DSS does not clearly improve the detection of RAMs in ART-naive patients, as compared with RSS. NGS allows detection of additional minority RAMs; however, their clinical relevance requires further investigation.

We investigated the presence of stop codons (SC) and/or hypermutation (HM) in HIV-1 DNA sequences generated for routine drug resistance testing in proviral HIV-1 DNA, and sought for associated factors. At least one SC was identified in 6.2% of HIV-1 DNA sequences, among which 54.8% were hypermutated. The defective virus group (SC w/o HM) was similar to the non-SC group regarding the characteristics of HIV-1 infection, and before drug exposure. In addition, the HIV-1 DNA levels were not different between both groups. Sequences with SC/HM displayed a higher proportion of RAMs. The impact of the SC/HM associated RAMs on clinical responses requires further investigation. K E Y W O R D S drug resistance, HIV-1 DNA, hypermutation, mutations, sequencing, stop codons J Med Virol. 2019;91:1684-1687. wileyonlinelibrary.com/journal/jmv 1684 | Abbreviations: HM, hypermutation; IN, integrase INI: integrase inhibitor; NNRTI: nonnucleoside reverse transcriptase inhibitor; NRTI: nucleos(t)ide reverse transcriptase inhibitor; PR, protease; PRI: protease inhibitor; RAM, resistance associated mutations; RT, reverse transcriptase; SC, stop codons; w/o, with or without. SUPPORTING INFORMATION Additional supporting information may be found online in the Supporting Information section at the end of the article. How to cite this article: Alidjinou EK, Deldalle J, Robineau O, et al. Routine drug resistance testing in proviral HIV-1 DNA: Prevalence of stop codons and hypermutation, and associated factors.