title: Modeling sequence evolution in HIV-1 infection with recombination.
abstract: Previously we proposed two simplified models of early HIV-1 evolution. Both showed that under a model of neutral evolution and exponential growth, the mean Hamming distance (HD) between genetic sequences grows linearly with time. In this paper we describe a more realistic continuous-time, age-dependent mathematical model of infection and viral replication, and show through simulations that even in this more complex description, the mean Hamming distance grows linearly with time. This remains unchanged when we introduce recombination, though the confidence intervals of the mean HD obtained ignoring recombination are overly conservative.
authors.affiliation: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
authors.forename: Elena E
authors.initials: EE
authors.lastname: Giorgi
authors.forename: Bette T
authors.initials: BT
authors.lastname: Korber
authors.forename: Alan S
authors.initials: AS
authors.lastname: Perelson
authors.forename: Tanmoy
authors.initials: T
authors.lastname: Bhattacharya
mesh_terms: D000208:Acute Disease; D019143:Evolution, Molecular; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000235:genetics* / Q000502:physiology; D006801:Humans; D008957:Models, Genetic; D009154:Mutation; D011995:Recombination, Genetic / Q000235:genetics*; D013997:Time Factors; D014779:Virus Replication / Q000235:genetics