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Title: Metagenomic analysis of the turkey gut RNA virus community

Author
item Day, James
item Ballard, Linda
item Duke, Mary
item Scheffler, Brian
item Zsak, Laszlo

Submitted to: Virology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/4/2010
Publication Date: 11/12/2010
Citation: Day, J.M., Ballard, L.L., Duke, M.V., Scheffler, B.E., Zsak, L. 2010. Metagenomic analysis of the turkey gut RNA virus community. Virology Journal. 7:313.

Interpretive Summary: Enteric disease syndromes such as Poult Enteritis Mortality Syndrome in young turkeys and Runting Stunting syndrome in chickens cause a great deal of economic loss to the poultry industry worldwide. It has been long suspected that these enteric syndromes are caused by avian viruses such as astrovirus, reovirus and rotavirus. However, it has been difficult for researchers to reproduce the enteric syndromes in experimental turkeys and chickens using viruses isolated from the field. Complicating the problem is the fact that many of the suspect viruses are often detected in flocks that are not exhibiting the classical signs of enteric disease such as diarrhea and stunted growth. We utilized a powerful new technology to detect and sequence the nucleic acid of all of the viruses present in the intestinal tract of enteric syndrome affected turkeys flocks. This intestinal virus "metagenome" contained thousands of pieces of nucleic acid representing many groups of known and previously unknown turkey viruses. Work remains to be done to determine if the new viruses detected in the turkey gut play a role in the development of enteric disease, but this approach to viral discovery in complex samples appears to be valid, with great promise for helping to understand the viral constituency in poultry.

Technical Abstract: Poultry enteric disease syndromes present an ongoing economic burden to poultry producers worldwide. Despite considerable research into the viral agents associated with these enteric disease syndromes, no single virus has emerged as a likely causative agent and target for prevention and control efforts. Recent national and regional surveys using up-to-date molecular diagnostic tests have revealed that suspect viruses continuously circulate on poultry farms in the United States, with many viruses appearing concomitantly and in otherwise healthy birds. Ultra high-throughput nucleic acid pyrosequencing has emerged as a powerful diagnostic technology that can be applied to determine the full genomic repertoire present in a complex environmental sample. In the present analysis, we utilized the Roche/454 Life Sciences Genome Sequencer-FLX (GS-FLX) pyrosequencing platform to compile a ribonucleic acid (RNA) virus metagenome from turkey flocks experiencing enteric disease. This approach yielded numerous sequences homologous to viruses in the non-redundant (nr) protein database, many of which have not been described in turkeys. In particular, numerous sequences from “small, round” RNA viruses were identified; the present analysis focuses in particular on the turkey-origin members of the Piconavirales, the Caliciviridae, and the turkey Picobirnaviruses.