HIV-1 Drug Resistance Mutations: Potential Applications for Point-of-Care Genotypic Resistance Testing

Abstract Transmission of HIV-1 resistance mutations among therapy-naïve patients impairs the efficiency of antiretroviral therapy (ART). Therefore, genotypic resistance testing of patients is recommended at baseline, as this both allows for the selection of the correct ART regimen and for surveillance of transmitted drug resistance mutations (TDRM) among therapy naive HIV-1 patients. In Denmark, the occurrence of TDRM in newly diagnosed and therapy naïve HIV-1 patients is monitored through the SERO project. Here, we investigated if the prevalence of TDRM differed between patients within and outside of phylogenetically identified transmission clusters. Samples from 1,227 newly diagnosed HIV-1 patients were sent along with epidemiological information to the Virological Surveillance and Research group at Statens Serum Institut. HIV-1 RNA extraction, RT-PCR and Sanger sequencing of the pol gene was performed using an in-house assay. The sequences were analyzed using BioNumerics v. 6.6 and manually checked for the presence of mixed mutations and analyzed for mutations using the HIVDB 8.4 algorithm implemented at the Stanford database. Sequence alignments were performed in Mafft, and phylogenetic analysis was performed using Mega 6.0 using the Maximum likelihood general time reversible model with 100 bootstrap replicates. Clusters were identified with ClusterPicker at default settings (cluster support = 90%, genetic distance 4.5%). Active clusters contained newly diagnosed patients from the 2015 to 2017 period. HIV-1 sequences from 588 patients belonged to one of 154 clusters, and sequences from 639 patients did not belong to a cluster. Patients in clusters were significantly more likely to be men who have sex with men and subtype B and significantly less likely to be late presenters (Fisher’s test P < 0.05). The TDRM prevalence was significantly higher for patients outside of clusters than within clusters, 16.6 per cent versus 12.1 per cent, respectively (Fisher’s test P < 0.05); however, no significant differences were found in the TDRM prevalence between the 75 active and 79 inactive clusters, nor between small (<3 patients) and large (≥3 patients) clusters. E138A, V179D, and K103N were the three most prevalent TDRMs for both patient groups, whereas M41L differed between them. In Denmark, the TDRM prevalence is lower within clusters than outside, indicating that TDRM cases are either imported and/or belong to yet unidentified clusters.

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Distribution of Human Immunodeficiency Virus Type 1 Protease and Reverse Transcriptase Mutation Patterns in 4,183 Persons Undergoing Genotypic Resistance Testing

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.48.8.3122-3126.2004 ◽

2004 ◽

Vol 48 (8) ◽

pp. 3122-3126 ◽

Cited By ~ 61

Author(s):

Soo-Yon Rhee ◽

Tommy Liu ◽

Jaideep Ravela ◽

Matthew J. Gonzales ◽

Robert W. Shafer

Keyword(s):

Human Immunodeficiency Virus ◽

Reverse Transcriptase ◽

Resistance Testing ◽

Resistance Mutations ◽

Genotypic Resistance ◽

Drug Resistance Mutations ◽

Genotypic Resistance Testing ◽

Immunodeficiency Virus

ABSTRACT In a sample of 6,156 sequences from 4,183 persons, the top 30 patterns of protease inhibitor, nucleoside reverse transcriptase (RT) inhibitor, and nonnucleoside RT inhibitor mutations accounted for 55, 46, and 66%, respectively, of sequences with drug resistance mutations. Characterization of the phenotypic and clinical significance of these common patterns may lead to improved treatment recommendations for a large proportion of patients for whom antiretroviral therapy is failing.

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Detectable viral load among HIV -1 positive pregnant women on ART (Option B +) in northern Tanzania: Baseline results from the HIVDR study

East Africa Science ◽

10.24248/easci-d-20-00009 ◽

2021 ◽

Vol 3 (1) ◽

pp. 44-50

Author(s):

Nicholaus Steven Mazuguni ◽

Festo Mazuguni ◽

Eva Prosper Muro

Keyword(s):

Drug Resistance ◽

Viral Load ◽

Virological Failure ◽

Virologic Failure ◽

Resistance Mutation ◽

Resistance Testing ◽

Resistance Mutations ◽

Drug Resistance Mutations ◽

Hiv 1 ◽

Level Resistance

Introduction: In Tanzania, the Ministry of Health, Community Development, Gender, Elderly and Children (MoHCDEC) has implemented the Option B+ as one of the strategies to facilitate achievement of elimination of mother to child transmission of HIV. To prevent emergence of drug resistance mutations early identification of option B+ failure is critical. The emergence of drug resistance mutation and subsequent treatment failure poses a major concern for HIV program in low- and middle-income resource settings where treatment options are limited. Methodology: We recruited treatment naïve, treatment experienced HIV-1 positive pregnant women and those who had prophylaxis in their previous pregnancy in Kilimanjaro, northern Tanzania August 2016 to February 2017. Whole blood (2ml) for biochemistry, viral load and drug resistance testing were taken at baseline. ARV drug resistance testing was done on women with VL ≥ 1000 copies/ml. We used descriptive statistic and logistic regression to determine the strength of association between virologic outcome (virologic failure) and independent predictors. Results: One hundred and forty eight (148) pregnant HIV-positive women were enrolled in the study with mean age of 29.82 years (SD=6.17) from August, 2016 to February, 2017. Virologic failure was demonstrated in 34 (23%) with viral load ≥ 1,000 copies/ml. Genotyping results were available from 26 women, mutations associated with ARV resistance were detected in 23.1% (n = 6/26). Among the six women with ARV resistance mutation 4(66.7%) had high level resistance and 2(33.3%) had low level resistance. Among the 26 samples genotyped 15(58%) viruses were subtype A, while eight were subtype C (31%) and three subtypes D (11%). The most dominant drug resistance mutations against the reverse transcriptase inhibitors for the women with high level resistance were K103N, Y188L, D67N, K70R, M184V, T215F, K219EQ, and the low-level resistance was E138A. The older age was associated with virological failure compared to those who were < 20 year of age. Conclusion: Viral load testing should be done on women who were already on antiretroviral treatment on their first antenatal visit to ensure early detection of virological failure and enable clinicians to take an appropriate course of action on their management. Educational intervention on adherence should be targeted at an early stage to women with virological failure during pregnancy to reduce the emergence of HIV-1 drug resistance mutations.

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Genetic Consequences of Antiviral Therapy on HIV-1

Computational and Mathematical Methods in Medicine ◽

10.1155/2015/395826 ◽

2015 ◽

Vol 2015 ◽

pp. 1-9 ◽

Cited By ~ 9

Author(s):

Miguel Arenas

Keyword(s):

Enzyme Inhibitors ◽

Resistance Testing ◽

Evolutionary Analysis ◽

Resistance Mutations ◽

Genotypic Resistance ◽

Antiviral Therapies ◽

Genotypic Resistance Testing ◽

Before And After ◽

Emergence Of Resistance ◽

Hiv 1

A variety of enzyme inhibitors have been developed in combating HIV-1, however the fast evolutionary rate of this virus commonly leads to the emergence of resistance mutations that finally allows the mutant virus to survive. This review explores the main genetic consequences of HIV-1 molecular evolution during antiviral therapies, including the viral genetic diversity and molecular adaptation. The role of recombination in the generation of drug resistance is also analyzed. Besides the investigation and discussion of published works, an evolutionary analysis of protease-coding genes collected from patients before and after treatment with different protease inhibitors was included to validate previous studies. Finally, the review discusses the importance of considering genetic consequences of antiviral therapies in models of HIV-1 evolution that could improve current genotypic resistance testing and treatments design.

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Increase in HIV-1 transmitted drug resistance among untreated 16~25-y-old youths in the China-Myanmar border areas during 2009~2017

10.21203/rs.3.rs-42813/v1 ◽

2020 ◽

Author(s):

Yibo DING ◽

Min CHEN ◽

Jibao WANG ◽

Yuecheng YANG ◽

Yi FENG ◽

...

Keyword(s):

