HIV-1 Drug Resistance Mutations Research Articles

Establishment and application of a method of tagged-amplicon deep sequencing for low-abundance drug resistance in HIV-1

In the latest HIV-1 global drug resistance report released by WHO, countries are advised to strengthen pre-treatment monitoring of drug resistance in AIDS patients. In this study, we established an NGS-based segmented amplification HIV-1 drug resistance mutation detection method. The pol region of HIV-1 was divided into three short fragments for NGS. The entire amplification and sequencing panel were more cost-effective and batched by using the barcode sequence corresponding to the sample. Each parameter was evaluated using samples with known resistance variants frequencies. The nucleotide sequence error rate, amino acid error rate, and noise value of the NGS-based segmented amplification method were both less than 1%. When the threshold was 2%, the consensus sequences of the HIV-1 NL4-3 strain were completely consistent with the Sanger sequences. This method can detect the minimum viral load of the sample at 102 copies/ml, and the input frequency and detection frequency of HIV-1 resistance mutations within the range of 1%–100% had good conformity (R2 = 0.9963; R2 = 0.9955). This method had no non-specific amplification for Hepatitis B and C. Under the 2% threshold, the incidence of surveillance drug resistance mutations in ART-naive HIV-infected patients was 20.69%, among which NRTIs class resistance mutations were mainly.

Point-of-care HIV viral load and targeted drug resistance mutation testing versus standard care for Kenyan children on antiretroviral therapy (Opt4Kids): an open-label, randomised controlled trial

Feasible, scalable, and cost-effective approaches to ensure virological suppression among children living with HIV are urgently needed. The aim of the Opt4Kids study was to determine the effect of point of care viral load and targeted drug resistance mutation testing in improving virological suppression among children on antiretroviral therapy (ART) in Kenya. In this open-label, individually randomised controlled trial, we enrolled children living with HIV aged 1-14 years and who were either newly initiating or already receiving ART at five study facilities in Kenya. Participants were randomly allocated 1:1 to receive the intervention of point-of-care viral load testing every 3 months, targeted drug resistance mutation testing, and clinical decision support (point-of-care testing) or to receive the standard care (control group), stratified by facility site and age groups (1-9 years vs 10-14 years). Investigators were masked to the randomised group. The primary efficacy outcome was virological suppression (defined as a viral load of <1000 copies per mL) by point-of-care viral load testing at 12 months after enrolment in all participants with an assessment. This study is registered with ClinicalTrials.gov, NCT03820323. Between March 7, 2019, and December 31, 2020, we enrolled 704 participants. Median age at enrolment was 9 years (IQR 7-12), 344 (49%) participants were female and 360 (51%) were male, and median time on ART was 5·8 years (IQR 3·1-8·6). 536 (76%) of 704 had documented virological suppression at enrolment. At 12 months after enrolment, the proportion of participants achieving virological suppression in the intervention group (283 [90%] of 313 participants with a 12 month point-of-care viral load test) did not differ from that in the control group (289 [92%] of 315; risk ratio [RR] 0·99, 95% CI 0·94-1·03; p=0·55). We identified 138 episodes of viraemia in intervention participants, of which 107 (89%) samples successfully underwent drug resistance mutation testing and 91 (85%) had major drug resistance mutations. The median turnaround time for viral load results was 1 day (IQR 0-1) in the intervention group and 15 days (10-21) in the control group. Point-of-care viral load testing decreased turnaround time and targeted drug resistance mutation testing identified a high prevalence of HIV drug resistance mutations in children living with HIV, but the combined approach did not increase rates of virological suppression. Further research in combination interventions, including point-of-care viral load and drug resistance mutation testing coupled with psychosocial support, is needed to optimise virological suppression for children living with HIV. National Institutes of Mental Health of the US National Institutes of Health, Thrasher Research Fund.

Next-generation sequencing (NGS) reveals low-abundance HIV-1 drug resistance mutations among patients experiencing virological failure at the time of therapy switching in Uganda

