**1. Introduction**

Human immunodeficiency virus (HIV) and the acquired immunodeficiency syndrome (AIDS) it causes, pose significant public health concern at a global level. With the enhanced access and improved efficacy of antiretroviral therapy (ART), HIV/AIDS has become a manageable chronic reaction in resource-permitted settings [1]. ART improves the lives of people living with HIV, and it also plays a vital role in reducing HIV transmission and HIV incidence [2]. However, HIV drug resistance (HIVDR) significantly decreases the ART efficacy and undermines its benefits. Over 27.5 million people were receiving ART globally by the end of 2020, but up to 24% of pre-treatment patients and 50~90% of patients failing ART may harbor ART-resistant variants [3,4]. Among many recommendations from the 2017 World Health Organization (WHO) Global Action Plan on HIVDR are the expanded coverage and improved effectiveness of genotypic HIVDR testing (HIVDRT) for surveillance and clinical purposes [4]. Any strategy that promotes the access, affordability, sensitivity, and accuracy of HIVDRT would benefit HIVDR managemen<sup>t</sup> globally. The appropriate selection of clinical specimen or analyte plays a vital role in the assay performance and subsequent HIVDR data interpretation and application.

Current HIVDRTs examine the presence of drug resistance-associated mutation (DRM) either via allele-specific assays targeting specific viral mutation(s) or by HIVDR genotyping, which sequences the ART-targeted HIV-1 genes and analyzes all potential DRMs collectively. Any HIV-positive specimen or analyte that contains HIV ribonucleic acid (RNA) or deoxyribonucleic acid (DNA) for the target HIV gene(s) could be used for HIVDRT. Unsurprisingly, a broad spectrum of analytes has been applied or attempted in HIVDRT. Most of such analytes are also applicable for other HIV molecular assays, such as viral load (VL) determination. This HIVDR thematic article provides a focused overview of various analytes' performance, strengths, and weaknesses while applied in HIVDRT.

#### **2. Varied Analytes for HIVDRT**

The commonly-used analytes are summarized as below: (Table 1).

**Citation:** Ji, H.; Sandstrom, P. Overview of the Analytes Applied in Genotypic HIV Drug Resistance Testing. *Pathogens* **2022**, *11*, 739. https://doi.org/10.3390/ pathogens11070739

Academic Editor: Ayalew Mergia

Received: 27 April 2022 Accepted: 28 June 2022 Published: 29 June 2022

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