis of the ORF2 of human astroviruses reveals lineage diversification, recombination and rearrangement and provides the basis for a novel sub-classification system",
abstract = "Canonical human astroviruses (HAstVs) are important enteric pathogens that can be classified genetically and antigenically into eight types. Sequence analysis of small diagnostic regions at either the 5′ or 3′ end of ORF2 (capsid precursor) is a good proxy for prediction of HAstV types and for distinction of intratypic genetic lineages (subtypes), although lineage diversification/classification has not been investigated systematically. Upon sequence and phylogenetic analysis of the full-length ORF2 of 86 HAstV strains selected from the databases, a detailed classification of HAstVs into lineages was established. Three main lineages could be defined in HAstV-1, four in HAstV-2, two in HAstV-3, three in HAstV-4, three in HAstV-5 and two in HAstV-6. Intratypic (inter-lineages) ORF2 recombinant strains were identified in type 1 (1b/1d) and type 2 (2c/2b) with distinct crossover points. Other potential intratypic recombinant strains were identified in type 3, type 5 and type 6. In addition, a type-1b strain with a large insertion (~600 bp) of heterologous RNA in the N-terminal region and a type-6 strain with a large RNA rearrangement in the hypervariable region were identified. The classification scheme was integrated in a novel nomenclature system suitable for designation of HAstV strains.",
author = "Vito Martella and Pierfrancesco Pinto and Fabio Tummolo and {De Grazia}, Simona and Giammanco, {Giovanni M.} and Medici, {Maria C.} and Balasubramanian Ganesh and Yvan L’Homme and Tibor Farkas and F. Jakab and K. B{\'a}nyai",
year = "2014",
doi = "10.1007/s00705-014-2153-9",
language = "English",
volume = "159",
pages = "3185--3196",
journal = "Archives of Virology",
issn = "0304-8608",
publisher = "Springer Wien",
number = "12",

}

TY - JOUR

T1 - Analysis of the ORF2 of human astroviruses reveals lineage diversification, recombination and rearrangement and provides the basis for a novel sub-classification system

AU - Martella, Vito

AU - Pinto, Pierfrancesco

AU - Tummolo, Fabio

AU - De Grazia, Simona

AU - Giammanco, Giovanni M.

AU - Medici, Maria C.

AU - Ganesh, Balasubramanian

AU - L’Homme, Yvan

AU - Farkas, Tibor

AU - Jakab, F.

AU - Bányai, K.

PY - 2014

Y1 - 2014

N2 - Canonical human astroviruses (HAstVs) are important enteric pathogens that can be classified genetically and antigenically into eight types. Sequence analysis of small diagnostic regions at either the 5′ or 3′ end of ORF2 (capsid precursor) is a good proxy for prediction of HAstV types and for distinction of intratypic genetic lineages (subtypes), although lineage diversification/classification has not been investigated systematically. Upon sequence and phylogenetic analysis of the full-length ORF2 of 86 HAstV strains selected from the databases, a detailed classification of HAstVs into lineages was established. Three main lineages could be defined in HAstV-1, four in HAstV-2, two in HAstV-3, three in HAstV-4, three in HAstV-5 and two in HAstV-6. Intratypic (inter-lineages) ORF2 recombinant strains were identified in type 1 (1b/1d) and type 2 (2c/2b) with distinct crossover points. Other potential intratypic recombinant strains were identified in type 3, type 5 and type 6. In addition, a type-1b strain with a large insertion (~600 bp) of heterologous RNA in the N-terminal region and a type-6 strain with a large RNA rearrangement in the hypervariable region were identified. The classification scheme was integrated in a novel nomenclature system suitable for designation of HAstV strains.

AB - Canonical human astroviruses (HAstVs) are important enteric pathogens that can be classified genetically and antigenically into eight types. Sequence analysis of small diagnostic regions at either the 5′ or 3′ end of ORF2 (capsid precursor) is a good proxy for prediction of HAstV types and for distinction of intratypic genetic lineages (subtypes), although lineage diversification/classification has not been investigated systematically. Upon sequence and phylogenetic analysis of the full-length ORF2 of 86 HAstV strains selected from the databases, a detailed classification of HAstVs into lineages was established. Three main lineages could be defined in HAstV-1, four in HAstV-2, two in HAstV-3, three in HAstV-4, three in HAstV-5 and two in HAstV-6. Intratypic (inter-lineages) ORF2 recombinant strains were identified in type 1 (1b/1d) and type 2 (2c/2b) with distinct crossover points. Other potential intratypic recombinant strains were identified in type 3, type 5 and type 6. In addition, a type-1b strain with a large insertion (~600 bp) of heterologous RNA in the N-terminal region and a type-6 strain with a large RNA rearrangement in the hypervariable region were identified. The classification scheme was integrated in a novel nomenclature system suitable for designation of HAstV strains.

UR - http://www.scopus.com/inward/record.url?scp=84922100993&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84922100993&partnerID=8YFLogxK

U2 - 10.1007/s00705-014-2153-9

DO - 10.1007/s00705-014-2153-9

M3 - Article

C2 - 25326755

AN - SCOPUS:84922100993

VL - 159

SP - 3185

EP - 3196

JO - Archives of Virology

JF - Archives of Virology

SN - 0304-8608

IS - 12

ER -