Coalescent estimates of HIV-1 generation time in vivo

Allen G. Rodrigo*, Eugene G. Shpaer, Eric L. Delwart, Astrid K.N. Iversen, Michael V. Gallo, Jürgen Brojatsch, Martin S. Hirsch, Bruce D. Walker, James I. Mullins

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

91 Citations (Scopus)

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 vital dynamics, coalescent modeling also allows us to simulate the evolutionary behavior of samples of sequences obtained over time.

Original languageEnglish
Pages (from-to)2187-2191
Number of pages5
JournalProceedings of the National Academy of Sciences of the United States of America
Volume96
Issue number5
DOIs
Publication statusPublished - 2 Mar 1999
Externally publishedYes

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