HIV Drug Susceptibility and Resistance Tests

Number: 0316

Table Of Contents

Policy
Applicable CPT / HCPCS / ICD-10 Codes
Background
References

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Policy

Scope of Policy

This Clinical Policy Bulletin addresses HIV drug susceptibility and resistance tests.

1. Medical Necessity

   1. Aetna considers HIV drug susceptibility and resistance tests (phenotypic or genotypic) medically necessary for any of the following groups:

      1. During acute (new onset) HIV infection to determine if a drug-resistant viral strain was transmitted and plan regimen accordingly; or
      2. Members with suboptimal suppression of viral load after initiation of anti-retroviral therapy to determine the role of resistance and maximize the number of active drugs in the new regimen if indicated; or
      3. Members with virologic failure during highly activated anti-retroviral therapy (HAART) to determine the role of resistance in drug failure and maximize the number of active drugs in the new regimen if indicated.

   2. Aetna considers both HIV phenotypic and genotypic tests when performed at the same time not medically necessary because this approach is duplicative.  Upon review, the alternate type of HIV resistance assay (either phenotypic or genotypic) may be considered medically necessary on an exception basis for members with virologic failure (indicated by a rising plasma HIV RNA concentration (viral load) in HIV-infected individuals receiving adequate doses of antiretroviral therapy where other potential causes of virologic failure have been excluded) despite apparent lack of drug resistance by one type of HIV resistance assay (either phenotypic or genotypic).

   3. Aetna considers phenotypic recombinant virus assays/HIV tropism testing (i.e., Trofile) or genotypic HIV V3-loop assays medically necessary for determining virus tropism of HIV-infected persons before commencement of a chemokine receptor 5 (CCR5) antagonist (e.g., maraviroc [Selzentry]).

2. Experimental and Investigational

   The following procedures are considered experimental and investigational because the effectiveness of these approaches has not been established:

   1. Drug resistance testing for members who have discontinued the use of anti-retroviral drugs because drug resistance mutations may become minor species in the absence of selective drug pressure.  Current tests may not detect minor drug resistant species
   2. Drug resistance testing for members who have HIV viral loads of less than 1,000 HIV RNA copies/ml because available tests cannot reliably detect this low level of viral load
   3. HIV drug resistance and susceptibility tests for all other indications not listed above
   4. HIV tropism testing for other indications not listed above (e.g., during or after failure of a CCR5 antagonist treatment, or for predicting disease progression)
   5. Repeat phenotypic recombinant virus assays/HIV tropism testing (i.e., Trofile) or genotypic HIV V3-loop assays during or after CCR5 antagonist therapy (eg, maraviroc) 
   6. Sentosa SQ HIV-1 genotyping assay for use in drug susceptibility phenotype prediction

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Table:

CPT Codes / HCPCS Codes / ICD-10 Codes

Code	Code Description
Information in the [brackets] below has been added for clarification purposes.   Codes requiring a 7th character are represented by "+":
CPT codes covered if selection criteria are met:
81400 - 81408	Molecular pathology
87900	Infectious agent drug susceptibility phenotype prediction using regularly updated genotypic bioinformatics
87901	Infectious agent genotype analysis by nucleic acid (DNA or RNA); HIV 1, reverse transcriptase and protease
87903	Infectious agent phenotype analysis by nucleic acid (DNA or RNA) with drug resistance tissue culture analysis, HIV 1; first through 10 drugs tested
+ 87904	each additional drug tested (List separately in addition to code for primary procedure)
87906	Infectious agent genotype analysis by nucleic acid (DNA or RNA); HIV-1, other region(e.g. integrase, fusion)
CPT codes not covered for indications listed in the CPB:
0219U	Infectious agent (human immunodeficiency virus), targeted viral next-generation sequence analysis (ie, protease [PR], reverse transcriptase [RT], integrase [INT]), algorithm reported as prediction of antiviral drug susceptibility
ICD-10 codes covered if selection criteria are met:
B20	Human immunodeficiency virus [HIV] disease
B97.35	Human immunodeficiency virus, type 2 [HIV-2], as the cause of diseases classified elsewhere
Z21	Asymptomatic human immunodeficiency virus [HIV] infection status

