Family Genomoviridae: 2021 taxonomy update

Abstract

The family Genomoviridae (phylum Cressdnaviricota, class Repensiviricetes, order Geplafuvirales) includes viruses with circular single-stranded DNA genomes encoding two proteins, the capsid protein and the rolling-circle replication initiation protein. The genomes of the vast majority of members in this family have been sequenced directly from diverse environmental or animal-and plant-associated samples, but two genomoviruses have been identified infecting fungi. Since the last taxonomic update of the Genomoviridae, a number of new members of this family have been sequenced. Here, we report on the most recent taxonomic update, including the creation of one new genus, Gemytripvirus, and classification of ~420 new genomoviruses into 164 new species. We also announce the adoption of the "Genus + freeform epithet" binomial system for the naming of all 236 officially recognized species in the family Genomoviridae. The updated taxonomy presented in this article has been accepted by the International Committee on Taxonomy of Viruses (ICTV).

Viral Metagenomic Data Analyses of Five New World Bat Species from Argentina: Identification of 35 Novel DNA Viruses

“…On the basis of the Rep amino acid sequence phylogeny, the novel genomoviruses belonged to the genera Gemycircular-(MAVGs13, 14, 15, 19, 23 and 25), Gemykibi-(MAVGs12, 16, 17, 18, 21, 22 and 24), Gemykronza-(MAVG26, MAVG29), and Gemygorvirus (MAVG20) (Figure 2). With the exception of MAVG15, all other genomoviral MAVGs represented novel species, according to the suggested species demarcation threshold [27]. The MAVGs 12 and 24 represented the same viral species of the genus Gemycircularvirus.…”

“…The final taxonomic classifications were assigned according to the contemporary taxonomic guidelines of ICTV and taxonomic updates that had been recently published and were not yet included in the official ICTV taxonomy, as in the case of Genomoviridae [27], Smacoviridae [28], and Anelloviridae [29]. In addition, novel papillomavirus (PV) nucleotide sequences were subsequently submitted to the Animal Papillomavirus Reference Center (http://www.animalpv.org/, accessed on 25 September 2021) [30] for their confirmation and official designation.…”

Virome in Fecal Samples From Wild Giant Pandas (Ailuropoda Melanoleuca)

“…The Rep protein of Pgenomo2 was closely related to Turdus pallidus Genomoviridae sp. (QTE03681), sharing 67.92% amino acid identity with it, but the genome-wide nucleotide identity was 81.70%; based on the genome-wide pairwise sequence identity threshold of 78%, this virus cannot be considered as a new species ( 26 ). The amino acid sequence identity between Pgenomo3 and its best matching Tarsiger cyanurus Genomoviridae sp.…”

A variety of highly divergent eukaryotic ssDNA viruses in sera of pigs

“…The Genomoviridae is a large viral family, currently divided into 10 genera (Gemycircularvirus, Gemyduguivirus, Gemygorvirus, Gemykibivirus, Gemykolovirus, Gemykrogvirus, Gemykrozvirus, Gemytondvirus, Gemytripvirus and Gemyvongvirus ) and 237 species [68]. Genomovirus genomes (~2 kb) are bidirectionally organized (Type II) with two or three ORFs encoding a Rep (often spliced) and a RepA in the complementary sense strand (unspliced smaller Rep-like protein with an endonuclease domain).…”

“…By phylogenetic inference, PoGV-1 was classified in the genus Gemykibivirus , whereas PoGV-2 and PoGV-3 were classified in the genus Gemykrogvirus (). Following the species demarcation criteria for Genomoviridae family members (78 % genome-wide identity) [68, 70], PoGV-1 was classified as the species Gemykibivirus anima1 . It shared >99 % genome-wide identity with other genomoviruses previously detected in pig faeces (KY214433) [63] and arthropods (MN379617, MH545498) [7] (Supplementary Material S6).…”