Genetic Diversity of Protease and Reverse Transcriptase Sequences in Non-Subtype-B Human Immunodeficiency Virus Type 1 Strains: Evidence of Many Minor Drug Resistance Mutations in Treatment-Naive Patients

Abstract

Most human immunodeficiency virus (HIV) drug susceptibility studies have involved subtype B strains. Little information on the impact of viral diversity on natural susceptibility to antiretroviral drugs has been reported. However, the prevalence of non-subtype-B (non-B) HIV type 1 (HIV-1) strains continues to increase in industrialized countries, and antiretroviral treatments have recently become available in certain developing countries where non-B subtypes predominate. We sequenced the protease and reverse transcriptase (RT) genes of 142 HIV-1 isolates from antiretroviral-naive patients: 4 belonged to group O and 138 belonged to group M (9 subtype A, 13 subtype B, 2 subtype C, 5 subtype D, 2 subtype F1, 9 subtype F2, 4 subtype G, 5 subtype J, 2 subtype K, 3 subtype CRF01-AE, 67 subtype CRF02-AG, and 17 unclassified isolates). No major mutations associated with resistance to nucleoside reverse transcriptase inhibitors (NRTIs) or protease inhibitors were detected. Major mutations linked to resistance to non-NRTI agents were detected in all group O isolates (A98G and Y181C) and in one subtype J virus (V108I). In contrast, many accessory mutations were found, especially in the protease gene. Only 5.6% of the 142 strains, all belonging to subtype B or D, had no mutations in the protease gene. Sixty percent had one mutation, 22.5% had two mutations, 9.8% had three mutations, and 2.1% (all group O strains) had four mutations. In order of decreasing frequency, the following mutations were identified in the protease gene: M36I (86.6%), L10I/V (26%), L63P (12.6%), K20M/R (11.2%), V77I (5.6%), A71V (2.8%), L33F (0.7%), and M46I (0.7%). R211K, an accessory mutation associated with NRTI resistance, was also observed in 43.6% of the samples. Phenotypic and clinical studies are now required to determine whether multidrug-resistant viruses emerge more rapidly during antiretroviral therapy when minor resistance-conferring mutations are present before treatment initiation.

Absence of genotypic drug resistance and presence of several naturally occurring polymorphisms of human immunodeficiency virus‐1 CRF06_cpx in treatment‐naive patients in Estonia

“…The growing number of studies on non-B HIV-1 subtypes has indicated the presence of several polymorphisms in PR region. The limited data about predominant subtypes of this study, CRF06_cpx, from Burkina Faso, France, Italy, and Australia suggest that in this regard this subtype is not different from others [Vergne et al, 2000;Montavon et al, 2002;Monno et al, 2005;Lawrence et al, 2006;Ndembi et al, 2008] On the other hand, PR polymorphisms G17E and L63H also frequently seen by us have been rarely found in other subtypes or CRFs [Kantor et al, 2005;van de Vijver et al, 2006], (http://hivdb.stanford.edu/). Despite the clinical relevance of several PR polymorphisms being largely unknown, some studies have shown that the outcome of ART is dependent on the viral subtype [Perno et al, 2001;Kantor et al, 2005;Pillay et al, 2005].…”

HIV‐1 subtypes and circulating recombinant forms (CRFs) from HIV‐infected patients residing in two regions of central and southern Italy

“…We are aware that the phylogenetic analysis of the pol gene for HIV-1 subtyping provides only partial information, and the possibility does exist that other regions might pertain to different subtypes. Nevertheless, a number of recent studies successfully adopted this approach to evaluate the spread of non-B variants in previously B-restricted countries [Vergne et al, 2000;Balotta et al, 2001;Gonzales et al, 2001;Papa et al, 2002]. Moreover, our data can be considered reliable because of the high concordance between the countries of origin of the patients and the most common viral strains circulating within those countries.…”

“…Historically, HIV-1 subtypes have been phylogenetically classified according to sequence variation within the env gene [McCutchan et al, 1996]. However, reverse transcriptase (RT) and protease (PR) genes of isolates throughout the world differ from one another, thereby allowing subtype grouping [Vergne et al, 2000;Gonzales et al, 2001]. Consequently, pol sequences, now readily available to clinicians for the evaluation of antiretroviral drug susceptibility, may permit the concurrent identification of HIV subtypes without additional costs.…”

Virological outcome and patterns of HIV‐1 drug resistance in patients with 36 months’ antiretroviral therapy experience in Cameroon

“…Briefly, viral RNA was extracted from the plasma using the QIAamp Viral RNA kit (Qiagen, Courtaboeuf, France), and amplified fragments covering the viral protease (amino acids 1Á99) and reverse transcriptase (amino acids 1Á310) were generated with outer G25REV-IN3 and inner AV150-polM4 primers. The assay detected mutants that comprise at least 20% of the virus population [10]. Amino acid sequences were analyzed to identify relevant drug resistance mutations (DRMs), using the Agence Nationale de Recherche sur le Sida et les Hépatites (ANRS) interpretation algorithm, version May 2011 (http://www.hivfrenchresistance.org/).…”