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GENOTYPIC ASSAYS: Genotype analysis identifies mutations associated with phenotypic resistance. Testing may be performed using commercial kits or "home brews." There is 98% concordance when two commercial kits are tested by the same laboratory (Antivir Ther 2000;5 suppl 4:60; Antivir Ther 2000; suppl 3:53). Another study found a 0.3% frequency of false positive results and a 6.4% frequency of false negative results (Antivir Ther 2001;6 suppl 1:1). Assays vary in cost, number of mutations tested, and method of reporting and interpreting results. The methodology involves: 1) amplification of the reverse transcriptase (RT) and protease (Pr) gene, by RT PCR. 2) DNA sequencing of amplicons generated for the dominant species (mutations are limited to those present in >20% of plasma virions). 3) Reporting of mutations for each gene using a letter-number-letter standard, in which the first letter indicates the amino acid at the designated codon with wild-type virus, the number is the codon position, and the second letter indicates the amino acid substituted in the mutation. Thus, the RT mutation K103N indicates that asparagine (N) has replaced lysine (K) on codon 103. Table 2-9 (below) shows the amino acids and corresponding letter codes used to describe mutations in genotype analyses. Interpretation is based on judgement using lists of drug resistance mutations or computerized rules-based algorithms. Updated information on resistance testing can be obtained at http://www.iasusa.org or http://hivdb.stanford.edu and www.isausa.org. Mutations associated with HIV resistance are summarized in Tables 2-10 to 2-13.
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TABLE 2-9: