Genotypic antiretroviral drug resistance testing at low viral loads in the UK

High prevalence of pre-treatment and acquired HIV-1 drug resistance mutations among non-citizens living with HIV in Botswana

Background

Approximately 30,000 non-citizens are living with HIV in Botswana, all of whom as of 2020 are eligible to receive free antiretroviral treatment (ART) within the country. We assessed the prevalence of HIV-1 mutational profiles [pre-treatment drug resistance (PDR) and acquired drug resistance (ADR)] among treatment-experienced (TE) and treatment-naïve (TN) non-citizens living with HIV in Botswana.

Methods

A total of 152 non-citizens living with HIV were enrolled from a migrant HIV clinic at Independence Surgery, a private practice in Botswana from 2019-2021. Viral RNA isolated from plasma samples were genotyped for HIV drug resistance (HIVDR) using Sanger sequencing. Major known HIV drug resistance mutations (DRMs) in the pol region were determined using the Stanford HIV Drug Resistance Database. The proportions of HIV DRMs amongst TE and TN non-citizens were estimated with 95% confidence intervals (95% CI) and compared between the two groups.

Results

A total of 60/152 (39.5%) participants had a detectable viral load (VL) >40 copies/mL and these were included in the subsequent analyses. The median age at enrollment was 43 years (Q1, Q3: 38-48). Among individuals with VL > 40 copies/mL, 60% (36/60) were treatment-experienced with 53% (19/36) of them on Atripla. Genotyping had a 62% (37/60) success rate - 24 were TE, and 13 were TN. A total of 29 participants (78.4, 95% CI: 0.12-0.35) had major HIV DRMs, including at least one non-nucleoside reverse transcriptase inhibitor (NNRTI) associated DRM. In TE individuals, ADR to any antiretroviral drug was 83.3% (20/24), while for PDR was 69.2% (9/13). The most frequent DRMs were nucleoside reverse transcriptase inhibitors (NRTIs) M184V (62.1%, 18/29), NNRTIs V106M (41.4%, 12/29), and K103N (34.4%, 10/29). No integrase strand transfer inhibitor-associated DRMs were reported.

Conclusion

We report high rates of PDR and ADR in ART-experienced and ART-naïve non-citizens, respectively, in Botswana. Given the uncertainty of time of HIV acquisition and treatment adherence levels in this population, routine HIV-1C VL monitoring coupled with HIVDR genotyping is crucial for long-term ART success.

HIV-1C in-House RNA-Based Genotyping Assay for Detection of Drug Resistance Mutations in Samples with Low-Level Viral Loads

Purpose

Monitoring HIV-1 drug resistance mutations (DRM) in treated patients on combination antiretroviral therapy (cART) with a detectable HIV-1 viral load (VL) is important for the selection of appropriate cART. Currently, there is limited data on HIV DRM at low-level viremia (LLV) (VL 401-999 copies/mL) due to the use of a threshold of VL ≥1000 copies/mL for HIV DRM testing. We here assess the performance of an in-house HIV drug resistance genotyping assay using plasma for the detection of DRM at LLV.

Methods

We used a total of 96 HIV plasma samples from the population-based Botswana Combination Prevention Project (BCPP). The samples were stratified by VL groups: 50 samples had LLV, defined as 401-999 copies/mL, and 46 had ≥1000 copies/mL. HIV pol (PR and RT) region was amplified and sequenced using an in-house genotyping assay with BigDye sequencing chemistry. Known HIV DRMs were identified using the Stanford HIV Drug Resistance Database. Genotyping success rate between the two groups was estimated and compared using the comparison of proportions test.

Results

The overall genotyping success rate was 79% (76/96). For VL groups, the genotyping success was 72% (36/50) at LLV and 87% (40/46) at VL ≥1000 copies/mL. Among generated sequences, the overall prevalence of individuals with at least 1 major or intermediate-associated DRM was 24% (18/76). The proportions of NNRTI-, NRTI- and PI-associated resistance mutations were 28%, 24%, and 0%, respectively. The most predominant mutations detected were K103N (18%) and M184V (12%) in NNRTI- and NRTI-associated mutations, respectively. The prevalence of DRM was 17% (6/36) at LLV and 30% (12/40) at VL ≥1000 copies/mL.