Background: The emergence and spread of antiretroviral drug resistant HIV-1 variants is one of the major factors associated with therapeutic failure in persons living with HIV (PLWH) as it jeopardizes the efforts to reduce the progression to AIDS. Whereas Sanger sequencing is the most appropriate conventional method for HIV drug resistance testing, it has limited capacity to detect low-abundance variants. This study assessed the suitability of next generation sequencing (NGS) to reveal low-abundance HIV-1 drug resistance mutations amongst patients experiencing virological failure at the time of therapy switching in Uganda. Methods: Archived blood samples previously collected from 60 PLWH were used in this study. Briefly HIV viral RNA was extracted and performed targeted NGS of portions of both the HIV protease and reverse transcriptase genes on the illumina MiSeq. For performance comparison, Sanger sequencing was also performed for all the samples targeting the highlighted genes. The sequence data generated was analyzed using HyDRA bioinformatics pipeline, accompanied by the Stanford HIV drug resistance database, to annotate and report drug resistance mutations/variants. Results: Out of the 60 samples, 58 passed preliminary quality control and were considered for subsequent analysis—of which 38/58 (65.5%) registered low-abundance HIV drug resistance variants. Overall, 757 variants from the NGS data and 90 variants from the Sanger data were identified. The most prevalent minority variants included; K65R (65.5%), K14R (63.8%), K45R (63.8%), L63P (63.8%), I15V (63.8%), K70R (60.3%), V77I (60.3%), L283I (60.3%), G16E (58.6%) and L282C (58.6%). Conclusion: An estimated 65.5% of the sampled population harbors low-abundance HIV-1 variants, most of which are associated with virological failure, and consequently antiviral drug resistance. NGS suitably detects drug resistance mutations even at frequencies below 20% of the viral quasi species that are occasionally missed by Sanger sequencing.

Epidemic Characteristics of HIV Drug Resistance in Hefei, Anhui Province.

To study the characteristics of HIV pretreatment drug resistance (PDR) and acquired drug resistance (ADR) in Hefei, a cross-sectional survey was used to collect 816 samples from newly reported HIV infections from 2017 to 2020 and 127 samples from HIV infections with virological failure from 2018 to 2019 in Hefei. HIV drug resistance levels and drug resistance mutations were interpreted using the Stanford Drug Resistance Database. Molecular networks were constructed by HIV-TRACE. Among the newly reported infections in Hefei, the prevalence of PDR was 6.4% (52/816). The drug resistance mutations were mainly V179E/D/T (12.4%), K103N (1.3%), and V106I/M (1.3%). In addition, it was found that the CRF55_01B subtype had a higher drug resistance rate than other subtypes (p < 0.05). Molecular network analysis found that K103N and V179E may be transmitted in the cluster of the CRF55_01B subtype. The prevalence of ADR among HIV infections with virological failure was 38.6% (49/127), and the drug resistance mutations were mainly M184V (24.4%), K103N/S (15.7%), Y181C (11.0%), G190S/A/E (10.2%), and V106M/I (10.2%). The molecular network was constructed by combining HIV infections with virological failure and newly reported infections; M184V and Y181C may be transmitted between them. The chi-square trend test results indicated that the higher the viral load level, the greater the number of newly reported infections linked to the infections with virological failure in the molecular network. In conclusion, interventions should focus on infections of the CRF55_01B subtype to reduce the transmission of drug-resistant strains. However, improving the treatment effect of HIV infections is beneficial for reducing the second-generation transmission of HIV.

Detection of Patient HIV-1 Drug Resistance Mutations in Russia's Northwestern Federal District in Patients with Treatment Failure.

Highly active antiretroviral therapy (HAART) is currently a combination of three (less frequently four) antiretroviral drugs; these target pathways involved in various stages of HIV replication in the body. Treatment failure is a problem facing doctors and patients using HAART. The most common cause of therapeutic failure is the development of HIV drug resistance. The emergence of resistance is associated with processes involving mutation occurring in the viral genome under the influence of evolutionary factors. Sequencing reactions were performed using the AmpliSens HIV Resist-Seq. Assembly of consensus sequences from fragments obtained during sequencing was carried out using Unipro UGENE softwar. Isolate genotyping was performed using the MEGA-X software with the Neighbor-joining algorithm. According to the analysis, 72.05% of patients had at least one significant mutation associated with drug resistance for the corresponding viral subtype. HIV-1 A6 remains the predominant HIV-1 genetic variant in Russia’s Northwestern Federal District. Among samples with drug resistance mutations, in all cases, mutations associated with pharmacological resistance to two or three drug groups were found. Given the high incidence of resistance mutations in patients on ineffective ART, surveillance of HIV-1 drug resistance, in both ART-receiving and ART-naive individuals, appears necessary. A lack of vigilance and control measures may lead to the spread of primary ART-resistant HIV strains.

Low-frequency HIV-1 drug resistance mutations in antiretroviral naïve individuals in Botswana.

