Molecular Evolution of Infectious Bronchitis Virus and the Emergence of Variant Viruses Circulating in the United States.

Infectious bronchitis virus (IBV) is a highly infectious and transmissible gammacoronavirus that is nearly impossible to control through biosecurity. Coronaviruses are RNA viruses with an enormous capacity for rapid replication and high rates of mutation, leading to a tremendous amount of genetic diversity. Viral evolution occurs when selection working on genetic diversity leads to new mutations being fixed in the population over time. For IBV, the emergence of variant viruses is likely due to a combination of selection acting on existing genetic diversity, as well as on newly created mutations as the virus replicates, or genetic drift. Immunity against IBV creates a strong selection pressure; however, immunity can also reduce the viral load, decreasing replication and the development of new mutations. Examining the balance between immunity reducing infection, replication, and genetic diversity, and immune pressure selecting for new variants, is extremely difficult at best. Nonetheless, vaccination and immunity do play a role in the emergence of new antigenic variants of IBV. To complicate the situation even more, coronaviruses can undergo recombination, and several studies in the literature report recombination between IBV vaccines and field viruses. However, to our knowledge, unlike genetic drift, recombination alone has not been shown to result in a new antigenic and pathogenic IBV type emerging to cause widespread disease in poultry. Vaccines against IBV that result in an immune population can reduce transmission (basic reproductive number less than 1), making vaccines for IBV the best control strategy available. However, IBV control remains extremely challenging because of the high number of antigenic variants causing disease in poultry and a limited number of vaccines that mostly provide only partial protection against infection and replication of those variants. Currently, there is one major variant IBV circulating in all sectors of US commercial poultry production: DMV/1639/11. This virus was initially detected in 2011, but only began causing significant disease in 2014/2015. Since then, it has affected all three sectors of poultry production (layers, breeders, broilers) and continues to predominate in certain regions of the United States. Additionally, a previously classified variant IBV, which is no longer considered a variant virus, GA08, is highly prevalent. This is attributed to heavy GA08-type IBV vaccine usage because disease caused by the GA08-type virus is rare. Interestingly, the major IBV detected in poultry for several decades, ArkDPI, is no longer among the most detected viruses in the United States. This change corresponds to the shift away from ArkDPI vaccine usage in the broiler sector as GA08 vaccine usage has increased and highlights the role IBV vaccines play in influencing viral populations in commercial chickens.