Full-spectrum HIV drug resistance mutation detection by high-resolution complete pol gene sequencing

• Published in: Journal of clinical virology Vol. 164; p. 105491
• Main Authors: Faraci, Gina, Park, Sung Yong, Dubé, Michael P., Lee, Ha Youn
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01-07-2023
• Subjects: Anti-HIV Agents - pharmacology; Anti-HIV Agents - therapeutic use; Cross-resistance; Drug resistance mutations; Drug Resistance, Viral - genetics; Genes, pol; Genotype; HIV; HIV Infections - drug therapy; HIV-1 - genetics; Humans; Minority variants; Mutation; Reverse Transcriptase Inhibitors - therapeutic use; Minority variants; Drug resistance mutations; HIV; Cross-resistance
• ISSN: 1386-6532; 1873-5967; 1873-5967
• DOI: 10.1016/j.jcv.2023.105491

•We produced 358 full-length HIV pol gene sequences by combining microdroplet amplification, unique molecular identifier labeling, and long-read high-throughput sequencing.•We detected linked cross-class drug resistance mutations (PI+NRTI, PI+NNRTI, and NRTI+NNRTI), which conferred cross-resistance to multiple drugs from different classes.•We detected minority drug resistance mutations, which were present with frequencies ranging from 3.2% to 19%.•A putative transmitted drug resistance mutation (TDRM) was identified in a treatment-naïve individual at the acute stage of infection before seroconversion, which persisted for over seven months.
Drug resistance mutation testing is a key element for HIV clinical management, informing effective treatment regimens. However, resistance screening in current clinical practice is limited in reporting linked cross-class resistance mutations and minority variants, both of which may increase the risk of virological failure.
To address these limitations, we obtained 358 full-length pol gene sequences from 52 specimens of 20 HIV infected individuals by combining microdroplet amplification, unique molecular identifier (UMI) labeling, and long-read high-throughput sequencing.
We conducted a rigorous assessment of the accuracy of our pipeline for precision drug resistance mutation detection, verifying that a sequencing depth of 35 high-throughput reads achieved complete, error-free pol gene sequencing. We detected 26 distinct drug resistance mutations to Protease Inhibitors (PIs), Nucleoside Reverse Transcriptase Inhibitors (NRTIs), Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs), and Integrase Strand Transfer Inhibitors (INSTIs). We detected linked cross-class drug resistance mutations (PI+NRTI, PI+NNRTI, and NRTI+NNRTI) that confer cross-resistance to multiple drugs in different classes. Fourteen different types of minority mutations were also detected with frequencies ranging from 3.2% to 19%, and the presence of these mutations was verified by Sanger reference sequencing. We detected a putative transmitted drug resistance mutation (TDRM) in one individual that persisted for over seven months from the first sample collected at the acute stage of infection prior to seroconversion.
Our comprehensive drug resistance mutation profiling can advance clinical practice by reporting mutation linkage and minority variants to better guide antiretroviral therapy options.