Drug Resistance ◽

Phylogenetic Trees ◽

Cd4 Count ◽

Molecular Networks ◽

Resistance Testing ◽

Transmitted Drug Resistance ◽

Resistance Mutations ◽

Drug Resistance Mutations ◽

The Mean ◽

Hiv 1

Abstract Background Transmitted drug resistance (TDR) can affect antiretroviral therapy (ART) efficacy. Surveillance drug resistance mutations in untreated youths newly reported with HIV-1 are highly representative of local TDR. We investigated HIV-1 TDR, TDR transmission based on molecular networks, and the effect of TDR mutations (TDRMs) on the CD4 count among youths in the China-Myanmar border area near the "Golden Triangle" to better understand TDR and guide ART.Methods From 2009 to 2017, 573 ART-naïve youths (16~25 y) newly reported with HIV-1 were enrolled. CD4 counts were obtained from whole blood. HIV pol gene sequences were amplified from RNA extracted from plasma. The Stanford REGA program and phylogenetic trees were used to determine genotypes. TDRMs were analyzed using the Stanford Calibrated Population Resistance tool. TDR transmission was evaluated from molecular networks of HIV-1 pol genes.Results The average prevalence of TDR was 6.3%, and the resistance to NNRTIs, NRTIs, and PIs was 3.49%, 2.62%, and 0.52%, respectively. TDR prevalence increased significantly during the period 2009~2017 (3.92%~9.48%, p<0.05). The mean CD4 count was significantly lower among individuals with TDRMs (373/mm3 vs. 496/mm3, p=0.013). The rate of network entry of youths harboring TDRMs (63.89%) was significantly higher than that of youths without TDRMs (44.9%).Conclusions The HIV-1 TDR increase and low CD4 count of patients with TDRMs in Dehong at the China-Myanmar border suggest the need for early ART and completion of resistance testing before initiating ART in HIV hotspots. Youths with TDRMs are likely to have links to others, necessitating intervention in onward transmission.

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Development and Evaluation of a National Reference Panel of HIV-1 Protease and Reverse Transcriptase Drug-Resistance Mutations for HIV-1 Genotypic Resistance Assays in China

Molecular Diagnosis & Therapy ◽

10.1007/bf03256351 ◽

2010 ◽

Vol 14 (1) ◽

pp. 31-41 ◽

Cited By ~ 5

Author(s):

Sihong Xu ◽

Jingyun Li ◽

Zuoyi Bao ◽

Hui Xing ◽

Ping Zhong ◽

...

Keyword(s):

Drug Resistance ◽

Reverse Transcriptase ◽

Reference Panel ◽

Resistance Mutations ◽

Genotypic Resistance ◽

National Reference ◽

Drug Resistance Mutations ◽

Hiv 1

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The frequency of HIV-I drug resistance mutations among treatment-naïve individuals at a tertiary care centre in south India

International Journal of STD & AIDS ◽

10.1258/ijsa.2008.008403 ◽

2009 ◽

Vol 20 (8) ◽

pp. 522-526 ◽

Cited By ~ 12

Author(s):

A J Kandathil ◽

R Kannangai ◽

O C Abraham ◽

P Rupali ◽

S A Pulimood ◽

...

Keyword(s):

Drug Resistance ◽

Tertiary Care ◽

Resistance Mutations ◽

Tertiary Care Centre ◽

Genotypic Resistance ◽

Drug Resistance Mutations ◽

Clade B ◽

Clade C ◽

Treatment Naïve ◽

Hiv 1

Antiretroviral treatment (ART) use in India requires information on baseline drug resistance mutations and polymorphisms in the protease (Pr) and reverse transcriptase (RT) genes of HIV-1 strains from treatment-naïve individuals. We report resistance predictor mutations and polymorphisms in the Pr and the RT sequence of non-clade B HIV-1 strains from ART naïve individuals. The genotypic resistance assay was done on 93 treatment-naïve individuals. The sequences were analysed by Stanford HIV drug resistance data for genotypic drug resistance analysis and REGA HIV-1 subtyping tool. Phylogenetic tree was generated with MEGA 4 for quality control. Ninety-two strains belonged to clade C and one to clade A (A1). Amino acid substitutions were seen at positions associated with drug resistance in Pr gene – 10, 24, 74 (each 3%) and position 82 (11%). Substitutions were seen at positions 41 (1%), 100 (1%), 101 (6%), 103 (2%), 179 (6%) and 181 (1%) of the RT sequence known to confer drug resistance in clade B. Polymorphisms in HIV-1 pol gene among treatment-naïve individuals were similar when compared with previous data. One strain each had Y181C substitution, T74S and E35G substitutions in the Pr and one had A98G, K101R and L210FL substitutions in RT.

