ANI analysis of poxvirus genomes reveals its potential application to viral species rank demarcation

Abstract

Average nucleotide identity (ANI) is a prominent approach for rapidly classifying archaea and bacteria by recruiting both whole genomic sequences and draft assemblies. To evaluate the feasibility of ANI in virus taxon demarcation, 685 poxviruses were assessed. Prior to the analysis, the fragment length and threshold of the ANI value were optimized as 200 bp and 98 per cent, respectively. After ANI analysis and network visualization, the resulting sixty-one species (ANI species rank) were clustered and largely consistent with the groupings found in National Center for Biotechnology Information Virus [within the International Committee on Taxonomy of Viruses (ICTV) Master Species List]. The species identities of thirty-four other poxviruses (excluded by the ICTV Master Species List) were also identified. Subsequent phylogenetic analysis and Guanine-Cytosine (GC) content comparison done were found to support the ANI analysis. Finally, the BLAST identity of concatenated sequences from previously identified core genes showed 91.8 per cent congruence with ANI analysis at the species rank, thus showing potential as a marker gene for poxviruses classification. Collectively, our results reveal that the ANI analysis may serve as a novel and efficient method for poxviruses demarcation.

Comparative genomic analysis of alloherpesviruses: Exploring an available genus/species demarcation proposal and method

“…However, the cumbersome steps and parameters optimization process make it inconvenient for users. In our previous study, we have demonstrated the potential of ANI analysis for viral classification at species rank ( Deng et al., 2022 ). Herein, although both ANI and AAI analyses were not suitable at the genus rank, they were applicable for species rank demarcation ( Figs.…”

Exploration of the genetic landscape of bacterial dsDNA viruses reveals an ANI gap amidst extensive mosaicism

“…The coverage for a genome pair using FastANI is quantified as the proportion of query genome fragments that successfully map to the reference genome, and hence directly comparable to MANIAC’s estimate of AF. We ran FastANI (version 1.33) with the following parameters: k=15 (following the recommended length for Mash), fragLen=500 (based on the fragment length analysis by 32 ), and minFraction=0.1 (to capture pairs with low AF but avoiding noise stemming from short alignments). The ANI of each pair was then taken as the mean of the query-reference ANI and query/fragment AF was reported as the coverage calculated by FastANI.…”

“…Notably, the ICTV's Bacterial Viruses Subcommittee recommends using nucleotide identity cut-offs across the genome lengths at 95% for the species rank and 70% for the genus rank for tailed dsDNA phages of the class Caudoviricetes. While threshold-based analyses have been previously used for species delineation among bacterial viruses 31,32 , to our knowledge there have been no attempts to systematically examine the genus assignment in dsDNA bacterial viruses depending on the values of both ANI and AF for various modes of their calculation.…”

“…Even though applications of ANI in evolutionary microbiology have been extensive, most of the focus has been on bacteria rather than viruses. At the same time, in recent years ANI has been increasingly used in viral genomics, with important applications like identification of new viruses from metagenomes 23,24 , decontamination of bacterial strains from viral sequences 25 , taxonomic assignment of new viral strains 26,27,28,29 and studying genetic boundaries between viral populations 30,31,32 . However, currently available tools have been primarily optimised for bacterial genomes, mainly to delineate them at the species level of approximately 95% of ANI.…”

Genomic characteristics of an avipoxvirus 282E4 strain

“…Poxviruses replicate in the cytoplasm of the cell and bud through cellular endocytosis. ( Mosad et al., 2020 ; Deng et al., 2022 ; Walker et al., 2021 ). Avipoxviruses extensively infect nonmammalian hosts including more than 300 species of birds ( Bolte et al., 1999 ).…”