Characterization and Structural Analysis of Novel Mutations in Human Immunodeficiency Virus Type 1 Reverse Transcriptase Involved in the Regulation of Resistance to Nonnucleoside Inhibitors

Abstract

Resistance to antivirals is a complex and dynamic phenomenon that involves more mutations than are currently known. Here, we characterize 10 additional mutations (L74V, K101Q, I135M/T, V179I, H221Y, K223E/Q, and L228H/R) in human immunodeficiency virus type 1 (HIV-1) reverse transcriptase which are involved in the regulation of resistance to nonnucleoside reverse transcriptase inhibitors (NNRTIs). These mutations are strongly associated with NNRTI failure and strongly correlate with the classical NNRTI resistance mutations in a data set of 1,904 HIV-1 B-subtype pol sequences from 758 drug-naïve patients, 592 nucleoside reverse transcriptase inhibitor (NRTI)-treated but NNRTI-naïve patients, and 554 patients treated with both NRTIs and NNRTIs. In particular, L74V and H221Y, positively correlated with Y181C, were associated with an increase in Y181C-mediated resistance to nevirapine, while I135M/T mutations, positively correlated with K103N, were associated with an increase in K103N-mediated resistance to efavirenz. In addition, the presence of the I135T polymorphism in NNRTI-naïve patients significantly correlated with the appearance of K103N in cases of NNRTI failure, suggesting that I135T may represent a crucial determinant of NNRTI resistance evolution. Molecular dynamics simulations show that I135T can contribute to the stabilization of the K103N-induced closure of the NNRTI binding pocket by reducing the distance and increasing the number of hydrogen bonds between 103N and 188Y. H221Y also showed negative correlations with type 2 thymidine analogue mutations (TAM2s); its copresence with the TAM2s was associated with a higher level of zidovudine susceptibility. Our study reinforces the complexity of NNRTI resistance and the significant interplay between NRTI-and NNRTI-selected mutations. Mutations beyond those currently known to confer resistance should be considered for a better prediction of clinical response to reverse transcriptase inhibitors and for the development of more efficient new-generation NNRTIs.

Resistance pathways of human immunodeficiency virus type 1 against the combination of zidovudine and lamivudine

“…We could not confirm some other previously reported interactions. Ceccherini-Silberstein et al (2007) reported a synergistic interaction between polymorphism 135T and mutation 103N for efavirenz resistance; however, in our analysis, 135T is linked to 60I. Mutation 60I has been found in patients treated with AZT (Shafer et al, 1995).…”

“…Mutations at position 228 have been linked to NRTI treatment (Deforche et al, 2008a;Gonzales et al, 2003;Rhee et al, 2005;Shahriar et al, 2009). Others have suggested a role in NNRTI resistance for mutations at this position (Ceccherini-Silberstein et al, 2007;Saracino et al, 2006). However, Saracino et al (2006) did not differentiate between mutations 228H and 228R, and their univariate analysis of the impact on susceptibility cannot exclude influences from other mutations present, whilst the study of Ceccherini-Silberstein et al (2007) only provides weak evidence for mutation 228H and rather suggests an involvement in NRTI resistance.…”

“…Others have suggested a role in NNRTI resistance for mutations at this position (Ceccherini-Silberstein et al, 2007;Saracino et al, 2006). However, Saracino et al (2006) did not differentiate between mutations 228H and 228R, and their univariate analysis of the impact on susceptibility cannot exclude influences from other mutations present, whilst the study of Ceccherini-Silberstein et al (2007) only provides weak evidence for mutation 228H and rather suggests an involvement in NRTI resistance. In our BN, mutation 228R is associated weakly with NNRTI treatment and position 215, so a dual role cannot be excluded.…”

HIV-I Reverse Transcriptase Variation in Plasma and Genital Secretion of Antiretroviral-Naive Females

“…26,27 This finding raises a possibility of differential selection process that leads to distinct drug-resistant variants under treatment because some of these mutations have been included as a candidate for positive reproductive fitness 28 and drug resistance. 8,29,30 The limitation of the current study is the smaller sample size, and the history on HIV seroconversion for the study population is unknown and hence the absence of genetic diversity between the compartments could not be related to the stage of HIV infection. In conclusion, in the present analysis, phylogenetic and mutational analysis of RT in plasma and genital secretions of HIV-1-infected ART-naive females demonstrated limited variation likely reflecting the absence of differential selection pressure and genetic diversity.…”

“…2,3 Because the envelope gene is a major determinant of cell tropism, 4,5 sequencing has been usually performed on this region, leaving other potentially important genes unexplored such as RT, that is primarily targeted by the cellular immune response and may also significantly impact viral quasi-species evolution and therefore drug resistance. [6][7][8] The purpose of this study is to ascertain whether RT is subjected to diverse selection pressure in plasma and genital secretions of antiretroviral treatment (ART)-naive females, which is critical to the development of an effective drug regimen against those variants residing in genital compartments.…”