Coalescent estimates of HIV-1 generation time in vivo.


Journal Article

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.

Full Text

Cited Authors

  • Rodrigo, AG; Shpaer, EG; Delwart, EL; Iversen, AK; Gallo, MV; Brojatsch, J; Hirsch, MS; Walker, BD; Mullins, JI

Published Date

  • March 1999

Published In

Volume / Issue

  • 96 / 5

Start / End Page

  • 2187 - 2191

PubMed ID

  • 10051616

Pubmed Central ID

  • 10051616

Electronic International Standard Serial Number (EISSN)

  • 1091-6490

International Standard Serial Number (ISSN)

  • 0027-8424

Digital Object Identifier (DOI)

  • 10.1073/pnas.96.5.2187


  • eng