Efficacy of genotypic drug resistance testing in patients with low-level plasma HIV-1 viremia

Drug resistance is common at low HIV viral loads and often requires modification of antiretroviral treatment, however commercial genotyping platforms are optimized for viremia >2000 copies/ml. Our aim was to analyze the results of drug resistance genotyping in samples with viral load <2000 copies/ml. Resistance testing was performed using combined commercial (Viroseq 2.8) and in-house bulk sequencing methodology in 18 treatment naive and 45 antiretroviral treated patients (in total 71 samples were analyzed). Drug resistance was evaluated based on the International AIDS Society-USA 2013 update. Sequencing success rate and drug resistance patterns were evaluated. Overall sequencing success rate was 87.4%. In viremia range of 50–1000 copies/ml 86.6% samples were successfully sequenced with 75.0% for levels of 50–200 copies/ml, 90.5% for 201–500 copies/ml, 91.7% for 501–1000 copies/ml and 88.46% for 1001–2000 copies/ml. Drug resistance mutations were found in 43.5% sequences, the overall resistance prevalence for NRTI was 30.65%, for NNRI: 19.35% and 11.29% for PI. In treatment naive patients 31.25% sequences with drug resistance mutations were found, among antiretroviral treatment failing patients in 52.17% samples. Across viremia ranges resistance was observed in 55.6% sequences for 50–200 copies/ml, 36.84% for 201–500 copies/ml and 36.36% for 501–1000 copies/ml and 47.83% for 1001–2000 copies/ml. Success rate for genotyping at low plasma viremia levels is high and allows to guide treatment optimization. As drug resistance is commonly found at low viral loads, genotyping should be attempted in every virologically failing patient regardless the plasma viremia.