Recombination in Avian Gamma-Coronavirus Infectious Bronchitis Virus

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.

Full genome analysis of Australian infectious bronchitis viruses suggests frequent recombination events between vaccine strains and multiple phylogenetically distant avian coronaviruses of unknown origin

“…1) supported previous suggestions that Australian strains of IBV have been diverging as an independent cluster (Quinteros et al, 2015). However, the representation of genetic divergence by a phylogenetic tree alone may not be accurate, because once a branch is created no further potential interactions between the branches are represented (Thor et al, 2011). In network trees, boxes represent the likelihood that there has been recombination between two different branches.…”

“…The seven methods used for the analysis were RDP (Martin et al, 2005), GENECONV (Padidam et al, 1999), BootScan/Rescan (Martin et al, 2005), Maximum Chi Square (MaxChi) (Smith, 1992), Chimaera (Posada and Crandall, 2001), SiScan (Gibbs et al, 2000) and 3Seq (Boni et al, 2007). Automasking was used for the optimal detection of recombination breakpoints (Thor et al, 2011). Default settings were used for most algorithms.…”

“…Changes from default settings were the window size for RDP (60) and Bootscan (500), the window and step size for SiScan (500 and 20, respectively), and the number of variable sites per window for MaxChi and Chimaera (120). The size of the window was increased from the default to reduce masking of recombination signals within IBV, which has a high mutation rate (Thor et al, 2011). The recombination breakpoint plot was calculated with a window of 200 nt.…”

“…The emergent virulent strain Ark DPI appears to have originated from recombination between four different IBV strains (Ammayappan et al, 2008). Additionally, the emergence of new strains of IBV in the USA has been reported to have arisen from recombination events between the Massachusetts (Mass), Conn and Holte strains and field strains (Thor et al, 2011).…”

Identification of a novel recombinant virulent avian infectious bronchitis virus

“…Recombination can cause the emergence and evolution of different IBV genotypes and different species of coronaviruses (Jackwood et al, 2010). More and more recombination events have been reported in IBV, and they are distributed throughout the entire genome (Brooks et al, 2004;Kuo et al, 2013;Thor et al, 2011). Recently, a new recombinant cluster of nephropathogenic IBVs able to cause death, respiratory signs and nephritis in infected chickens emerged in Korea (Lim et al, 2011(Lim et al, , 2015.…”