Conclusion

The in-house HIV genotyping assay successfully genotyped 72% of LLV samples and was able to detect 17% of DRM amongst them. Our results highlight the possibility and clinical significance of genotyping HIV among individuals with LLV.

Graphical analysis of guideline adherence to detect systemwide anomalies in HIV diagnostic testing

Background

Analyses of electronic medical databases often compare clinical practice to guideline recommendations. These analyses have a limited ability to simultaneously evaluate many interconnected medical decisions. We aimed to overcome this limitation with an alternative method and apply it to the diagnostic workup of HIV, where misuse can contribute to HIV transmission, delay care, and incur unnecessary costs.

Methods

We used graph theory to assess patterns of HIV diagnostic testing in a national healthcare system. We modeled the HIV diagnostic testing guidelines as a directed graph. Each node in the graph represented a test, and the edges pointed from one test to the next in chronological order. We then graphed each patient’s HIV testing. This set of patient-level graphs was aggregated into a single graph. Finally, we compared the two graphs, the first representing the recommended approach to HIV diagnostic testing and the second representing the observed patterns of HIV testing, to assess for clinical practice deviations.

Results

The HIV diagnostic testing of 1.643 million patients provided 8.790 million HIV diagnostic test results for analysis. Significant deviations from recommended practice were found including the use of HIV resistance tests (n = 3,007) and HIV nucleic acid tests (n = 16,567) instead of the recommended HIV screen.

Conclusions

We developed a method that modeled a complex medical scenario as a directed graph. When applied to HIV diagnostic testing, we identified deviations in clinical practice from guideline recommendations. The model enabled the identification of intervention targets and prompted systemwide policy changes to enhance HIV detection.

Sanger and Next Generation Sequencing Approaches to Evaluate HIV-1 Virus in Blood Compartments

The implementation of antiretroviral treatment combined with the monitoring of drug resistance mutations improves the quality of life of HIV-1 positive patients. The drug resistance mutation patterns and viral genotypes are currently analyzed by DNA sequencing of the virus in the plasma of patients. However, the virus compartmentalizes, and different T cell subsets may harbor distinct viral subsets. In this study, we compared the patterns of HIV distribution in cell-free (blood plasma) and cell-associated viruses (peripheral blood mononuclear cells, PBMCs) derived from ART-treated patients by using Sanger sequencing- and Next-Generation sequencing-based HIV assay. CD4⁺CD45RA⁻RO⁺ memory T-cells were isolated from PBMCs using a BD FACSAria instrument. HIV pol (protease and reverse transcriptase) was RT-PCR or PCR amplified from the plasma and the T-cell subset, respectively. Sequences were obtained using Sanger sequencing and Next-Generation Sequencing (NGS). Sanger sequences were aligned and edited using RECall software (beta v3.03). The Stanford HIV database was used to evaluate drug resistance mutations. Illumina MiSeq platform and HyDRA Web were used to generate and analyze NGS data, respectively. Our results show a high correlation between Sanger sequencing and NGS results. However, some major and minor drug resistance mutations were only observed by NGS, albeit at different frequencies. Analysis of low-frequency drugs resistance mutations and virus distribution in the blood compartments may provide information to allow a more sustainable response to therapy and better disease management.

HIV drug resistance testing among patients failing second line antiretroviral therapy. Comparison of in-house and commercial sequencing

INTRODUCTION

HIV genotyping is often unavailable in low and middle-income countries due to infrastructure requirements and cost. We compared genotype resistance testing in patients with virologic failure, by amplification of HIV pol gene, followed by "in-house" sequencing and commercial sequencing.

