Dynamics of haplotype frequency change in a CD8+TL epitope of simian immunodeficiency virus

Deep pyrosequencing of a CD8+TL epitope from the Tat protein of simian immunodeficiency virus (SIV) from four infected rhesus macaques carrying the restricting MHC allele (Mamu-A*01) for that epitope, revealed that natural selection favoring escape mutations led to an increase in the frequency of haplotypes in the epitope region that differed from the inoculum. After 20 weeks of infection, a new sequence haplotype in the epitope region had increased to a frequency greater than 50% in each of the four monkeys (range 57.9-98.9%); but the predominant haplotype was not the same in all four monkeys. Thus, even under strong selection favoring escape from CD8+TL recognition, the random nature of mutation itself is the primary factor affecting which escape mutation is likely to become predominant within an individual host. The relationship between the frequency of the inoculum haplotype in the epitope region and time post-infection approximated a simple hyperbola. On this assumption, the expected ratio of the frequencies at the inoculum at two times t(1) and t(2), f(i)(t(2))/f(i)(t(1)), will be given by t(1)/t(2). Because standard phylogenetic methods for reconstructing ancestral sequences failed to predict the inoculum sequence correctly, we used this relationship to predict the inoculum sequence with 100% accuracy, given data on haplotype frequencies at different time periods.