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

Abstract

Currently, many viruses are classified based on their genome organization and nucleotide/amino acid sequence identities of their capsid and replication-associated proteins. Although biological traits such as vector specificities and host range are also considered, this later information is scarce for the majority of recently identified viruses, characterized only from genomic sequences. Accordingly, genomic sequences and derived information are being frequently used as the major, if not only, criteria 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 an updated set of demarcation criteria based on a process involving pairwise identity analyses and phylogenetics. The proposed framework has been designed to solve the majority of current conundrums in taxonomy and to facilitate future virus classification. Finally, the analyses performed herein, alongside the proposed approaches, could be used as a blueprint for virus classification at-large.

Grapevine virus P: a novel vitivirus found through virome analysis of bulk grape genetic resources in Japan

“…Regardless of a possible recombination event for GVP that is not analyzed here, the current and proposed new criteria [20,32] indicate that GVP is distinct from other vitiviruses and may be a novel species in the genus.…”

“…From the molecular aspect, GVP shares a maximum of 52.5% aa (57.5% nt) RAP and 72.7% aa (68.3% nt) CP sequence identity with the vitiviruses (Table 3). The molecular species demarcation criteria for members of the genus Vitivirus are the same as those applied throughout the family Beta exiviridae: isolates sharing less than 72% nt sequence identity between their CP or RAP genes or 80% aa sequence identity between their respective products should be considered different species [20,32].…”

Genomic analyses of a widespread blueberry virus in the United States

“…While this is lower than the ICTV species demarcation, the rest of the proteins share >93% aa identity. A recent update of the Betaflexiviridae taxonomic criteria has been proposed; where in instances that the aa identity of one protein is close to the cutoff threshold, (which in BlVL case the lowest aa identity is 88.5% with a cutoff value of 90%) then the aa identity of an additional protein is considered ( Silva et al., 2022 ). Therefore, taking into consideration all other aa% identities of BlVL, all isolates presented here are the same species.…”

Meta-Transcriptomic Analysis Uncovers the Presence of Four Novel Viruses and Multiple Known Virus Genera in a Single Hibiscus rosa-sinensis Plant in Colombia

“…Recombination events were detected using several recombination analysis programs built into the Recombination Detection Program (RDP v4.101) with default parameter values [ 46 ]. A cutoff of at least five different methods detecting the same event at p -value < 0.05 was used to determine true positives [ 47 ].…”