Frontiers in Clinical Drug Research - HIV: Volume 5

Atta-ur-Rahman

• Publisher: Bentham Science Publishers
• Year: 2021
• ISBN:
  9789811464454
• Topic: Medicine
• Subtopic: AIDS & HIV

Frontiers in Clinical Drug Research – HIV is a book series that brings updated reviews to readers interested in learning about advances in the development of pharmaceutical agents for the treatment of acquired immune deficiency syndrome (AIDS) and other disorders associated with human immunodeficiency virus (HIV) infection. The scope of the book series covers a range of topics including the medicinal chemistry and pharmacology of natural and synthetic drugs employed in the treatment of AIDS (including HAART) and resulting complications, and the virology and immunological study of HIV and related viruses. Frontiers in Clinical Drug Research – HIV is a valuable resource for pharmaceutical scientists, clinicians and postgraduate students seeking updated and critically important information for developing clinical trials and devising research plans in HIV/AIDS research.
The fifth volume of this series features 5 chapters that cover these topics:
- Clinical Eradication of Latent HIV Reservoirs: Where Are We Now?
- HIV-1 Genotypic Drug Resistance Testing and Next-Generation Sequencing
- Current and Promising Multiclass Drug Regimens and Long-Acting Formulation Drugs in HIV Therapy
- Role of Nanotechnology in HIV Diagnosis and Prognosis
- Preventive and Therapeutic Features of Combination Therapy for HIV

HIV-1 Genotypic Drug Resistance Testing and Next-Generation Sequencing

Binhua Liang^{1, 2, *}, Melanie Murray^{3, 4}, Raghavan Sampathkumar^{1, 5}, Ma Luo^{1, 6}

¹ JC Wilt Infectious Disease Research Center, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada

² Department of Biochemistry & Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada

³ Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, Canada

⁴ The Oak Tree Clinic, British Columbia Women’s Hospital, Vancouver, Canada

⁵ ATPC, Regional Centre for Biotechnology, Haryana, India

⁶ Department of Medical Microbiology & Infectious Diseases, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada

Abstract

The emergence and spread of HIV drug resistance (DR) is threatening the global advances gained from antiretroviral therapy (ART) in suppressing HIV-1 infection and reducing AIDS-related morbidity and mortality over the last decade. Next-generation sequencing (NGS) has fundamentally altered the landscape of HIV-1 DR testing through widely and deep sequencing in a much more cost effective and rapid manner. NGS is improving our ability to understand, diagnose, and prevent HIV DR by accurately identifying low abundant (< 20%) HIV DR variants (LADRVs) relevant to ART outcomes. NGS has been increasingly adopted by research and clinical laboratories for research, surveillance, and clinical monitoring of HIV DR in the last decade. However, NGS faces a number of limitations in its application of HIV DR testing, including sequencing error management, standardization of NGS procedures and instruments, external quality assurance of laboratories, computational and bioinformatics challenges. In this chapter, we will review the HIV-1 genotypic DR testing methods with the focus on the main NGS platforms available for HIV-1 DR diagnosis, their characteristics, applications, and limitations. In addition, we will systematically review LADRV in its distribution, prevalence, mechanism, and impact on ART outcomes. In the end, we will review the host factors, including the human leukocyte antigen (HLA), which effects the efficacy of ART.

Keywords: Allele-specific assays, Antiretroviral therapy, Drug resistance, HIV-1, Low abundant HIV-1 drug-resistant variants, MiSeq, Next-generation Sequencing, Roche 454, Sanger Sequencing.

---

^* Corresponding author Binhua Liang: JC Wilt Infectious Disease Research Center, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada; Tel: [phone]; E-mail: [email protected]

HIV-1 DRUG RESISTANCE TESTING

INTRODUCTION

With the availability of numerous antiretroviral (ARV) medications from a variety of classes and the standard use of combined antiretroviral therapy (ART) for human immunodeficiency virus (HIV), there are now multiple ARV regimen options available for the treatment of persons living with HIV (PLWH). However, resistance to ARVs remains a barrier to obtaining the 90-90-90 targets set forth by UNAIDS [1]. Understanding why HIV resistance emerges, and how best we can detect and manage it, is an important step forward in ending the HIV epidemic.

