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Journal of Virology, October 1999, p. 8167-8178, Vol. 73, No. 10
0022-538X/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.

Search for the Mechanism of Genetic Variation in the pro Gene of Human Immunodeficiency Virus

I. M. Rouzine* and J. M. Coffin

Department of Molecular Biology and Microbiology, School of Medicine, Tufts University, Boston, Massachusetts 02111

Received 24 February 1999/Accepted 23 June 1999

To study the mechanism of evolution of the human immunodeficiency virus (HIV) protease gene (pro), we analyzed a database of 213 pro sequences isolated from 11 HIV type 1-infected patients who had not been treated with protease inhibitors. Variation in pro is restricted to rare variable bases which are highly diverse and differ in location among individuals; an average variable base appears in about 16% of individuals. The average intrapatient distance per individual variable site, 27%, is similar for synonymous and nonsynonymous sites, although synonymous sites are twice as abundant. The latter observation excludes selection for diversity as an important, permanently acting factor in the evolution of pro and leaves purifying selection as the only kind of selection. Based on this, we developed a model of evolution, both within individuals and along the transmission chain, which explains variable sites as slightly deleterious mutants slowly reverting to the better-fit variant during individual infection. In the case of a single-source transmission, genetic bottlenecks at the moment of transmission effectively suppress selection, allowing mutants to accumulate along the transmission chain to high levels. However, even very rare coinfections from independent sources are, as we show, able to counteract the bottleneck effect. Therefore, there are two possible explanations for the high mutant frequency. First, the frequency of coinfection in the natural host population may be quite low. Alternatively, a strong variation of the best-adapted sequence between individuals could be caused by a combination of an immune response present in early infection and coselection.

* Corresponding author. Mailing address: Department of Molecular Biology and Microbiology, School of Medicine, Tufts University, 136 Harrison Ave., Boston, MA 02111. Phone: (617) 636-0917. Fax: (617) 636-4086. E-mail: irouzine{at}emerald.tufts.edu.

Journal of Virology, October 1999, p. 8167-8178, Vol. 73, No. 10
0022-538X/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.


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