Abstract
Recombination in the family Coronaviridae has been well documented and is thought to be a contributing factor in the emergence and evolution of different coronaviral genotypes as well as different species of coronavirus. However, there are limited data available on the frequency and extent of recombination in coronaviruses in nature and particularly for the avian gamma-coronaviruses where only recently the emergence of a turkey coronavirus has been attributed solely to recombination. In this study, the full-length genomes of eight avian gamma-coronavirus infectious bronchitis virus (IBV) isolates were sequenced and along with other full-length IBV genomes available from GenBank were analyzed for recombination. Evidence of recombination was found in every sequence analyzed and was distributed throughout the entire genome. Areas that have the highest occurrence of recombination are located in regions of the genome that code for nonstructural proteins 2, 3 and 16, and the structural spike glycoprotein. The extent of the recombination observed, suggests that this may be one of the principal mechanisms for generating genetic and antigenic diversity within IBV. These data indicate that reticulate evolutionary change due to recombination in IBV, likely plays a major role in the origin and adaptation of the virus leading to new genetic types and strains of the virus.
Highlights
Avian infectious bronchitis virus (IBV) is a gamma-coronavirus in the family Coronaviridae, the order Nidovirales, and the genus Coronavirus that causes a highly contagious upper-respiratory disease of domestic chickens
The polyproteins are post-translationally cleaved into 15 non-structural proteins, nsp 2–16 (IBV does not have an nsp1) that make up the replication complex
Breakpoints in the 1ab polyprotein gene have the potential to alter pathogenicity of the virus, and breakpoints near or in spike have the potential to lead to the emergence of new serotypes of IBV or new coronaviruses
Summary
Avian infectious bronchitis virus (IBV) is a gamma-coronavirus in the family Coronaviridae, the order Nidovirales, and the genus Coronavirus that causes a highly contagious upper-respiratory disease of domestic chickens. The 3' end of the genome encodes four structural proteins; spike (S), envelope (E), membrane (M) and nucleocapsid (N) as well as several non-structural proteins [1]. Spike is post-translationally cleaved into S1 and S2 subunits with the S1 subunit forming the outermost portion and S2 forming a stalk-like structure that is embedded in the viral membrane. Spike is involved in membrane fusion and viral entry into the host cell. The polyproteins are post-translationally cleaved into 15 non-structural proteins (nsps), nsp 2–16 (IBV does not have an nsp1) that make up the replication complex. Include a papain-like protease 2 (PLP2) within nsp 3, a main protease (Mpro) within nsp 5, and the RNA-dependent RNA-polymerase (RdRp) within nsps 11 and 12
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