Resistance to ARVs emerges as a result of the fact that HIV couples a high replication rate (approximately 10¹⁰ virions per day) with a low fidelity reverse transcriptase enzyme (2.6 x 10^-4 errors/base) [2] to produce an immense variety of viral variants each day [3]. Because of these extraordinary rates, low frequency drug resistant viral variants are already present prior to the start of therapy. In this setting, any situation whereby an antiretroviral drug is present at the same time as replicating HIV may result in the selection and amplification of viral variants resistant to the drug(s) present. Examples of this include the step-wise introduction and use of monotherapy/dual therapy with ARVs as they became available in the late 1980s and 1990s, or for the prevention of mother to child HIV transmission [4, 5], the presence of pretreatment HIV drug resistance [6^-8], and imperfect adherence to ART [9, 10]. ARV resistance to one or more drugs thus remains fairly common. In addition, the lack of access to drug resistance testing, with reported testing rates of 0-2% in developing nations, has added to the emergence of drug resistance in patients who have started on standard therapies in the setting of pretreatment drug resistance (DR), and subsequently, failed these regimens [7].

Standard HIV drug resistance testing (genotyping) is usually carried out using standard Sanger sequencing techniques capable of detecting virus variants comprising greater than or equal to 20% of the HIV viral population present in the individual [11]. With the exception of the cited study by Taffa et al [12] which uses an allele-specific assay, studies presented herein represent results from in-house or kit-based population-based Sanger sequencing methods.

Rates of ARV Drug Resistance

Resistance of the HIV virus to ARV therapy may be classified into two forms. Resistance transmitted from one person to another at the time of infection is known as transmitted drug resistance (TDR), while resistance to ARVs that arises at any point after infection, usually as a result of exposure to ARV drugs is known as acquired drug resistance (ADR). In this chapter, “baseline” resistance testing will refer to any testing done prior to initiation of ARVs.

ARV drug resistance testing is an important part of clinical care. When done during acute infection or when infection is recent, resistance testing may identify cases of TDR and thus allow physicians to start patients on a fully active ARV regimen. When done before therapy initiation, but after infection has been present for many months to years, resistance testing may still be useful in identifying TDR, through predominant virus may by this time have reverted to wild type.

Later, testing identifies ADR in those individuals for whom therapy has failed and guides next line ARV regimen selection. A 2015 study by Baxter et al. examined baseline drug resistance testing at several international sites. Testing rates were 0.1% in Africa and 1.8% in South America.

In contrast, testing frequencies were much higher in resource-rich settings, ranging from 81.3% in the United States (US) to 86.7% in Europe and 89.9% in Australia [7].

Resource-Rich Settings

Studies from resource-rich settings examining TDR by Sanger sequencing have demonstrated pre-treatment rates of resistance varying between 6.6% and 19.4% depending on study date and cohort [13^-18]. Transmitted resistance was mainly toward nucleos(t)ide reverse transcriptase inhibitors (NRTI’s) 0.9-9.5% and/or non-nucleoside reverse transcriptase inhibitors (NNRTIs) 1.9-4.5%, while resistance to protease inhibitors (PIs) was less frequent ranging from 0.4-2.7% [13, 15, 16, 19, 20]. Only one of these studies reported resistance to integrase inhibitors (INSTI) with 1/461 patients, exhibiting a major integrase strand transfer inhibitor (INSTI) mutation [17]. In some resource-rich settings, rates of TDR decreased over time, while in others, rates have stayed the same. Specifically, in the large European CASCADE cohort study, the estimated TDR prevalence was 19.4% in 1996, a number that decreased significantly to 8.5% by 2012 [13]. Simila...