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ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » Exotic & Emerging Avian Viral Diseases Research » Research » Publications at this Location » Publication #389794

Research Project: Control Strategies to Prevent and Respond to Diseases Outbreaks Caused by Avian Influenza Viruses

Location: Exotic & Emerging Avian Viral Diseases Research

Title: Diverse single-stranded DNA viruses identified in chicken buccal swabs

item CHRZASTEK, KLAUDIA - Orise Fellow
item KRABERGER, SIMONA - Arizona State University
item SCHMIDLIN, KARA - Arizona State University
item FONTENELE, RAFAELA - Arizona State University
item KULKARNI, ARUN - Georgia Poultry Laboratory Network
item CHAPPELL, LEN - Georgia Poultry Laboratory Network
item DUFOR-ZAVALA, LOUISE - Georgia Poultry Laboratory Network
item Kapczynski, Darrell
item VARSANI, ARVIND - Arizona State University

Submitted to: Microorganisms
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/13/2021
Publication Date: 12/16/2021
Citation: Chrzastek, K., Kraberger, S., Schmidlin, K., Fontenele, R.S., Kulkarni, A., Chappell, L., Dufor-Zavala, L., Kapczynski, D.R., Varsani, A. 2021. Diverse single-stranded DNA viruses identified in chicken buccal swabs. Microorganisms. 9(12):2602.

Interpretive Summary: High-throughput sequencing (HTS) has emerged as a promising tool for the detection and discovery of known and novel infectious agents in clinical specimens. HTS-based approaches for clinical samples provide an alternative solution to conventional culture-based method for rapid pathogen identification with no prior sequence knowledge. A large proportion of novel viruses have been discovered using HTS-based approaches directly from clinical samples of humans and animals. In these studies we utilized HTS on poultry samples to identify novel unclassified DNA viruses belonging Circoviridae, Genomoviridae and Smacoviridae families. Use of these technologies will enable scientists to further characterize the poultry microbiome.

Technical 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.