Individuals living with human immunodeficiency virus (HIV) who experience virological failure (VF) after combination antiretroviral therapy (cART) initiation may have had low-frequency drug resistance mutations (DRMs) at cART initiation. There are no data on low-frequency DRMs among cART-naïve HIV-positive individuals in Botswana. We evaluated the prevalence of low-frequency DRMs among cART-naïve individuals previously sequenced using Sanger sequencing. The generated pol amplicons were sequenced by next-generation sequencing. We observed low-frequency DRMs (detected at <20% in 33/103 (32%) of the successfully sequenced individuals, of whom four also had mutations detected at >20%. K65R was the most common low-frequency DRM detected in 8 individuals. Eighty-two of the 103 individuals had follow-up viral load data while on cART. Twenty-seven of the 82 individuals harbored low-frequency DRMs. Only 12 of 82 individuals experienced VF. The following low-frequency DRMs were observed in four individuals experiencing VF: K65R, K103N, V108I, and Y188C. No statistically significant difference was observed in the prevalence of low-frequency DRMs between individuals experiencing VF (4/12) and those not experiencing VF (23/70) (P = .97). However, individuals with non-nucleoside reverse transcriptase inhibitors-associated low-frequency DRMs were 2.68 times more likely to experience VF (odds ratio, 2.68; 95% confidential interval, 0.4-13.9) compared with those without (P = .22). Next-generation sequencing was able to detect low-frequency DRMs in this cohort in Botswana, but these DRMs did not contribute significantly to VF.

Correction for Kouamou et al., "Diagnostic Accuracy of Pan-Degenerate Amplification and Adaptation Assay for HIV-1 Drug Resistance Mutation Analysis in Low- and Middle-Income Countries".

Volume 58, no. 9, e01045-20, 2020, https://doi.org/10.1128/JCM.01045-20. In Table 2, the revised kappa (95% confidence interval) values for NRTI DRMs and NNRTI DRMs are as follows: for NRTI DRMs, 0.97 (0.94–1.00); for NNRTI DRMs, 0.81 (0.71–0.92).

Next generation sequencing reveals low-abundance HIV-1 drug resistance mutations among patients experiencing virological failure at the time of therapy switching in Uganda

Next generation sequencing reveals low-abundance HIV-1 drug resistance mutations among patients experiencing virological failure at the time of therapy switching in Uganda

High Levels of Pretreatment HIV-1 Drug Resistance Mutations Among South African Women Who Acquired HIV During a Prospective Study.

Pretreatment HIV drug resistance (PDR) undermines individual treatment success and threatens the achievement of UNAIDS 95-95-95 targets. In many African countries, limited data are available on PDR as detection of recent HIV infection is uncommon and access to resistance testing is limited. We describe the prevalence of PDR among South African women with recent HIV infection from the Evidence for Contraceptive Options and HIV Outcomes (ECHO) Trial. HIV-uninfected, sexually active women, aged 18-35 years, and seeking contraception were enrolled in the ECHO Trial at sites in South Africa, from 2015 to 2018. HIV testing was done at trial entry and repeated quarterly. We tested stored plasma samples collected at HIV diagnosis from women who seroconverted during follow-up and had a viral load >1000 copies/mL for antiretroviral resistant mutations using a validated laboratory-developed population genotyping assay, which sequences the full protease and reverse transcriptase regions. Mutation profiles were determined using the Stanford Drug Resistance Database. We sequenced 275 samples. The median age was 23 years, and majority (98.9%, n = 272) were infected with HIV-1 subtype C. The prevalence of surveillance drug resistance mutations (SDRMs) was 13.5% (n = 37). Nonnucleoside reverse transcriptase inhibitor (NNRTI) mutations were found in 12.4% of women (n = 34). Few women had NRTI (1.8%, n = 5) and protease inhibitor (1.1%, n = 3) mutations. Five women had multiple NRTI and NNRTI SDRMs. The high levels of PDR, particularly to NNRTIs, strongly support the recent change to the South African national HIV treatment guidelines to transition to a first-line drug regimen that excludes NNRTIs.

Acquired HIV drug resistance among adults living with HIV receiving first-line antiretroviral therapy in Rwanda: A cross-sectional nationally representative survey.

