Stanford University Medical Center Diagnostic Virology Lab
Contacts To order tests or for more information:
Mary Arroyo
Supervisor of Virology
Stanford Clinical Microbiology/Virology Laboratory (650) 723-6671
Stanford University is a full-service clinical diagnostic laboratory that performs a non-kit-based genotypic assay.**
GENERAL INFORMATION
Assay Name
HIV RT and Protease Genotype
Collaborators/Distributors
None
Availability
Commercially available for research use only.
Regulatory Status
CAP accredited and CLIA certified laboratory. The assays are non-kit-based.** The FDA does not currently regulate non-kit-based tests through published regulations or site inspections.
Proprietary/Non-kit-based assays are sometimes referred to as "home brew" assays. See the background article regarding FDA regulation of kit- vs. non-kit-based assays.
ASSAY INFORMATION
Assay
Codons Interrogated
Turnaround time
Sensitivity
RT
PI
Full sequence assay
1–300
1–99
14 days
500 RNA copies/ml
METHODOLOGY
HIV RT and Protease Genotype is a full sequencing assay. Viral RNA is extracted from plasma and amplified through RT-PCR. The products undergo automated dye terminator sequencing of the entire protease gene and approximately the first 300 codons of the RT gene. Commercial software is used to assemble the sequences and an in-house program, HIV-SEQ, is used to compare sequences to the HIV subtype B consensus reference sequence. The program and its description can be found on the web (http://hivdb.stanford.edu/hiv/programs.htm). Software similar to the Stanford HIV RT and Protease Sequence Database Sequence Analyzer (beta test version) is then used to compare the sequences with wild type viral sequences to determine the resistance mutations. Each sequence is also examined manually. Final interpretations are performed by Dr. Robert Shafer. For purposes of quality control, the laboratory sequences a control virus sample in parallel with each batch of routine clinical samples. Occasionally, information obtained in this way will over-rule the software program's output. Comments are added when unusual mutations are observed.
REPORT INFORMATION
Report
Drug Resistance Interpretation
Genotype
Yes
The report includes an algorithm for interpretation that utilizes three tables with rules, one each for NRTI, NNRTI, and PI. Each row in the table has a score or penalty for a drug depending on the codon and the specific mutation. If multiple mutations influence a drug's susceptibility then that drug's final score will be the sum of the individual mutations scores. If a mutation causes hypersusceptibility then it confers a negative score. A final interpretation includes a resistance description based on sequence and five levels of resistance to all approved HIV drugs: susceptible, potential low-level resistance, low-level resistance, intermediate resistance, and high-level resistance. Comments are added to clarify unusual results.
500 RNA copies/ml