Clinical Virology In the Department of Pathology

Viral Genotyping and Antiviral Resistance Testing

HIV-1 genotyping and antiretroviral resistance testing by sequence analysis.



The Stanford Clinical Virology Laboratory is widely recognized as a pioneer in HIV-1 genotyping and antiviral resistance testing. This testing has revolutionized thecare of HIV infected patients and significantly advanced HIV research. With it, physicians can now closely monitor the emergence of drug resistance mutations and optimize the management of patients infected with drug resistant HIV.


The Stanford Clinical Virology Laboratory has been offering HIV-1 genotyping since 1997.  We use an in-house sequencing assay that was first developed at the Center for AIDS Research at Stanford in the mid-1990's.  As an acknowledged leader in clinical HIV research, our laboratory has played a critical role in numerous studies of HIV drug resistance, including an ongoing collaboration with the Centers for Disease Control and Prevention (CDC).
Our HIV genotyping and drug resistance testing results are reviewed by Dr. Robert Shafer, an expert in the mechanisms and consequences of HIV evolution and the architect of the world-renown HIV Drug Resistance Database (see next section).  Dr. Shafer has over 25 years of experience in the area of HIV/AIDS and is available for consultation at 650-725-2946.

The HIV Drug Resistance Database

The HIV Drug Resistance Database ( is designed to provide a publicly available resource for those performing HIV drug resistance surveillance, interpreting HIV drug resistance tests, and developing new antiretroviral drugs.  It contains over 90,000 HIV sequences from more than 80,000 distinct virus isolations obtained from nearly 40,000 individuals.  When presented with an HIV sequence, the genotypic resistance interpretation algorithm found on the site draws on this wealth of sequence information and takes into consideration (1) Correlations between genotypic data with the treatments of persons from whom sequenced HIV-1 isolates have been obtained (genotype-treatment); (2) Correlations between genotype and in vitro drug susceptibility (genotype-phenotype); and (3) Correlations between genotype and the clinical response to a new treatment regimen (genotype-outcome) to render an interpretation.

This drug resistance interpretation system is similar to the one used by the Stanford Clinical Virology Laboratory with several significant differences.  First, each sequence is automatically compared to previous sequences from the same patient to facilitate the monitoring of resistance development and to act as a means of quality control.  Second, Dr. Shafer reviews each report before it is released to the ordering physician.  For example reports, please click on the links in the section below.

Our Tests

The Stanford Clinical Virology Laboratory offers two HIV-1 genotyping and antiretroviral resistance tests.  The first evaluates HIV-1 reverse transcriptase and protease gene sequences and provides inferred resistance information for 19 commonly prescribed reverse transcriptase and protease inhibitors.  The HIV-1 subtype is also included in the report.
Recently, we expanded our test menu to include HIV-1 integrase antiretroviral resistance testing.  This test utilizes sequence analysis of the HIV-1 integrase gene to identify mutations that confer raltegravir or elvitegravir resistance. Raltegravir, brand name Isentress, is a first-in-its-class oral integrase inhibitor that prevents HIV-1 replication by inhibiting the insertion of virally encoded DNA into the human genome. The addition of raltegravir to optimized background therapy in treatment-experienced HIV infected patients results significant reductions in HIV viral loads and increases CD4 counts (for review see Hicks and Glick. Clin Infect Dis. 2009;48(7):931-9). However, in a recent study, nearly one quarter of raltegravir treated patients developed virologic failure associated with genotypic evidence of integrase resistance (Cooper et al. N Engl J Med. 2008;359(4):355-65), suggesting that integrase resistance testing may be a critical component of the management of patients on integrase inhibitor therapy.  Elvitegravir is an investigational integrase inhibitor currently undergoing Phase III clinical trials.

In addition to HIV-1 genotypic testing, we also perform Hepatitis C virus (HCV) genotyping.  HCV genotyping is recommended prior to the start of therapy as the genotype predicts the likelihood of treatment response, influences antiviral dosing, and determines the optimal duration of treatment with pegylated-interferon alpha plus ribavirin (Hadziyannis et al., Ann Intern Med. 2004; 140(5):346-55).  There are at least 6 HCV genotypes, each with multiple subtypes (a,b,c…).  This sequencing assay targets the core region of the HCV genome and provides both genotype and subtype information
Example HIV-1 Reports

Reverse Transcriptase and Protease Report
Integrase Report


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