Cookies on this website

We use cookies to ensure that we give you the best experience on our website. If you click 'Accept all cookies' we'll assume that you are happy to receive all cookies and you won't see this message again. If you click 'Reject all non-essential cookies' only necessary cookies providing core functionality such as security, network management, and accessibility will be enabled. Click 'Find out more' for information on how to change your cookie settings.

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.

Original publication

DOI

10.1073/pnas.96.5.2187

Type

Journal article

Journal

Proc Natl Acad Sci U S A

Publication Date

02/03/1999

Volume

96

Pages

2187 - 2191

Keywords

DNA, Viral, Evolution, Molecular, Genes, env, HIV Seropositivity, HIV-1, Homosexuality, Male, Humans, Male, Models, Genetic, Models, Statistical, Molecular Sequence Data, Phylogeny, Time Factors, Virus Replication