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

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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.

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Acknowledgements

This investigation was supported by the Grant “MicroMap (PON01_02589)”. KB was supported by the Momentum program awarded by the Hungarian Academy of Sciences.

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Authors and Affiliations

  1. Dipartimento di Medicina Veterinaria, Università Aldo Moro di Bari, Valenzano, Italy

    Vito Martella & Pierfrancesco Pinto

  2. Unità di Microbiologia e Virologia, Dipartimento di Medicina Clinica e Sperimentale, Università degli Studi di Parma, Parma, Italy

    Fabio Tummolo & Maria C. Medici

  3. Dipartimento di Scienze per la Promozione della Salute e Materno Infantile “G. D’Alessandro”, Università di Palermo, Palermo, Italy

    Simona De Grazia & Giovanni M. Giammanco

  4. Division of Virology, National Institute of Cholera and Enteric Diseases (NICED), Kolkata, West Bengal, India

    Balasubramanian Ganesh

  5. Canadian Food Inspection Agency, St-Hyacinthe Laboratory, St-Hyacinthe, QC, Canada

    Yvan L’Homme

  6. Cincinnati Children’s Hospital Medical Center, Cincinnati, USA

    Tibor Farkas

  7. Virological Research Group, Faculty of Sciences, Institute of Biology, University of Pécs, Pecs, Hungary

    Ferenc Jakab

  8. Centre for Agricultural Research, Veterinary Medical Research Institute, Hungarian Academy of Sciences, Budapest, Hungary

    Krisztián Bányai

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  1. Vito Martella
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Correspondence to Vito Martella.

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Martella, V., Pinto, P., Tummolo, F. et al. Analysis of the ORF2 of human astroviruses reveals lineage diversification, recombination and rearrangement and provides the basis for a novel sub-classification system. Arch Virol 159, 3185–3196 (2014). https://doi.org/10.1007/s00705-014-2153-9

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