METHODS

Remnant plasma samples from adults and children failing second-line ART were amplified and sequenced using in-house and commercial di-deoxysequencing, and analyzed in Harare, Zimbabwe and at Stanford, U.S.A, respectively. HIV drug resistance mutations were determined using the Stanford HIV drug resistance database.

RESULTS

Twenty-six of 28 samples were amplified and 25 were successfully genotyped. Comparison of average percent nucleotide and amino acid identities between 23 pairs sequenced in both laboratories were 99.51 (±0.56) and 99.11 (±0.95), respectively. All pairs clustered together in phylogenetic analysis. Sequencing analysis identified 6/23 pairs with mutation discordances resulting in differences in phenotype, but these did not impact future regimens.

CONCLUSIONS

The results demonstrate our ability to produce good quality drug resistance data in-house. Despite discordant mutations in some sequence pairs, the phenotypic predictions were not clinically significant.

Predicting resistance as indicator for need to switch from first-line antiretroviral therapy among patients with elevated viral loads: development of a risk score algorithm

Background

In resource-limited settings, where resistance testing is unavailable, confirmatory testing for patients with high viral loads (VL) delays antiretroviral therapy (ART) switches for persons with resistance. We developed a risk score algorithm to predict need for ART change by identifying resistance among persons with persistently elevated VL.

Methods

We analyzed data from a Phase IV open-label trial. Using logistic regression, we identified demographic and clinical characteristics predictive of need for ART change among participants with VLs ≥1000 copies/ml, and assigned model-derived scores to predictors. We designed three models, including only variables accessible in resource-limited settings.

Results

Among 290 participants with at least one VL ≥1000 copies/ml, 51 % (148/290) resuppressed and did not have resistance testing; among those who did not resuppress and had resistance testing, 47 % (67/142) did not have resistance and 53 % (75/142) had resistance (ART change needed for 25.9 % (75/290)). Need for ART change was directly associated with higher baseline VL and higher VL at time of elevated measure, and inversely associated with treatment duration. Other predictors included body mass index and adherence. Area under receiver operating characteristic curves ranged from 0.794 to 0.817. At a risk score ≥9, sensitivity was 14.7–28.0 % and specificity was 96.7–98.6 %.

Conclusions

Our model performed reasonably well and may be a tool to quickly transition persons in need of ART change to more effective regimens when resistance testing is unavailable. Use of this algorithm may result in public health benefits and health system savings through reduced transmissions of resistant virus and costs on laboratory investigations.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-016-1611-2) contains supplementary material, which is available to authorized users.

Reliability and clinical relevance of the HIV-1 drug resistance test in patients with low viremia levels

BACKGROUND

We evaluated reliability and clinical usefulness of genotypic resistance testing (GRT) in patients for whom combination antiretroviral therapy (cART) was unsuccessful with viremia levels 50-1000 copies/mL, for whom GRT is generally not recommended by current guidelines.

METHODS

The genotyping success rate was evaluated in 12 828 human immunodeficiency virus type 1 (HIV-1) plasma samples with viremia >50 copies/mL, tested using the commercial ViroSeq HIV-1 Genotyping System or a homemade system. Phylogenetic analysis was performed to test the reliability and reproducibility of the GRT at low-level viremia (LLV). Drug resistance was evaluated in 3895 samples from 2200 patients for whom treatment was unsuccessful (viremia >50 copies/mL) by considering the resistance mutations paneled in the 2013 International Antiviral Society list.

RESULTS

Overall, the success rate of amplification/sequencing was 96.4%. Viremia levels of 50-200 and 201-500 copies/mL afforded success rates of 67.2% and 88.1%, respectively, reaching 93.2% at 501-1000 copies/mL and ≥97.3% above 1000 copies/mL. A high homology among sequences belonging to the same subject for 96.4% of patients analyzed was found. The overall resistance prevalence was 74%. Drug resistance was commonly found also at LLV. In particular, by stratifying for different viremia ranges, detection of resistance was as follows: 50-200 copies/mL = 52.8%; 201-500 = 70%; 501-1000 = 74%; 1001-10 000 = 86.1%; 10 001-100 000 = 76.7%; and >100 000 = 63% (P < .001). Similar bell-shaped results were found when the GRT analysis was restricted to 2008-2012, although at a slightly lower prevalence.

