Patent ID: 8637252

Claim:
A method for determining whether a human immunodeficiency virus 1 (HIV-1) has reduced susceptibility to a non-nucleoside reverse transcriptase inhibitor (NNRTI), comprising: (a) detecting the presence or absence of a mutation at codon 399 in combination with mutations in at least two of codons 103, 179, or 190 in a pol gene encoding reverse transcriptase of the HIV-1 using radioactive or fluorescent DNA sequencing, polymerase chain reaction (PCR), reverse transcription PCR (RTPCR), allele-specific restriction-endonuclease cleavage, mismatch-repair detection, binding of MutS protein, denaturing-gradient gel electrophoresis, single-strand-conformation polymorphism detection, RNAase cleavage at mismatched base-pairs, chemical or enzymatic cleavage of heteroduplex DNA, methods based on oligonucleotide-specific primer extension, genetic bit analysis, oligonucleotide-ligation assay, oligonucleotide-specific ligation chain reaction (LCR), gap-LCR, peptide nucleic acid (PNA) assays, Southern Blot analyses, or single stranded conformational polymorphism analyses (SSCP), wherein the codon number of said reverse transcriptase corresponds to the codon number in the wild type HIV-1 isolate NL4-3 sequence, and wherein the mutation at codon 399 encodes aspartic acid (D) instead of glutamic acid (E); the mutation at codon 103 encodes asparagine (N), arginine (R), serine (S), glutamine (Q), or threonine (T) instead of lysine (K); the mutation at codon 179 encodes aspartic acid (D) instead of valine (V); and the mutation at codon 190 encodes serine (S) instead of glycine (G); and (b) determining that the HIV-1 has reduced susceptibility to the NNRTI if the mutations are present.