Application of an allele‐specific PCR to clinical HIV genotyping samples detects additional K103N mutations in both therapy naïve and experienced patients

Low‐level drug resistance is not detected by routine consensus sequence genotype analysis (CSA) but low levels of specific mutations, such as the non‐nucleoside reverse transcriptase inhibitor (NNRTI)‐resistant mutation K103N, can be quantitated by allele‐specific PCR (ASP). This study has applied an ASP to quantitate low‐level K103N in patients presenting for clinical HIV genotyping and assess the correlation with antiretroviral treatment history and outcomes. HIV RNA was extracted from patient plasma and subjected to PCR amplification of the reverse transcriptase (RT) region followed by genotyping by CSA and real‐time ASP for K103N. When applied to samples from patients presenting for genotyping, the ASP detects K103N, not K103 nor K103R, but cross‐reacts with K103S. ASP identified all samples that were K103N by CSA (10.5%) and an additional 14% by ASP only, representing patients who were therapy naïve and with NNRTI treatment history. ASP detected therapy‐acquired K103N at low levels up to 6 years after cessation of NNRTI therapy. In three patients with new HIV diagnosis and K103N detected by ASP only, K103N virus declined rapidly from the circulation but persisted in PBMC DNA at >12 months post‐diagnosis. Efavirenz (EFV) combination therapy in three patients with low‐level K103N suppressed successfully viral load, although one patient developed failure and CSA‐detectable K103N after 15 months of therapy. Thus, analysis of K103N by ASP in conjunction with CSA genotyping provides additional information that reflects K103N transmission and persistence but detection of low‐level K103N does not preclude successful EFV‐containing combination therapy. J. Med. Virol. 81:1983–1990, 2009. © 2009 Wiley‐Liss, Inc.