Genomic sequencing and phylogenetic analysis reveals recombination and mutational changes contributing to the emergence and evolution of coronaviruses

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 is limited data available on the frequency and extent of recombination in coronaviruses in nature. In this study, the full-length genomes of three alphacoronaviruses, three betacoronaviruses and eight avian gamma-coronavirus infectious bronchitis virus (IBV) isolates were sequenced and along with other full-length coronavirus genomes available from GenBank were analyzed for recombination. Evidence of recombination was found in almost every sequence analyzed and was distributed throughout the entire genome. Areas that have the highest occurrence of recombination are located in similar regions for the three coronavirus genera. For both the alpha-and beta coronaviruses these regions were the region that encodes nonstructural protein 3 and the gene for the structural spike glycoprotein. The areas identified for the gammacoronaviruses were the regions of the genome that code for nonstructural proteins 2, 3 and 16, and the structural spike glycoprotein. Our analysis revealed novel recombination events occurring in the evolution of coronaviruses and revealed no evidence of recombination between the alpha- and betacoronaviruses. The extent of the recombination observed suggests that recombination may be one of the principal mechanisms for generating genetic and antigenic diversity within coronaviruses. These data indicate that reticulate evolutionary change, due to recombination in coronaviruses, likely plays a major role in the origin and adaptation of the virus leading to new genetic types and strains of the virus.