Coalescent estimates of HIV-1 generation time in vivo

Abstract

The generation time of HIV Type 1 (HIV-1) in vivo has previously been estimated using a mathematical model of viral dynamics and was found to be on the order of one to two days per generation. Here, we describe a new method based on coalescence theory that allows the estimate of generation times to be derived by using nucleotide sequence data and a reconstructed genealogy of sequences obtained over time. The method is applied to sequences obtained from a long-term nonprogressing individual at five sampling occasions. The estimate of viral generation time using the coalescent method is 1.2 days per generation and is close to that obtained by mathematical modeling (1.8 days per generation), thus strengthening confidence in estimates of a short viral generation time. Apart from the estimation of relevant parameters relating to viral dynamics, coalescent modeling also allows us to simulate the evolutionary behavior of samples of sequences obtained over time.

Figure 1

The genealogy of partial HIV env sequences obtained from sample 1 (○) and a later sample 2 (▴). Sequences from the later sample cluster together more than one would expect by chance alone, and 11 of the 14 possible coalescent events occur between lineages that exclusively include sequences from the later time point only. ∗ marks the nodes where sequences from different time points share close common ancestors.

Figure 2

Joint phylogeny of sequences obtained from all five samples. See text for details on phylogenetic tree reconstruction. The tree was rooted using the reference sequence HIVRF (data not shown).