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Journal of Virology, March 2004, p. 2242-2246, Vol. 78, No. 5
0022-538X/04/$08.00+0     DOI: 10.1128/JVI.78.5.2242-2246.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Genetic Basis of Hypersusceptibility to Protease Inhibitors and Low Replicative Capacity of Human Immunodeficiency Virus Type 1 Strains in Primary Infection

Andrew J. Leigh Brown,1* Simon D. W. Frost,2 Benjamin Good,2 Eric S. Daar,3 Viviana Simon,4 Martin Markowitz,4 Ann C. Collier,5 Elizabeth Connick,6 Brian Conway,7 Joseph B. Margolick,8 Jean-Pierre Routy,9 Jacques Corbeil,2 Nicholas S. Hellmann,10 Douglas D. Richman,2,11 and Susan J. Little2

University of Edinburgh, Edinburgh, Scotland,1 University of California, San Diego,2 VA San Diego Healthcare System, La Jolla,11 Harbor-UCLA, Los Angeles,3 ViroLogic Inc., South San Francisco, California,10 Aaron Diamond AIDS Research Center, New York, New York,4 University of Washington, Seattle, Washington,5 University of Colorado Health Sciences Center, Denver, Colorado,6 University of British Columbia, Vancouver,7 McGill University Health Centre, Montreal, Canada,9 Johns Hopkins University, Baltimore, Maryland8

Received 27 May 2003/ Accepted 17 October 2003

The initial virus strains from as many as 12% of individuals with primary human immunodeficiency virus (HIV) infection have a 50% inhibitory concentration <=0.4-fold that of HIV type 1NL4-3 (HIV-1NL4-3) to ritonavir (hypersusceptibility [HS]). There is also substantial variation in replicative capacity (RC) or an in vitro assay of the contributions of protease (PR) and reverse transcriptase to viral fitness. In chronically infected antiretrovirally treated patients, amprenavir HS has been associated with the mutation N88S in PR, but this mutation is not seen in untreated patients. In this study, virus strains from 182 cases of primary HIV infection were analyzed, and a highly significant association between HS and low RC (<=10% that of HIV-1NL4-3) was observed (P < 10-6). Multivariate analysis was used to determine the genotypic basis of ritonavir HS, analyzing all polymorphic amino acid sites and insertions from p7gag through PR. Decision tree models developed on the entire Gag-plus-PR data set and on PR alone gave overall correct classifications of 73 and 72%, respectively, on cross-validation. They were also able to predict low RC, with sensitivities of 69 and 62% and specificities of 84 and 70%, respectively. The analysis shows that ritonavir HS in untreated primary HIV infection is not associated with single mutations but with combinations of amino acids at polymorphic sites and that the same genotypes which confer HS to PR inhibitors confer low RC. This supports the view that variation in PR function is directly responsible for variation in fitness among strains in primary infection.

* Corresponding author. Mailing address: ICAPB, University of Edinburgh, West Mains Rd., Edinburgh EH9 3JT, Scotland. Phone: 44-131-650-5523. Fax: 44-131-650-6564. E-mail: A.Leigh-Brown{at}ed.ac.uk.

Journal of Virology, March 2004, p. 2242-2246, Vol. 78, No. 5
0022-538X/04/$08.00+0     DOI: 10.1128/JVI.78.5.2242-2246.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



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