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Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays
1Department of Molecular Biology, Affymetrix, Santa Clara, California 95051, USA.
Nature Medicine
|July 1, 1996
Summary
Naturally occurring mutations in HIV protease were highly variable in treatment-naive patients. Many drug resistance mutations were found as natural polymorphisms, impacting HIV therapy outcomes.
Area of Science:
- Virology
- Genetics
- Drug Resistance
Background:
- Naturally occurring mutations in Human Immunodeficiency Virus type 1 (HIV-1) impact therapy and clinical study outcomes.
- Prevalence of mutations conferring resistance to HIV-1 protease inhibitors in treatment-naive patients is largely unknown.
Purpose of the Study:
- To investigate the prevalence of mutations conferring resistance to HIV-1 protease inhibitors in isolates from patients naive to such inhibitors.
- To analyze the genetic diversity of HIV-1 clade B proteases in the USA.
Main Methods:
- High-density oligonucleotide array sequencing was used for the first time in a clinical application.
- Sequencing of 167 viral isolates from 102 patients.
Main Results:
- The DNA sequence of USA HIV-1 clade B proteases exhibited extreme variability, with 47.5% of 99 amino acid positions varying.
- This amino acid diversity (47.5%) exceeds previously known diversity across all worldwide HIV-1 clades (40%).
- Many amino acid changes associated with drug resistance were identified as natural polymorphisms in isolates from protease inhibitor-naive patients.
Conclusions:
- Significant natural genetic diversity exists in HIV-1 protease, even in treatment-naive individuals.
- The presence of natural polymorphisms conferring drug resistance has critical implications for HIV therapy and clinical trial design.
- Further research is needed to understand the clinical impact of these naturally occurring resistance mutations.
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