**1. Introduction**

The scale-up of antiretroviral therapy (ART) has reduced HIV-related deaths and prevented new HIV infections [1]. By the end of 2019, 25.4 million people globally had received ART, with an increase of 19 million when compared with 2009 [2]. However, while the number of patients with ART increases, so does the number of patients with treatment

**Citation:** Li, M.; Liang, S.; Zhou, C.; Chen, M.; Liang, S.; Liu, C.; Zuo, Z.; Liu, L.; Feng, Y.; Song, C.; et al. HIV Drug Resistance Mutations Detection by Next-Generation Sequencing during Antiretroviral Therapy Interruption in China. *Pathogens* **2021**, *10*, 264. https://doi.org/10.3390/ pathogens10030264

Academic Editor: Hezhao Ji

Received: 22 January 2021 Accepted: 20 February 2021 Published: 25 February 2021

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interruption. The rate of ART discontinuation ranges from 10% to 78% under different settings [3–6] and keeps rising with ART prolonged [7]. Patients with ART interruption have decreased CD4+ T cell counts [8], a higher risk of AIDS or death [9] and are a potential source of HIV transmission.

The emergence of HIV drug resistance (HIVDR) results from the low fidelity of HIV reverse transcriptase, the rapid replication of the virus and the selective pressure of antiretroviral drugs [10]. It will compromise the efficacy of ART, lead to virological failure and hamper the progress of HIV/AIDS treatment and prevention [11]. Under ART interruption, HIVDR variants may persist, or revert to wild-type strains or to a resistant revertant like T215rev [12,13]. In addition, new HIVDR variants may be selected by residual drugs with longer half-lives in combined antiretroviral regimens [14].

HIVDR assays are usually carried out using Sanger sequencing (SS), which can detect minority variants at a 15%–20% frequency in HIV viral populations (quasi species) within patients [15]. Next-generation sequencing (NGS) has been increasingly valued in recent years, having the ability to detect lower-frequency mutants and thus more HIVDR variants [16], with increased throughput and higher cost-efficiency [17]. The HIVDR mutation frequencies detected by NGS, but not SS, concentrate between 1.1% and 21.3% [18]. NGS could identify HIV drug-resistant variants at a frequency as low as 0.4% [19]. When patients with low-frequency HIVDR mutations receive ART again, the minority drug-resistant strains may return as predominant ones under the selective pressure of the drug [20]. In addition, multiple studies have shown that the presence of low-frequency HIVDR mutations is often related to treatment failure [21,22].

In this study, we conducted a cross-sectional survey among patients under ART interruption, and compared the mutation detection between NGS and SS using plasma samples from patients with ART interruption, to provide more information about detecting lowfrequency drug resistance mutations and further assistance in implementing ultrasensitive HIVDR surveillance in routine assays and to guide the choice of treatment regimen.