CONCLUSIONS

In patients failing cART with LLV, HIV-1 genotyping provides reliable and reproducible results that are informative about emerging drug resistance.

[Consensus Statement by GeSIDA/National AIDS Plan Secretariat on antiretroviral treatment in adults infected by the human immunodeficiency virus (Updated January 2013)]

OBJECTIVE

This consensus document is an update of combined antiretroviral therapy (cART) guidelines for HIV-1 infected adult patients.

METHODS

To formulate these recommendations a panel composed of members of the GeSIDA/National AIDS Plan Secretariat (Grupo de Estudio de Sida and the Secretaría del Plan Nacional sobre el Sida) reviewed the efficacy and safety advances in clinical trials, cohort and pharmacokinetic studies published in medical journals (PubMed and Embase) or presented in medical scientific meetings. The strength of the recommendations and the evidence which support them are based on a modification of the criteria of Infectious Diseases Society of America.

RESULTS

cART is recommended in patients with symptoms of HIV infection, in pregnant women, in serodiscordant couples with high risk of transmission, in hepatitisB co-infection requiring treatment, and in HIV nephropathy. cART is recommended in asymptomatic patients if CD4 is <500cells/μl. If CD4 are >500cells/μl cART should be considered in the case of chronic hepatitisC, cirrhosis, high cardiovascular risk, plasma viral load >100.000 copies/ml, proportion of CD4 cells <14%, neurocognitive deficits, and in people aged >55years. The objective of cART is to achieve an undetectable viral load. The first cART should include 2 reverse transcriptase inhibitors (RTI) nucleoside analogs and a third drug (a non-analog RTI, a ritonavir boosted protease inhibitor, or an integrase inhibitor). The panel has consensually selected some drug combinations, for the first cART and specific criteria for cART in acute HIV infection, in tuberculosis and other HIV related opportunistic infections, for the women and in pregnancy, in hepatitisB or C co-infection, in HIV-2 infection, and in post-exposure prophylaxis.

CONCLUSIONS

These new guidelines update previous recommendations related to first cART (when to begin and what drugs should be used), how to monitor, and what to do in case of viral failure or adverse drug reactions. cART specific criteria in comorbid patients and special situations are similarly updated.

[Consensus document of Gesida and Spanish Secretariat for the National Plan on AIDS (SPNS) regarding combined antiretroviral treatment in adults infected by the human immunodeficiency virus (January 2012)]

This consensus document has been prepared by a panel consisting of members of the AIDS Study Group (Gesida) and the Spanish Secretariat for the National Plan on AIDS (SPNS) after reviewing the efficacy and safety results of clinical trials, cohort and pharmacokinetic studies published in medical journals, or presented in medical scientific meetings. Gesida has prepared an objective and structured method to prioritise combined antiretroviral treatment (cART) in naïve patients. Recommendations strength (A, B, C) and the evidence which supports them (I, II, III) are based on a modification of the Infectious Diseases Society of America criteria. The current antiretroviral treatment (ART) of choice for chronic HIV infection is the combination of three drugs. ART is recommended in patients with symptomatic HIV infection, in pregnancy, in serodiscordant couples with high transmission risk, hepatitis B fulfilling treatment criteria, and HIV nephropathy. Guidelines on ART treatment in patients with concurrent diagnosis of HIV infection and an opportunistic type C infection are included. In asymptomatic patients ART is recommended on the basis of CD4 lymphocyte counts, plasma viral load and patient co-morbidities, as follows: 1) therapy should be started in patients with CD4 counts <350 cells/μL; 2) when CD4 counts are between 350 and 500 cells/μL, therapy will be recommended and only delayed if patient is reluctant to take it, the CD4 are stabilised, and the plasma viral load is low; 3) therapy could be deferred when CD4 counts are above 500 cells/μL, but should be considered in cases of cirrhosis, chronic hepatitis C, high cardiovascular risk, plasma viral load >10(5) copies/mL, proportion of CD4 cells <14%, and in people aged >55 years. ART should include 2 reverse transcriptase inhibitors nucleoside analogues and a third drug (non-analogue reverse transcriptase inhibitor, ritonavir boosted protease inhibitor or integrase inhibitor). The panel has consensually selected and given priority to using the Gesida score for some drug combinations, some of them co-formulated. The objective of ART is to achieve an undetectable viral load. Adherence to therapy plays an essential role in maintaining antiviral response. Therapeutic options are limited after ART failures, but an undetectable viral load may be possible nowadays. Adverse events are a fading problem of ART. Guidelines in acute HIV infection, in women, in pregnancy, and to prevent mother-to-child transmission and pre- and post-exposition prophylaxis are commented upon. Management of hepatitis B or C co-infection, other co-morbidities, and the characteristics of ART in HIV-2 infection are included.