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Background

Evidence suggests that HIV viral drug resistance is correlated with poor virological response to new therapy.  In-vitro phenotypic and genotypic tests for HIV drug resistance are now available.  A phenotypic test measures the drug susceptibility of the virus by determining the concentration of drug that inhibits viral replication in vitro.  A genotypic test identifies the presence of mutations that are known to confer reduced drug susceptibility.  Several studies have suggested that resistance testing may be useful in assessing the success of salvage anti-retroviral therapy, and improving short-term virological response.  Resistance testing is presently recommended to help guide the choice of new drugs for patients with HIV-1 infection after treatment has failed.  Guidelines also state that resistance testing should be considered in patients with acute HIV infection to assess whether a drug-resistant virus was transmitted.

Phenotypic and genotypic tests appear to provide similar results.  The latter is more commonly used because tests are more readily available and results are available more quickly.  Currently, there is insufficient information as to which approach is preferable in any particular clinical setting.  The Panel on Clinical Practices for Treatment of HIV Infection (2004) concluded that: "There are currently no prospective data to support the use of one type of resistance assay over the other (i.e., genotyping vs. phenotyping) in different clinical situations.  Therefore, one type of assay is generally recommended per sample; however, in the setting of a complex prior treatment history, both assays may provide important and complementary information."

Current evidence for combined genotyping and phenotyping is limited to non-randomized studies; no randomized studies have compared the combination of genotyping and phenotyping directed therapy compared to either genotyping or phenotyping alone.

Commercially available HIV drug susceptibility and resistance tests include genotypic tests (e.g., ABI Gene Sequencing; TrueGene HIV Genotyping GeneKit; HIV-1 GeneSeek Test; Murex LiPA HIV-1 RT; ViroSeq Genotyping System, and Affymetrix GeneChip HIV PRT Assay) and phenotypic tests (e.g., PhenoSense HIV, and Virco Antivirogram).

Napravnik et al (2010) examined the suitability of the ExaVir Load and ExaVir Drug assays for use in patient monitoring.  Specimens from 108 adults were used to compare ExaVir Load HIV-1 RT to Amplicor HIV-1 Monitor HIV-1 RNA, and ExaVir Drug phenotype to HIV GenoSure genotype.  HIV-1 RT and HIV-1 RNA levels were comparable (Pearson correlation coefficient 0.83).  Most (94 %) had detectable results in both assays.  The mean difference (HIV-1 RT minus HIV-1 RNA) was -0.21 log(10)cps/mLequiv.  Relationship between HIV-1 RT and HIV-1 RNA was not affected by RT mutations, CD4 cell count, or efavirenz (EFV) or nevirapine (NVP) use.  Phenotypes were generally consistent with genotype findings for EFV, but not for NVP.  Most patients (93.9 %) with phenotypic EFV resistance had at least 1 EFV mutation, while 78.0 % of patients with phenotypic NVP resistance had at least 1 NVP mutation.  Eleven of 49 samples tested for EFV susceptibility were found resistant (n = 2) or with reduced susceptibility (n = 9) despite the absence of genotypic resistance.  Eleven of 45 samples tested for NVP susceptibility were found resistant (n = 9) or with reduced susceptibility (n = 2) with no evidence of genotypic mutations.  The authors concluded that the ExaVir Load assay performed well and may be an alternative to amplification based techniques for HIV-1 RNA quantification.  On the other hand, the ExaVir Drug assay for phenotypic resistance testing requires further evaluation, especially for NVP.

Human immunodeficiency virus (HIV) phenotypic tropism testing (ie,Trofile) is a molecular assay that identifies the tropism of an individual’s HIV strain to determine if the virus has the ability to invade cells that have the CCR5 marker. This test helps to identify those who may benefit from treatment with maraviroc (Selzentry), a CCR5-receptor antagonist. Viral load must be at least 1,000 copies/ml to determine viral tropism. 

