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Enteric Viruses Detected By Molecular Methods In Commercial Chicken and Turkey Flocks In the United States Between 2005 and 2006

Study Result Intestinal samples collected from 43 commercial broiler and 33 commercial turkey flocks from all regions of the United States during 2005 and 2006, were examined for the presence of astrovirus, rotavirus, reovirus, and coronavirus by RT-PCR, and for the presence of groups I and II adenovirus by PCR. Phylogenetic analysis was performed to further characterize the viruses and to evaluate species association and geographic patterns. Astroviruses were identified in samples from 86% of the chicken flocks and 100% of the turkey flocks. Both chicken astrovirus and avian nephritis virus (ANV) were identified in chicken samples and often both viruses were detected in the same flock. Turkey astrovirus type-2 and turkey astrovirus type-1 were found in 100% and 15.4% of the turkey flocks, respectively. In addition, 12.5% of turkey flocks were positive for ANV. Rotaviruses were present in 46.5% of the chicken, and 69.7% of the turkey flocks tested. Based upon the rotavirus NSP4 gene sequence, the chicken and turkey origin rotaviruses assorted in a species-specific manner. The turkey origin rotaviruses also assorted based upon geographical location. Reoviruses were identified in 62.8% and 45.5% of chicken and turkey flocks respectively. Based on the reovirus S4 gene segment, the chicken and turkey origin viruses assorted separately and were distinct from all previously reported avian reoviruses. Coronaviruses were detected in the intestinal contents of chickens, but not turkeys. Adenoviruses were not detected in any chicken or turkeys flocks. Of the 76 total chicken and turkey flocks tested, only 3 chicken flocks were negative for all viruses targeted by this study. Most flocks were positive for 2 or more of the viruses and overall no clear pattern of virus geographic distribution was evident.