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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Disease and Pest Management Research Unit » Research » Publications at this Location » Publication #395849
Research Project: Disease Management in Small Fruit and Nursery Crops Based on Knowledge of Pathogen Diversity, Biology, and Environmental Effects

Location: Horticultural Crops Disease and Pest Management Research Unit

Title: Virus classification based on in-depth sequence analyses and development of demarcation criteria using the Betaflexiviridae as a case study

Author
item SILVA, JOAO MARCOS F - University Of Brasilia
item MELO, FERNANDO LUCAS - University Of Brasilia
item ELENA, SANTIAGO - Santa Fe Community College
item CANDRESSE, THIERRY - Bordeaux University
item SABANADZOVIC, SEAD - Mississippi State University
item TZANETAKIS, IOANNIS - University Of Arkansas
item BLOUIN, ARNOUD - Agroscope
item VILLAMOR, DAN - University Of Arkansas
item Mollov, Dimitre
item CONSTABLE, FIONA - Agriculture Victoria
item CAO, MENGJI - Southwest University
item SALDARELLI, PASQUALE - Institute For Sustainable Agriculture
item CHO, WON KYONG - Sung Kyun Kwan University
item NAGATA, TATSUYA - University Of Brasilia

Submitted to: Journal of General Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/13/2022
Publication Date: 11/21/2022
Citation: Silva, J., Melo, F., Elena, S., Candresse, T., Sabanadzovic, S., Tzanetakis, I., Blouin, A., Villamor, D., Mollov, D.S., Constable, F., Cao, M., Saldarelli, P., Cho, W., Nagata, T. 2022. Virus classification based on in-depth sequence analyses and development of demarcation criteria using the Betaflexiviridae as a case study. Journal of General Virology. 103(11). Article 001806. https://doi.org/10.1099/jgv.0.001806.
DOI: https://doi.org/10.1099/jgv.0.001806

Interpretive Summary: The technological advancements of virus discovery and detection that produce vast amounts of genomic data have been utilized in virus taxonomy. In this research we evaluated the current criteria in one virus family and developed a step-wise process utilizing genomic data for virus classification. With this new approach many questions and disparities about proper taxonomy will be resolved. Additionally, this approach is applicable to all virus taxa, which will result in more unified virus classification across different taxonomic virus groups.

Technical Abstract: Currently, many viruses are classified based on their genome organization and nucleotide/amino acid sequence identities of their replication and capsid proteins. Although biological traits such as vector specificities and host range are also considered, this information is scarce for the majority of recently identified viruses, characterized only from genomic sequences. Accordingly, genomic sequences and derived information is being frequently used as the major, if not only, criterion for virus classification and this calls for a full review of the process. Herein, we critically addressed current issues concerning classification of viruses in the family Betaflexiviridae in the era of high-throughput sequencing and propose updated set of demarcation criteria based on a stepwise process involving pairwise identity analyses and phylogenetics. Proposed framework has been designed to solve majority of current enigmas in the betaflexivirus taxonomy and to facilitate future classification of viruses in the family. Finally, analyses performed in this study, along with proposed approaches, could be easily transferred and used as a blueprint for classification of viruses in other taxa as well.