Maraviroc (Selzentry) is indicated for use in combination with other anti-retroviral agents, for treatment-experienced adult patients infected with only chemokine receptor 5 (CCR5)-tropic HIV-1 detectable, who have evidence of viral replication and HIV-1 strains resistant to multiple anti-retroviral agents.  Tropism and treatment history should guide the use of maraviroc (Mueller and Bogner, 2007).

According to the manufacturer of maraviroc (Pfizer, 2008), the following points should be considered when initiating therapy with Selzentry:

• The safety and efficacy of Selzentry have not been established in treatment-naive adult patients or pediatric patients.
• Tropism testing and treatment history should guide the use of Selzentry.
• Use of Selzentry is not recommended in patients with dual/mixed or CXCR4-tropic HIV-1 as efficacy was not demonstrated in a phase 2 study of this patient group.

Also, there are no study results demonstrating the effect of Selzentry on clinical progression of HIV-1 (Pfizer, 2008).

Whitcomb et al (2007) stated that most HIV-1 strains require either the CXCR4 or CCR5 chemokine receptor to efficiently enter cells.  Blocking viral binding to these co-receptors is an attractive therapeutic target.  Currently, several co-receptor antagonists are being evaluated in clinical trials that require characterization of co-receptor tropism for enrollment.  These researchers described the development of an automated and accurate procedure for determining HIV-1 co-receptor tropism (Trofile) and its validation for routine laboratory testing.  HIV-1 pseudoviruses are generated using full-length env genes derived from patient virus populations.  Co-receptor tropism is determined by measuring the abilities of these pseudovirus populations to efficiently infect CD4+/U87 cells expressing either the CXCR4 or CCR5 co-receptor.  Viruses exclusively and efficiently infecting CXCR4+/CD4+/U87 cells are designated X4-tropic.  Conversely, viruses exclusively and efficiently infecting CCR5+/CD4+/U87 cells are designated R5-tropic.  Viruses capable of infecting both CXCR4+/CD4+/U87 and CCR5+/CD4+/U87 cells are designated dual/mixed-tropic.  Assay accuracy and reproducibility were established by evaluating the tropisms of well-characterized viruses and the variability among replicate results from samples tested repeatedly.  The viral subtype, hepatitis B virus or hepatitis C virus co-infection, and the plasma viral load did not affect assay performance.  Minority sub-populations with alternate tropisms were reliably detected when present at 5 to 10 %.  The plasma viral load above which samples can be amplified efficiently in the Trofile assay is 1,000 copies per ml of plasma.  Trofile has been automated for high-throughput use; it can be used to identify patients most likely to benefit from treatment regimens that include a co-receptor inhibitor and to monitor patients on treatment for the emergence of resistant virus populations that switch co-receptor tropism.

The Panel on Anti-retroviral Guidelines for Adults and Adolescents' guidelines on the use of anti-retroviral agents in HIV-1-infected adults and adolescents (DHHS, 2013) recommends that a co-receptor tropism assay should be performed whenever the use of a CCR5 co-receptor antagonist is being considered. The Panel also recommends that co-receptor tropism testing for patients who exhibit virologic failure on a CCR5 antagonist. The Panel stated that a phenotypic tropism assay is preferred to determine HIV-1 co-receptor usage, but that a genotypic tropism assay should be considered as an alternative test to predict HIV-1 co-receptor usage. The guideline explained that, compared to genotypic testing, phenotypic testing has more evidence supporting its usefulness. Therefore, a phenotypic test for co-receptor usage is generally preferred. However, because phenotypic testing is more expensive and requires more time to perform, a genotypic test to predict HIV-1 co-receptor usage should be considered as an alternative test

A European consensus panel on HIV tropism testing (Vandekerckhove et al, 2010; Vandekerckhove et al, 2011) concluded that both the phenotypic Trofile assay and genotypic population sequencing of the V3-loop are recommended for use in clinical practice.  Although the panel did not recommend one methodology over another, the panel stated that it anticipated that genotypic testing will be used more frequently because of its greater accessibility, lower cost and shorter turnaround time.

