Diverse Single-Stranded DNA Viruses Identified in Chicken Buccal Swabs

Abstract

High-throughput sequencing approaches offer the possibility to better understand the complex microbial communities associated with animals. Viral metagenomics has facilitated the discovery and identification of many known and unknown viruses that inhabit mucosal surfaces of the body and has extended our knowledge related to virus diversity. We used metagenomics sequencing of chicken buccal swab samples and identified various small DNA viruses with circular genome organization. Out of 134 putative circular viral-like circular genome sequences, 70 are cressdnaviruses and 26 are microviruses, whilst the remaining 38 most probably represent sub-genomic molecules. The cressdnaviruses found in this study belong to the Circoviridae, Genomoviridae and Smacoviridae families as well as previously described CRESS1 and naryavirus groups. Among these, genomoviruses and smacoviruses were the most prevalent across the samples. Interestingly, we also identified 26 bacteriophages that belong to the Microviridae family, whose members are known to infect enterobacteria.

Phylogenomic analysis expands the known repertoire of single-stranded DNA viruses in benthic zones of the South Indian Ocean

“…These sequences were predominantly assigned with categorical Groups 1–5 as well as Circoviridae , which are known to infect a wide range of hosts including mammals and diatoms [ 112–114 ]. Consistent with previous studies [ 41 , 115 ], these viruses were highly abundant in our samples. It is possible that these viruses may interact with phylogenetically diverse eukaryotic hosts.…”

Characterization of Diverse Anelloviruses, Cressdnaviruses, and Bacteriophages in the Human Oral DNA Virome from North Carolina (USA)

“…Microviruses are small ssDNA bacteriophages known to infect enterobacteria and to be relatively ubiquitous across metagenomic surveys [ 33 , 79 , 80 , 81 ]. Microvirus genomes are ~4–6 kb and usually contain multiple overlapping reading frames.…”

“…Microvirus genomes are ~4–6 kb and usually contain multiple overlapping reading frames. Their genomes typically encode a more conserved major capsid protein (MCP) along with a replication initiator protein (Rep) and scaffolding proteins [ 33 , 82 ]. The Microviridae family is currently composed of two sub-families, Gokushovirinae and Bullavirinae [ 80 ].…”

“…Cytoscape V3.8.2 [ 32 ] was used to visualize the resulting SSN. A similarity threshold of 60 has previously demonstrated family-level groupings for cressdnaviruses [ 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 ].…”

A New Circular Single-Stranded DNA Virus Related with Howler Monkey Associated Porprismacovirus 1 Detected in Children with Acute Gastroenteritis

“…The extensive use of next-generation sequencing on a variety of biological samples revealed an enormous variety of new viruses [ 1 , 2 , 3 ]. Particularly, viruses recently identified and coined as circular, Rep-encoding ssDNA (CRESS DNA) has a huge diversity and were detected in samples of eukaryotic hosts [ 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 ]. Many of the species belong to the phylum Cressdnaviricota and were classified into two genera, eight orders, eleven families, and sixty-six genera; many of the species are uncultured and remain unclassified [ 15 ].…”