HIV-1 Genotypic Resistance Testing Using Sanger and Next-Generation Sequencing in Adults with Low-Level Viremia in China

Qun Li; Fengting Yu; Chuan Song; Hongxin Zhao; Qing Xiao; Xiaojie Lao; Siyuan Yang; Yunxia Tang; Fujie Zhang

doi:10.2147/IDR.S387215

HIV-1 Genotypic Resistance Testing Using Sanger and Next-Generation Sequencing in Adults with Low-Level Viremia in China

Infect Drug Resist. 2022 Nov 21:15:6711-6722. doi: 10.2147/IDR.S387215. eCollection 2022.

Authors

Qun Li^{1

2}, Fengting Yu^{1

2}, Chuan Song^{1

2

3}, Hongxin Zhao^{1

2}, Qing Xiao^{1

2}, Xiaojie Lao^{1

2}, Siyuan Yang^{1

2}, Yunxia Tang^{1

2}, Fujie Zhang^{1

2}

Affiliations

¹ Beijing Ditan Hospital, Capital Medical University, Beijing, People's Republic of China.
² Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People's Republic of China.
³ Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, People's Republic of China.

Abstract

Objective: In this study, we aimed to determine drug-resistance mutations (DRMs) in HIV-1 patients with low-level viremia (LLV) and explored the performance of next-generation sequencing (NGS) in detecting HIV DRMs by using LLV samples.

Methods: Overall, 80 samples with LLV were amplified and sequenced using a commercial Sanger sequencing (SS) genotyping kit. Furthermore, 51 samples successfully sequenced using SS were simultaneously subjected to NGS. Genotyping success rates of various viremia categories by two sequencing methods were calculated. Stanford HIV-1 drug-resistance database (HIVdb version 8.9) was used to analyze the DRMs. In the NGS assay, a threshold of 5% was considered for reporting low-frequency variants, and the DRMs detected using SS and NGS were compared.

Results: The overall success rate of PR/RT regions was 88.1% (67/80) using SS and 86.3% (44/51) using NGS. Furthermore, a significant linear trend was noted between viral load and the genotyping success rate. A total of 38.8% (26/67) participants harbored at least one mutation, as revealed through SS. Moreover, the prevalence of DRMs in persistent LLV was significantly higher than that in intermittent LLV (62.1% vs. 21.1%; P < 0.05). A total of 69 DRMs were detected using the two sequencing methods at the threshold of 5%. Moreover, 10 DRMs missed by SS were detected using NGS, whereas 8 DRMs missed by NGS were detected by SS.

Conclusion: Our data suggested that the genotyping resistance testing is necessary to guide antiretroviral therapy optimization in LLV patients.

Keywords: HIV-1; drug-resistance mutation; low-level viremia; next-generation sequencing.

Grants and funding

This work was partly funded by The National 13th Five-Year Grand Program on Key Infectious Disease Control (2018ZX10302-102 to F.Z., 2018ZX10715-005 to H.Z.) and the R&D Program of Beijing Municipal Education Commission (KM202210025004).