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Title: A diarrheic chicken simultaneously co-infected with multiple picornaviruses: Complete genome analysis of avian picornaviruses representing up to six genera

Author
item BOROS, AKOS - Ántsz Regional Institute Of State Public Health Service
item PANKOVICS, PETER - Ántsz Regional Institute Of State Public Health Service
item ADONYI, ADAM - Ántsz Regional Institute Of State Public Health Service
item FENYVESI, HAJNALKA - Ántsz Regional Institute Of State Public Health Service
item Day, James
item GIA PHAN, TUNG - University Of California
item DELWART, ERIC - University Of California
item REUTER, GABOR - Ántsz Regional Institute Of State Public Health Service

Submitted to: Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/3/2015
Publication Date: 12/18/2015
Publication URL: http://handle.nal.usda.gov/10113/62860
Citation: Boros, A., Pankovics, P., Adonyi, A., Fenyvesi, H., Day, J.M., Gia Phan, T., Delwart, E., Reuter, G. 2015. A diarrheic chicken simultaneously co-infected with multiple picornaviruses: Complete genome analysis of avian picornaviruses representing up to six genera. Virology. 489:63-74. doi: 10.1016/j.virol.2015.12.002.

Interpretive Summary: Avian picornaviruses are being discovered and described with increasing frequency in the intestinal tracts of turkeys and chickens. The picornaviruses as a group are in a state of taxonomic flux, with many new species being characterized at an increasing rate. This manuscript details a study that detected several picornaviruses in a single fecal sample from a chicken raised in a backyard flock in Hungary. In fact, of the over 29 official and provisional genera that comprise the Family Picornaviridae, six of these genera were represented in this single chicken, with eight distinct picornaviruses present. Several of these picornaviruses were chosen for detailed genomic study, and a molecular assay was used to detect one novel type of picornavirus in several samples collected from chicken farms in the United States. Characterizing the complex viral community in the chicken gut will lead to a better understanding of the contribution of these viruses to animal health, well-being, and performance.

Technical Abstract: In this study all currently known chicken picornaviruses including a novel one (chicken phacovirus 1, KT880670) were identified by viral metagenomic and RT-PCR methods from a single specimen of a diarrheic chicken suffering from a total of eight picornavirus co-infections, in Hungary. The complete genomes of six picornaviruses were determined and their genomic and phylogenetic characteristics and UTR RNA structural models analyzed in details. Picornaviruses belonged to genera Sicinivirus (the first complete genome), Gallivirus, Tremovirus, Avisivirus and "Orivirus" (two potential genotypes). In addition, the unassigned phacoviruses were also detected in multiple samples of chickens in the USA. Multiple co-infections promote and facilitate the recombination and evolution of picornaviruses and eventually could contribute to the severity of the diarrhea in chicken, in one of the most important food sources of humans.