Attenuated live vaccine usage affects accurate measures of virus diversity and mutation rates in avian coronavirus infectious bronchitis virus

摘要: Abstract The full-length genomes of 11 infectious bronchitis virus (IBV) field isolates from three different types the virus; Massachusetts (Mass), Connecticut (Conn) and California (CAL) isolated over a 41, 25 8 year period respectively, were sequenced analyzed to determine mutation rates level polymorphisms across genome. Positive selection was not detected ranged 10 −4 −6  substitutions/site/year for Mass Conn IBV where attenuated live vaccines are routinely used control disease. In contrast, CAL type viruses, which no vaccine exists, positive fold higher ranging −2 −3  substitutions/site/year. Lower levels genetic diversity among viruses as well sequence similarities with suggest that origin all but one likely had been circulating in an unknown apparently short time. data also identified recombinant isolate 7 breakpoints distributed entire genome suggesting within same serotype can have high degree variability outside spike gene. These important because inaccurate measures could lead underestimates ability change potentially emerge cause