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Differentiation between Polymorphisms and Resistance-Associated Mutations in Human Cytomegalovirus DNA Polymerase

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00259-10 ◽

2010 ◽

Vol 54 (12) ◽

pp. 5004-5011 ◽

Cited By ~ 11

Author(s):

Meike Chevillotte ◽

Ina Ersing ◽

Thomas Mertens ◽

Jens von Einem

Keyword(s):

Drug Resistance ◽

Dna Polymerase ◽

Human Cytomegalovirus ◽

Antiviral Drug ◽

Drug Susceptibility ◽

Resistance Testing ◽

Resistance Mutations ◽

Genotypic Resistance ◽

Drug Resistance Testing ◽

Genotypic Resistance Testing

ABSTRACT Specific mutations in the human cytomegalovirus (HCMV) DNA polymerase (pUL54) are known to confer resistance against all currently licensed drugs for treatment of HCMV infection and disease. Following the widespread use of antivirals, the occurrence of HCMV drug resistance is constantly increasing. Recently, diagnostic laboratories have started to replace phenotypic drug resistance testing with genotypic resistance testing. However, the reliability and success of genotypic testing highly depend on the availability of high-quality phenotypic resistance data for each individual mutation and for combinations of mutations, with the latter being increasingly found in patients' HCMV isolates. We performed clonal marker transfer experiments to investigate the impacts of 7 different UL54 point mutations and also of combinations of these mutations on drug susceptibility and viral replicative fitness. We show that several mutations—S695T, A972V, K415R, S291P, and A692V—of suspected but uncertain drug susceptibility phenotype, either alone or in combination, were not relevant to antiviral drug resistance. In contrast, the combination of two mutations individually characterized previously—E756K and D413E—conferred high-grade loss of susceptibility to all three antivirals. Our results have been added to the newly available database of all published HCMV resistance mutations (http://www.informatik.uni-ulm.de/ni/mitarbeiter/HKestler/hcmv/index.html ). These data will allow better interpretation of genotypic data and further improve the basis for drug resistance testing.

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Application of HIV-1 genotypic-resistance testing prevents the evolution of further resistance mutations in heavily pretreated patients

Journal of Clinical Virology ◽

10.1016/s1386-6532(00)00183-9 ◽

2001 ◽

Vol 21 (1) ◽

pp. 37-45 ◽

Cited By ~ 3

Author(s):

Bernhard Zöllner ◽

Heinz-Hubert Feucht ◽

Lutwin Weitner ◽

Axel Adam ◽

Matthias Schröter ◽

...

Keyword(s):

Resistance Testing ◽

Resistance Mutations ◽

Genotypic Resistance ◽

Genotypic Resistance Testing ◽

Heavily Pretreated ◽

Pretreated Patients ◽

Hiv 1

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HIV-1 Subtype C Drug Resistance Mutations in Heavily Treated Patients Failing Integrase Strand Transfer Inhibitor-Based Regimens in Botswana

Viruses ◽

10.3390/v13040594 ◽

2021 ◽

Vol 13 (4) ◽

pp. 594

Author(s):

Kaelo K. Seatla ◽

Dorcas Maruapula ◽

Wonderful T. Choga ◽

Tshenolo Ntsipe ◽

Nametso Mathiba ◽

...

Keyword(s):

Drug Resistance ◽

Virologic Failure ◽

Resistance Testing ◽

Strand Transfer ◽

Resistance Mutations ◽

Subtype C ◽

Genotypic Resistance Testing ◽

Transfer Inhibitor ◽

Integrase Strand Transfer Inhibitor ◽

Hiv 1

There are limited real-world mutational and virological outcomes data of treatment-experienced persons diagnosed with HIV-1 subtype C (HIV-1 C) who are failing Integrase Strand Transfer Inhibitor-based regimens. Requisition forms sent for HIV-1 genotypic resistance testing (GRT) between May 2015 and September 2019 were reviewed and participants experiencing virologic failure while on dolutegravir (DTG) or raltegravir (RAL) cART at sampling recruited. Sanger sequencing of the HIV-1 Pol gene was performed from residual plasma samples and drug resistance mutational (DRM) analysis performed using the Stanford University HIV drug resistance database. 40 HIV-1C integrase sequences were generated from 34 individuals, 24 of whom were on DTG cART, three on RAL cART and seven on an unknown (DTG or RAL)-anchored cART at time of GRT. 11/34 (32%) individuals had DRMs to DTG and other integrase inhibitors. 7/11 (64%) patients had exposure to a RAL-based cART at the time of sampling. Out of the 11 individuals with DRMs, one (9%) had 2-class, 6 (55%) had 3-class, and 4 (36%) had 4-class multidrug-resistant HIV-1C. 7/11 individuals (64%) are currently virologically suppressed. Of the four individuals not virologically suppressed, three had extensive DRMs involving 4-classes of ARV drugs and one individual has demised. Resistance to DTG occurs more often in patients exposed to RAL cART. Individuals with 4-class DRMs plus integrase T97 and E157Q mutations appear to have worse outcomes. There is a need for frequent VL monitoring and GRT amongst treatment-experienced HIV-1C diagnosed individuals.

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