Perez-Olmeda and Alcami (2013) stated that assessment of HIV co-receptor tropism assay is recommended before starting therapy with CCR5 co-receptor antagonists.  So far, only maraviroc (MVC) has been approved for clinical use and a tropism assay is mandatory for patients with virologic failure or patients in which MVC is considered into future treatment options.  Viral tropism can be assessed with either genotypic or phenotypic methods and to this aim different techniques have been developed.  However, it is unclear which assay is more appropriate for routine testing.  In fact, although phenotypic assays are considered the gold standard as they directly measure the viral tropism and current versions allow detection of a lower threshold of minor CXCR4-dependent variants, the genotypic assays present major practical advantages for their use in the clinical setting.

The Department of Health and Human Services’ Panel on Antiretroviral Guidelines for Adults and Adolescents’ guidelines on "The use of antiretroviral agents in HIV-1-infected adults and adolescents" (2013) provided the following recommendations:

• A co-receptor tropism assay should be performed whenever the use of a CCR5 co-receptor antagonist is being considered (AI).
• Co-receptor tropism testing is also recommended for patients who exhibit virologic failure on a CCR5 antagonist (BIII).
• A phenotypic tropism assay is preferred to determine HIV-1 co-receptor usage (AI).
• A genotypic tropism assay should be considered as an alternative test to predict HIV-1 co-receptor usage (BII).

Mortier et al (2013) noted that determination of HIV-1 co-receptor use is a necessity before initiation of a CCR5 antagonist; but the longevity of a CCR5-use prediction remains unknown.  Genotypic co-receptor tropism determination was performed in 225 newly diagnosed individuals consulting an AIDS Reference Center.  Samples were collected at diagnosis and at initiation of anti-retroviral therapy or just before closure of the study for patients who did not initiate therapy.  For individuals with a discordant tropism prediction on the 2 longitudinal samples, analysis of intermediate samples and single genome sequencing of pro-viral DNA was performed to confirm the tropism switch.  Deep sequencing was done to identify minor CXCR4 or CCR5-using populations in the initial sample.  Overall, tropism switches were rare (7.6 %).  Only a geno2pheno false positive rate of less than 50 % at baseline was retained as predictive for a subsequent switch from CCR5-use only to predicted CXCR4-use.  Minor CXCR4-using virus populations were detected in the first sample of 9 of the 14 R5-to-X4 switchers, but the subsequent outgrowth of these minor populations was documented in only 3.  The authors concluded that with the current guidelines for treatment initiation at CD4(+) T cell counts of less than 500 cells/mm(3), co-receptor switch between diagnosis and starting anti-retroviral therapy is rare.  Patients with R5 viruses and a geno2pheno FPR of less than 50 % are more prone to subsequent co-receptor switch than patients with an FPR of greater than 50 % and will need repeat tropism testing if initiation of maraviroc is considered and previous testing dates from more than 1 year before.

The Panel on Treatment of HIV-Infected Pregnant Women and Prevention of Perinatal Transmission’s guideline on "Use of antiretroviral drugs in pregnant HIV-1-infected women for maternal health and interventions to reduce perinatal HIV transmission" (2014) noted that no validated HIV-2 genotype or phenotype resistance assays are available in the United States.

