Modeling sequence evolution in HIV-1 infection with recombination

• We describe a continuous time, age-dependent model of early HIV infection.
• We show that the new model yields the same results as a simplified model we published in 2009.
• We introduce recombination in the model.
• We show how recombination affects the results compared to our previous model.

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.