Genetic variation and evolution of equine infectious anemia virus rev quasispecies during long term persistent infection

Genetic variation has been observed in many viruses. Viruses that carry their genetic information in the form of RNA exhibit high mutation rates because the viral polymerase lacks proof-reading mechanisms commonly found in DNA polymerase complexes. The combination of high mutation rates, small genome size, and high replication rates results in a population of closely related viral genotypes, which are commonly referred to as a quasispecies. A consequence of the genetic variation in viruses is possible variation in viral phenotype of the quasispecies population. Furthermore, changes in viral phenotype may be a biologically important factor in progression of disease. Here, we undertook a longitudinal study to describe the quasispecies nature and genetic variation in a lentivirus regulatory protein, Rev, during the course of disease in a pony experimentally infected with equine infectious anemia virus (EIAV). This study examined rev variants that comprised the quasispecies population in sequential sera samples. Over the course of disease, there was continual appearance of novel rev variants, with some variants growing in frequency to predominate certain time points. Phylogenetic and cluster analyses suggested that the Rev quasispecies was comprised of two distinct populations that co-existed during infection. These two quasispecies populations differed in their pattern of evolution, with one population accumulating changes in a linear, time-dependent manner, while the other population evolved radially from a common variant. Changes in the population size of the two Rev quasispecies coincided with changes in the clinical stages of disease. Rev variants from each population were biologically tested, and significant differences in Rev activity were detected between the two populations. Together, these results suggested that the distinct Rev populations differed in selective advantage. A statistical correlation was found between Rev quasispecies activity and temperature of the pony over the course of infection. Furthermore, the Rev quasispecies activity differed significantly between different stages of clinical disease. This study suggests that distinct quasispecies populations, which differed in pattern of evolution and niche advantage, co-existed during long term persistent infection by EIAV. A multi-population quasispecies model challenges our current thinking of viral populations and may have significant biological implications