Anti-Retroviral Resistance Testing in HIV-Positive People

In a Cochrane review, Aves and colleagues (2018) examined the effectiveness of anti-retroviral resistance testing (genotypic or phenotypic) in reducing mortality and morbidity in HIV-positive people.  These investigators identified all relevant studies, regardless of language or publication status, through searches of electronic databases and conference proceedings up to  January 26, 2018.  They searched Medline, Embase, the Cochrane Central Register of Controlled Trials (CENTRAL), in the Cochrane Library, the World Health Organization (WHO) International Clinical Trials Registry Platform (ICTRP), and ClinicalTrials.gov to January 26, 2018.  These researchers searched Latin American and Caribbean Health Sciences Literature (LILACS) and the Web of Science for publications from 1996 to January 26, 2018.  They included all randomized controlled trials (RCTs) and observational studies that compared resistance testing to no resistance testing in people with HIV irrespective of their exposure to anti-retroviral therapy (ART).  Primary outcomes of interest were mortality and virological failure.  Secondary outcomes were change in mean CD4-T-lymphocyte count, clinical progression to AIDS, development of a second or new opportunistic infection, change in viral load, and quality of life (QOL).  Two review authors independently assessed each reference for pre-specified inclusion criteria; they then independently extracted data from each included study using a standardized data extraction form.  They analyzed data on an intention-to-treat (ITT) basis using a random-effects model.  These investigators performed subgroup analyses for the type of resistance test used (phenotypic or genotypic), use of expert advice to interpret resistance tests, and age (children and adolescents versus adults).  They followed standard Cochrane methodological procedures.  A total of 11 RCTs (published between 1999 and 2006), which included 2,531 participants, met the inclusion criteria.  All of these trials exclusively enrolled patients who had previous exposure to ART.  These researchers found no observational studies.  Length of follow-up time, study settings, and types of resistance testing varied greatly.  Follow-up ranged from 12 to 150 weeks.  All studies were conducted in Europe, USA, or South America; 7 studies used genotypic testing, 2 used phenotypic testing, and 2 used both phenotypic and genotypic testing.  Only 1 study was funded by a manufacturer of resistance tests.  Resistance testing made little or no difference in mortality (odds ratio (OR) 0.89, 95 % confidence interval (CI): 0.36 to 2.22; 5 trials, 1,140 participants; moderate-certainty evidence), and may have slightly reduced the number of people with virological failure (OR 0.70, 95 % CI: 0.56 to 0.87; 10 trials, 1,728 participants; low-certainty evidence); and probably made little or no difference in change in CD4 cell count (mean difference (MD) -1.00 cells/mm³, 95 % CI: -12.49 to 10.50; 7 trials, 1,349 participants; moderate-certainty evidence) or progression to AIDS (OR 0.64, 95 % CI: 0.31 to 1.29; 3 trials, 809 participants; moderate-certainty evidence).  Resistance testing made little or no difference in adverse events (AEs) (OR 0.89, 95 % CI: 0.51 to 1.55; 4 trials, 808 participants; low-certainty evidence) and probably reduced viral load (MD -0.23, 95 % CI: -0.35 to -0.11; 10 trials, 1,837 participants; moderate-certainty evidence).  No studies reported on development of new opportunistic infections or QOL.  These investigators found no statistically significant heterogeneity for any outcomes, and the I² statistic value ranged from 0 to 25 %.  They found no subgroup effects for types of resistance testing (genotypic versus phenotypic), the addition of expert advice to interpretation of resistance tests, or age.  Results for mortality were consistent when they compared studies at high or unclear risk of bias versus studies at low risk of bias.  The authors concluded that resistance testing probably improved virological outcomes in people who have had virological failure in trials conducted 12 or more years ago.  These researchers found no evidence in treatment-naive people; resistance testing did not demonstrate important patient benefits in terms of risk of death or progression to AIDS.  The trials included very few participants from low- and middle-income countries.

