Infectious Bronchitis Virus Surveillance in Broilers in California (2012-20).

Abstract

Infectious bronchitis virus (IBV) causes severe economic losses among chicken flocks worldwide. Although IBV molecular surveillance has been conducted in California broilers, seasonal and spatial-temporal trends in IBV prevalence are poorly defined. The goals of this study were to evaluate seasonal and spatial-temporal trends in IBV prevalence and to determine the predominant IBV genotypes obtained over the last 8 yr from a broiler company located in the California Central Valley. In total, 3439 broilers with a suspicion of IBV infection were submitted to the California Animal Health and Food Safety laboratories between January 2012 and February 2020. Swabs from tracheas, kidneys, and cecal tonsils from each submission were independently pooled and screened for IBV using reverse transcriptase quantitative PCR (RT-qPCR). Positive samples were submitted for virus isolation. Viral isolates were subject to a conventional RT-PCR targeting the S1 gene hypervariable region. Positive samples from this RT-PCR were sequenced, and phylogenetic analyses were performed. In total, 1243 pooled swab samples were positive for IBV. Positive results were more frequently detected in fall and winter months compared to spring. Spatial analyses revealed an IBV hot spot in the vicinity of Livingston, and two areas with a low prevalence (i.e., cold spots) around Riverdale. The IBV spatial-temporal distribution identified three significant clusters: one hot spot around Turlock from 2015 to 2016, a second hot spot around Merced from 2012 to 2016, and a cold spot around Fresno from 2017 to 2020. Predominant genotypes changed over time from IBV Cal 99, which was predominant between 2012 and 2014, to IBV 3099 in 2019. Vaccination efforts were initiated in 2018, and as a result, we detected an emerging variant with 92% similarity to CA 3099 in 2020. This work highlights the importance of ongoing surveillance in IBV prevention programs. Surveillance strategies are necessary to monitor trends in diseases such as infectious bronchitis, and the tools used for surveillance need to be sensitive enough to detect new variants and identify spatial-temporal trends.