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Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays

M J Kozal¹, N Shah, N Shen

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.

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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.