Sentosa SQ HIV-1 Genotyping Assay in Drug Susceptibility Phenotype Prediction

Dessilly and colleagues (2018) stated that the WHO urges action against the threat posed by HIV drug resistance.  It is well known that the sensitivity of next-generation sequencing (NGS) is greater than that of Sanger Sequencing (SS).  The se researchers examined the performance of the novel NGS HIV-1 drug resistance monitoring system.  NGS analyses were carried out on 67 plasma samples from HIV-1 infected patients using the Sentosa SQ HIV Genotyping Assay from Vela-Dx.  This kit was used on a semi-automated Ion Torrent-based platform.  Sequences were compared to those obtained by SS.  Samples were analyzed in the same, and in separate runs.  Quality controls (QC) were added to control sequencing processes of protease (PRO), reverse transcriptase (RT) and integrase (INT) regions.  Of the 41 analyzed samples, 33 (80.5 %) had identical drug resistance interpretation reports.  Discrepant results were observed for 8 samples; 5 of them were only detected by NGS and had drug resistance mutations (DRMs) with an allelic frequency below the limit of detection of the SS method (between 6.3 to 20.5 %); 2 DRMs were only identified using the SS method.  The sequences were similar in 98.2 % of cases (counting variants as mismatches) and homologous in 99.9 % if missed variants.  Duplicated samples in a single run were similar in 95.7 % (99.9 %) of cases.  Duplicated samples in 2 different runs were 98 % (100 %) homologous.  QC results were manually assessed with a score of 340/340 for detection of DRMs in PRO and RT and 100 % for INT sequencing.  The authors concluded that this was the 1st preliminary evaluation in Belgium employing the Sentosa SQ HIV Genotyping Assay.  The NGS appeared to be a promising tool for the detection of DRMs in HIV-1 patients and showed a higher sensitivity compared to SS.  Moreover, these researchers stated that large studies evaluating the clinical relevance of low frequency DRMs are needed.

Weber and associates (2019) noted that genotypic anti-retroviral drug resistance testing is a critical component of the global efforts to control the HIV-1 epidemic.  In a prospective, cohort study, these investigators examined the semi-automated, NGS-based Vela diagnostics Sentosa SQ HIV-1 genotyping assay in HIV-1-infected patients.  A total of 269 samples were successfully sequenced by both NGS and SS.  Among the 261 protease (PR)/RT sequences, a mean of 0.37 drug resistance mutations were identified by both Sanger and NGS, 0.08 by NGS alone, and 0.03 by Sanger alone.  Among the 50 integrase (IN) sequences, a mean of 0.3 drug resistance mutations were detected by both Sanger and NGS, and 0.08 by NGS alone.  NGS estimated higher levels of drug resistance to 1 or more anti-retroviral drugs for 6.5 % of PR/RT sequences and 4.0 % of IN sequences, whereas Sanger estimated higher levels of drug resistance for 3.8 % of PR/RT sequences.  Although the samples successfully sequenced by the Sentosa SQ HIV genotyping assay demonstrated similar predicted resistance compared with Sanger, 44 % of Sentosa runs failed quality control requiring 17 additional runs.  The authors concluded that this semi-automated NGS-based assay may aid in HIV-1 genotypic drug resistance testing, although numerous quality control issues were observed when this platform was used in a clinical laboratory setting.  These researchers stated that with additional refinement, the Sentosa SQ HIV-1 Genotyping Assay may contribute to the global efforts to control HIV-1.

The authors stated that drawbacks of this study included the predominance of subtype B viruses, although this reflected the distribution of subtypes in the U.S.  Future studies in Africa or Asia or targeting specific populations in the U.S. or Europe is needed to confirm performance with non-subtype B viruses.  Furthermore, the ability of the Sentosa SQ HIV-1 genotyping assay to sequence samples that were not amplifiable by in-house RT-PCR was not examined.  This question may need to be addressed in future studies, especially as the manufacturer incorporates updated and improved primer sets.  Finally, correlation of Sanger and NGS sequencing data with ART regimens was beyond the scope of this work and may be better addressed using samples from a laboratory with extensive local patient testing, or using archived specimens from therapeutic trials, such as from the AIDS Clinical Trial Group.

Alidjinou and co-workers (2019) stated that HIV-1 DNA genotypic drug resistance testing is increasingly conducted to guide treatment switching or simplification in controlled patients.  The Sentosa NGS platform is a fully automated system marketed for drug resistance testing on HIV-1 RNA samples.  These researchers examined this automated NGS solution for routine resistance genotypic resistance testing in pro-viral HIV-1 DNA; SS of the RT, PR and IN genes was performed using the French ANRS protocol.  NGS was performed retrospectively on frozen samples, using the Sentosa platform combined with the Sentosa SQ HIV genotyping Assay.  A total of 77 samples were run once using NGS.  A successful sequencing of the 3 HIV-1 genes (RT, PR, IN) was obtained for 45 samples.  The number of cumulated RAMs was 179, 185 and 219 with SS, NGS 20 % and NGS 10 %, respectively; however, most of them were minor mutations in the PR region.  The mutation detection rate was similar between SS and NGS 20 %.  Several discordances were observed between both methods in the RT and PR regions, mainly due to the use of different DNA extracts, and hypermutation.  The authors concluded that HIV-1 DNA genotypic resistance testing can be performed with the Sentosa platform; several technical optimizations still needed to include the extraction step and to improve the sequencing efficiency.

