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. 2024 Dec 18;6(4):lqae183.
doi: 10.1093/nargab/lqae183. eCollection 2024 Dec.

GRAViTy-V2: a grounded viral taxonomy application

Richard Mayne  1 , Pakorn Aiewsakun  2 , Dann Turner  3 , Evelien M Adriaenssens  4 , Peter Simmonds  1
Affiliations

GRAViTy-V2: a grounded viral taxonomy application

Richard Mayne et al. NAR Genom Bioinform. .

Abstract

Taxonomic classification of viruses is essential for understanding their evolution. Genomic classification of viruses at higher taxonomic ranks, such as order or phylum, is typically based on alignment and comparison of amino acid sequence motifs in conserved genes. Classification at lower taxonomic ranks, such as genus or species, is usually based on nucleotide sequence identities between genomic sequences. Building on our whole-genome analytical classification framework, we here describe Genome Relationships Applied to Viral Taxonomy Version 2 (GRAViTy-V2), which encompasses a greatly expanded range of features and numerous optimisations, packaged as an application that may be used as a general-purpose virus classification tool. Using 28 datasets derived from the ICTV 2022 taxonomy proposals, GRAViTy-V2 output was compared against human expert-curated classifications used for assignments in the 2023 round of ICTV taxonomy changes. GRAViTy-V2 produced taxonomies equivalent to manually-curated versions down to the family level and in almost all cases, to genus and species levels. The majority of discrepant results arose from errors in coding sequence annotations in INDSC records, or from inclusion of incomplete genome sequences in the analysis. Analysis times ranged from 1-506 min (median 3.59) on datasets with 17-1004 genomes and mean genome length of 3000-1 000 000 bases.

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Figures

Figure 1.
Figure 1.
GRAViTy-V2 process flow.
Figure 2.
Figure 2.
Comparison of ICTV and GRAViTy-V2 analyses for Nyamiviridae TP. (A) TP ML tree, from L protein AA alignment (22). (B) GRAViTy-V2 tree (Orinocovirus and Beihai rhabdo-like virus 3 omitted as genomes non-coding complete; bootstrap values <0.7 hidden). (C) GRAViTy-V2 heatmap, including neighbouring families Xinmoviridae and Bornaviridae. (Red text: sequences proposed as new taxa in TP).
Figure 3.
Figure 3.
GRAViTy-V2 analysis of Jingchuvirales TP. (A) Shared normalised PPHMM ratio matrix. (B) Barcode heatmap. (Blue lines: incomplete sequences; red text: sequences proposed as new taxa in TP).
Figure 4.
Figure 4.
Histogram of GRAViTy-V2 run time benchmarks showing positive correlation with both mean genome length and number of genomes analysed.
Figure 5.
Figure 5.
Comparison of ICTV and GRAViTy-V2 analyses for Phasmaviridae trees. (A) TP ML tree produced by alignment of L segment AA sequences (23). (B) GRAViTy-V2 tree, with colours adjusted to match TP. (Red text: sequences proposed as new taxa in TP; bootstrap values <0.7 hidden).
Figure 6.
Figure 6.
Comparison of ICTV and GRAViTy-V2 analyses for Jingchuvirales TP. (A) TP ML tree, from RdRp alignment (24). (B) GRAViTy-V2 tree (red: sequences proposed as new taxa in T; blue: family violations; green: genus violations; bootstrap values <0.7 hidden).
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