Genotypic resistance testing in routine clinical care

PURPOSE OF REVIEW

Genotypic resistance testing has become part of routine clinical management of HIV-infected patients. Focussing on observational studies, this review looks at recent advances in this area.

RECENT FINDINGS

Translation of the nucleotide sequence generated by the resistance test into clinically useful information remains a major challenge. A recent key development is the availability of therapy optimization tools to predict regimens that are most likely to achieve virological suppression. Standard genotypic resistance testing only examines protease and part of reverse transcriptase; as drugs are licensed to further targets, it has become necessary to expand the repertoire for testing. Traditionally, genotypic testing has not been attempted at viral loads less than 1000 copies/ml, but recent studies indicate that major mutations are often detected at much lower levels. Similarly, various methods have been developed for the detection of minority variants including allele-specific PCR, single-genome sequencing, and ultra-deep sequencing.

SUMMARY

The technology and interpretation of genotypic resistance tests is in a phase of rapid development. It remains uncertain which of these developments will become part of routine clinical practice.

Causes and consequences of incomplete HIV RNA suppression in clinical trials

The current goal of antiretroviral treatment is suppression of HIV RNA below 50 copies/mL. However, there is evidence for residual low-level plasma viraemia below 50 copies/mL for people with HIV RNA suppression on antiretroviral treatment. It is not clear whether more profound suppression of HIV RNA would lead to a lower risk of virological failure on antiretroviral treatment or emergent drug resistance. There is high variability in the currently used HIV RNA PCR assays for samples with HIV RNA levels close to the detection lower limit of 40-50 copies/mL. For patients who have HIV RNA levels just above 50 copies/mL (often called "single blips"), a repeat sample should be taken to investigate the possibility of technical error. In a systematic review of 48-week efficacy from randomized clinical trials (N = 8,083), patients were significantly more likely to show HIV RNA levels between 50-400 copies/mL while taking fi rst-line boosted PI-based HAART (7.3%) compared with fi rst-line NNRTI-based HAART (4.5%) (p < 0.01). However in a systematic review of emergent drug resistance at failure in the same trials, there was also a significantly lower risk of emerging drug resistance after virological failure of boosted PI-based HAART (p < 0.01). Therefore, HIV RNA blips between 50-400 copies/mL may have different consequences for different classes of antiretrovirals. The most widely used method to analyse HIV RNA in clinical trials - time to loss of virological response (TLOVR) - uses two consecutive HIV RNA measurements to define both virological success and failure. However, other methods may improve precision and increase statistical power.

HIV drug resistance testing

HIV genotypic resistance testing has become a routine test informing the management of HIV-positive patients. This chapter describes the background of this testing and provides a protocol for undertaking the assay by a home-brew method. Methods for interpretation of the data are also outlined.