Background:We assessed the prevalence of acquired HIV drug resistance (HIVDR) and associated factors among patients receiving first-line antiretroviral therapy (ART) in Rwanda.Methods:This cross-sectional study included 702 patients receiving first-line ART for at least 6 months with last viral load (VL) results ≥1000 copies/mL. Blood plasma samples were subjected to VL testing; specimens with unsuppressed VL were genotyped to identify HIVDR-associated mutations. Data were analysed using STATA/SE.Results:Median time on ART was 86.4 months (interquartile range [IQR], 44.8–130.2 months), and median CD4 count at ART initiation was 311 cells/mm3 (IQR, 197–484 cells/mm3). Of 414 (68.2%) samples with unsuppressed VL, 378 (88.3%) were genotyped. HIVDR included 347 (90.4%) non-nucleoside reverse transcriptase inhibitor- (NNRTI), 291 (75.5%) nucleoside reverse transcriptase inhibitor- (NRTI) and 13 (3.5%) protease inhibitor (PI) resistance-associated mutations. The most common HIVDR mutations were K65R (22.7%), M184V (15.4%) and D67N (9.8%) for NRTIs and K103N (34.4%) and Y181C/I/V/YC (7%) for NNRTIs. Independent predictors of acquired HIVDR included current ART regimen of zidovudine + lamivudine + nevirapine (adjusted odds ratio [aOR], 3.333 [95% confidence interval (CI): 1.022–10.870]; p = 0.046) for NRTI resistance and current ART regimen of tenofovir + emtricitabine + nevirapine (aOR, 0.148 [95% CI: 0.028–0.779]; p = 0.025), zidovudine + lamivudine + efavirenz (aOR, 0.105 [95% CI: 0.016–0.693]; p = 0.020) and zidovudine + lamivudine + nevirapine (aOR, 0.259 [95% CI: 0.084–0.793]; p = 0.019) for NNRTI resistance. History of ever switching ART regimen was associated with NRTI resistance (aOR, 2.53 [95% CI: 1.198–5.356]; p = 0.016) and NNRTI resistance (aOR, 3.23 [95% CI: 1.435–7.278], p = 0.005).Conclusion:The prevalence of acquired HIV drug resistance (HIVDR) was high among patient failing to re-suppress VL and was associated with current ART regimen and ever switching ART regimen. The findings of this study support the current WHO guidelines recommending that patients on an NNRTI-based regimen should be switched based on a single viral load test and suggests that national HIV VL monitoring of patients receiving ART has prevented long-term treatment failure that would result in the accumulation of TAMs and potential loss of efficacy of all NRTI used in second-line ART as the backbone in combination with either dolutegravir or boosted PIs.

A Partially Multiplexed HIV Drug Resistance (HIVDR) Assay for Monitoring HIVDR Mutations of the Protease, Reverse-Transcriptase (PRRT), and Integrase (INT).

ABSTRACTAs dolutegravir (DTG)-containing HIV regimens are scaled up globally, monitoring for HIV drug resistance (HIVDR) will become increasingly important. We designed a partially multiplexed HIVDR assay using Sanger sequencing technology to monitor HIVDR mutations in the protease, reverse-transcriptase (PRRT), and integrase (INT). A total of 213 clinical and analytical plasma and dried blood spot (DBS) samples were used in the evaluation. The assay detected a wide range of known HIV-1 subtypes and circulating recombinant forms (CRFs) of group M from 139 samples. INT accuracy showed that the average nucleotide (nt) sequence concordance was 99.8% for 75 plasma samples and 99.5% for 11 DBS samples compared with the reference sequences. The PRRT accuracy also demonstrated the average nucleotide sequence concordance was 99.5% for 57 plasma samples and 99.2% for 33 DBS samples. The major PRRT and INT DR mutations of all samples tested were concordant with those of the reference sequences using the Stanford HIV database (db). Amplification sensitivity of samples with viral load (VL) >5000 copies/mL showed plasma exceeded 95% of positivity, and DBS exceeded 90% for PRRT and INT. Samples with VL (1000 to 5000 copies/mL) showed plasma exceeded 90%, and DBS reached 88% positivity for PRRT and INT. Assay precision and reproducibility showed >99% nucleotide sequence concordance in each set of replicates for PRRT and INT. In conclusion, this HIVDR assay met WHO HIVDR assay performance criteria for surveillance, worked for plasma and DBS, used minimal sample volume, was sensitive, and was a potentially cost-effective tool to monitor HIVDR mutations in PRRT and INT.IMPORTANCE This HIVDR genotyping assay works for both plasma and DBS samples, requires low sample input, and is sensitive. This assay has the potential to be a user-friendly and cost-effective HIVDR assay because of its partially multiplexed design. Application of this genotyping assay will help HIVDR monitoring in HIV high-burdened countries using a DGT-based HIV drug regimen recommended by the U.S. President's Emergency Plan for AIDS Relief and the WHO.

