Smacoviridae: a new family of animal-associated single-stranded DNA viruses

Abstract

Smacoviruses have small (∼2.3-2.9 kb), circular single-stranded DNA genomes encoding rolling circle replication-associated proteins (Rep) and unique capsid proteins. Although smacoviruses are prevalent in faecal matter of various vertebrates, including humans, none of these viruses have been cultured thus far. Smacoviruses display ∼45% genome-wide sequence diversity, which is very similar to that found within other families of circular Rep-encoding single-stranded (CRESS) DNA viruses, including members of the families Geminiviridae (46% diversity) and Genomoviridae (47% diversity). Here, we announce the creation of a new family Smacoviridae and describe a sequence-based taxonomic framework which was used to classify 83 smacovirus genomes into 43 species within six new genera, Bovismacovirus (n=3), Cosmacovirus (n=1), Dragsmacovirus (n=1), Drosmacovirus (n=3), Huchismacovirus (n=7), and Porprismacovirus (n=28). As in the case of genomoviruses, the species demarcation is based on the genome-wide pairwise identity, whereas genera are established based on the Rep amino acid sequence identity coupled with strong phylogenetic support. A similar sequence-based taxonomic framework should guide the classification of an astonishing diversity of other uncultured and currently unclassified CRESS DNA viruses discovered by metagenomic approaches.

Alphasatellitidae: a new family with two subfamilies for the classification of geminivirus- and nanovirus-associated alphasatellites

“…The communication by Simmonds et al [41] addressed the classification of diverse groups of viral sequences derived from metagenomics approaches and this has resulted in significant changes in viral classification. For example, new families have been established to accommodate virophages and satellite viruses [23] and various novel groups of circular Rep encoding ssDNA viruses derived from environmental sources (with unknown hosts or pathology) [22,47,49]. In line with these significant changes on classification of viruses and viral-like elements, we communicate the establishment of a new family Alphasatellitidae with two sub-families Geminialphasatellitinae and Nanoalphasatellitinae for geminivirus-and nanovirus-alphasatellite molecules.…”

Novel smacoviruses identified in the faeces of two wild felids: North American bobcat and African lion

“…The phylogenetic tree was rooted with the Rep sequences of the nanoviruses. Based on the taxonomic guidelines put forward by the Smacoviridae subcommittee for the International Committee on Taxonomy of Viruses [19], the results of phylogenetic analysis and sequence comparisons support the assignment of each of these three smacoviruses to a distinct species.…”

“…The Smacoviridae are a family of circular single-stranded DNA viruses that have been identified in the faecal excrement of many mammals and birds, and a few arthropods [19]. The genomes of smacoviruses range from 2.3 to 3 kb in size and contain at least two bidirectionally transcribed open reading frames (ORFs), which encode a replicationassociated protein (Rep) and a capsid protein (CP).…”

A tripartite ssDNA mycovirus from a plant pathogenic fungus is infectious as cloned DNA and purified virions

“…Ostrich-associated gemytondvirus 1 Rabbit-associated gemykroznavirus 1 Bacilladnaviridae, Circoviridae, Geminiviridae, Genomoviridae, Nanoviridae, and Smacoviridae are the only six eukaryotic CRESS DNA viral families currently recognized by the ICTV (7,13,25). Among those, members of the Circoviridae, Geminiviridae, Genomoviridae, and Smacoviridae families are circular ssDNA viruses (2 to 3 kb in size) that encode a Rep and a CP in the same circular DNA molecule (9,13,25). Viruses of the family Bacilladnaviridae have larger genome sizes than other eukaryotic CRESS DNA viruses (~4.5 to 6 kb) (7).…”