Raymond and colleagues (2020) noted that patients on ART could benefit from HIV-1 DNA resistance genotyping for examining virologic failure with low viral load or to guide treatment simplification.  Few NGS data are available.  These investigators evaluated the Sentosa SQ HIV genotyping assay with automated extraction on 40 DNA longitudinal samples from treatment-experienced patients by comparison with SS; HIV drug resistance was interpreted using the ANRS algorithm (v29) at the threshold of 20 % and 3 %.  The Sentosa SQ HIV genotyping assay was 100 % successful to amplify and sequence PR and RT and 86 % to amplify and sequence IN when the HIV DNA load was greater than 2.5 log copies/million cells.  The Sentosa and Sanger sequencing were concordant for predicting PR-RT resistance at the threshold of 20 % in 14/18 samples successfully sequenced.  A higher level of resistance was predicted by Sentosa in 3 samples and by Sanger in 1 sample.  The prevalence of resistance was 7 % to PI, 59 % to NRTI, 31 % to NNRTI and 20 % to IN inhibitors using the Sentosa SQ genotyping assay at the threshold of 3 %; 7 additional mutations of less than 20 % were detected using the Sentosa assay.  The authors concluded that automated DNA extraction and sequencing using the Sentosa SQ HIV genotyping assay accurately predicted HIV DNA drug resistance by comparison with Sanger.  Moreover, these researchers stated that prospective studies are needed to examine the clinical interest of HIV DNA genotyping.

Gholami and associates (2020) noted that based on WHO recommendation, drug resistance assay should be performed in initial of treatment and after treatment for administering and monitoring of ART in HIV-1 infected patients.  In this study, NGS analyses were carried out on 41 plasma samples from HIV-1 affected patients using the Sentosa SQ HIV genotyping assay.  This system comprises a semi-automated Ion torrent-based platform and the sequencing results were analyzed based on ANRS, REGA and Stanford drug resistance algorithms.  Phylogenetic analysis was analyzed based on https://comet.lih.lu database as well as MEGA5 Software.  Drug resistances were identified in 33 samples (80 %) out of 41 samples.  The Phylogenetic analysis results showed that CRF-35AD (94 %) and subtypes B (2.4 %) and G (2.4 %) were dominant subtypes in this study.  NRTI and NNRTI associated dominant mutations were M184I/V and K103 N.  High-level resistance to lamivudine (3 TC) and Emtricitabine (FTC) were detected in 34.3 % of patients while 53.1 % were resistant to efavirenz (EFV) and nevirapine (NVP).  The protease inhibitor (PI) minor and major mutations were not reported but more than 95 % of samples had polymorphisms mutation in K20R, M36I, H69K, L89 M positions.  These mutations were subtype-dependent and were completely absent in subtype B virus.  The secondary mutations were reported in positions of E157Q, S230 N, and T97A of the IN gene and 4 samples represent low-level resistance to IN strand transfer inhibitor (INSTI).  The authors concluded that this was the 1st preliminary evaluation of HIV-1 drug resistance mutation (DRM) by using the Sentosa SQ HIV genotyping assay in Iran.  These researchers stated that the NGS represents a promising tool for the accurate detection of DRMs of CRF-35AD that is dominant subtype in Iranian HIV-1 infected population and for the 1st time revealed HIV-1 subtype G in Iranian population.  In the present study polymorphic mutation in the position of K20R, M36I, H69K, L89 M were properly reported in CRF35AD that is dominant in Iranian HIV patients.

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References