Diverse Single-Stranded DNA Viruses Identified in Chicken Buccal Swabs.

Klaudia Chrzastek,Len Chappell,Rafaela S Fontenele,Louise Dufour-Zavala,Kara Schmidlin,Simona Kraberger,Darrell R Kapczynski,Arun Kulkarni,Arvind Varsani

doi:10.3390/microorganisms9122602

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.

Highlights

High-throughput sequencing (HTS) has emerged as a promising tool for the detection and discovery of known and novel infectious agents in clinical samples
To increase our general knowledge of viruses that infect or are associated with the upper respiratory track of commercial chickens, we undertook shotgun metagenomics sequencing of DNA extracted from buccal swabs
We identified 665 de novo assembled viral-like contigs that share similarities to viruses in the families Ackermannviridae, Anelloviridae, Autographiviridae, Circoviridae, Demerecviridae, Genomoviridae, Herelleviridae, Inoviridae, Microviridae, Myoviridae, Parvoviridae, Podoviridae, Siphoviridae and Smacoviridae, and unclassified cressdnaviruses

Summary

Introduction

High-throughput sequencing (HTS) has emerged as a promising tool for the detection and discovery of known and novel infectious agents in clinical samples. A large proportion of novel viruses have been discovered directly from humans and animal clinical samples using HTS-based approaches [1,2,3], but this has raised issues of contamination with viral-like sequences from lab reagents and during library preparation [3,4,5,6]. Over the last several years, viral metagenomics has facilitated the discovery of hundreds of highly divergent single-stranded DNA (ssDNA) viruses that belong in the phylum. Cressdnaviricota [7], commonly referred to as circular replication-associated protein encoding single-stranded (CRESS) DNA viruses [3,8,9,10,11,12]. A large number of ssDNA bacteriophages in the family Microviridae [13,14] have been identified [15,16,17,18,19,20]

Methods

Results

Conclusion