HIV-1 Drug Resistance Mutations and Their Clinical Implications in South Korea

Jiwon Yun, M.D., Kiwook Jung, M.D., Jae Hyeon Park, M.D., Ji Hwan Bang, M.D., Namhee Kim, M.D., Eun Youn Roh, M.D., Sue Shin, M.D., Jong Hyun Yoon, M.D., Hyunwoong Park, M.D.. Lab Med Online 2022;12:100-8. https://doi.org/10.47429/lmo.2022.12.2.100

Pre-Treatment Integrase Inhibitor Resistance and Natural Polymorphisms among HIV-1 Subtype C Infected Patients in Ethiopia.

Dolutegravir-based antiretroviral therapy (ART) has been scaled up in many developing countries, including Ethiopia. However, subtype-dependent polymorphic differences might influence the occurrence of HIV-drug-resistance mutations (HIVDRMs). We analyzed the prevalence of pre-treatment integrase strand transfer inhibitor (INSTI) HIVDRMs and naturally occurring polymorphisms (NOPs) of the integrase gene, using plasma samples collected as part of the national HIVDR survey in Ethiopia in 2017. We included a total of 460 HIV-1 integrase gene sequences from INSTI-naïve (n = 373 ART-naïve and n = 87 ART-experienced) patients. No dolutegravir-associated HIVDRMs were detected, regardless of previous exposure to ART. However, we found E92G in one ART-naïve patient specimen and accessory mutations in 20/460 (4.3%) of the specimens. Moreover, among the 288 integrase amino acid positions of the subtype C, 187/288 (64.9%) were conserved (<1.0% variability). Analysis of the genetic barrier showed that the Q148H/K/R dolutegravir resistance pathway was less selected in subtype C. Docking analysis of the dolutegravir showed that protease- and reverse-transcriptase-associated HIVDRMs did not affect the native structure of the HIV-1 integrase. Our results support the implementation of a wide scale-up of dolutegravir-based regimes. However, the detection of polymorphisms contributing to INSTI warrants the continuous surveillance of INSTI resistance.

Analysis of HIV‐1 integrase genotypes and polymorphisms among integrase inhibitors‐based antiretroviral treatment naïve patients in South Sudan

HIV-1 genetic diversity and drug resistance mutations remain public health challenges especially in regions where treatment is limited. The aim of this study was to characterize the HIV-1 integrase (IN) subtype and the possible occurrence of drug-resistance mutations or polymorphisms in resource-poor settings in South Sudan. Dried blood spots from integrase inhibitor treatment (Integrase strand transfer inhibitor [INSTI]) naïve HIV-1 infected patients were subjected to DNA amplification and direct sequencing of integrase genes. The sequences were interpreted for drug resistance according to the Stanford algorithm and the International AIDS Society-USA guidelines. Phylogenetic analysis revealed that HIV-1 subtype D, C, G, A1, and recombinant forms accounted for 40%, 10%, 13.3%, 23.4%, and 13.3%, respectively. Furthermore, inter-subtype recombinants were interspersed within viral strains sampled in other African countries, highlighting complex transmission dynamics within a mobile host population. A total of 78 of 288 (27%) amino acid IN positions presented at least one polymorphism each. Major INSTI resistance mutations were absent, however, polymorphic accessory mutations at positions M50ILR (26.6%) and L74I (3.3%) were detected. Despite the limited size of the study population, our findings underscore the need for monitoring minor and natural polymorphisms that may influence the outcome of treatment regimens.

Genetic diversity and drug resistance mutations of HIV-1 in Leningrad Region

Introduction. The spread of the human immunodeficiency virus type 1 (HIV-1) has become a global concern and has approached the pandemic status. St. Petersburg, a major transportation, tourist, cultural, industrial center, and a border city, is characterized by high migration of the population. The growing number of migrants can contribute to importation and spread of new genetic variants of the virus and trigger recombination processes in the virus population in St. Petersburg and the Leningrad Region.The aim is to characterize the present-day HIV-1 subtype-specific profile and drug-resistance mutations among patients with virological failure on antiretroviral therapy (ART) in the Leningrad Region.Materials and methods. The study performed in 2016–2018 was based on clinical material from HIV-infected individuals living in the Leningrad Region and having confirmed virological failure on ART. The genetic diversity and distribution of drug-resistance mutations of the HIV-1 isolates were assessed through analysis of nucleotide sequences of the virus pol gene fragment that included regions encoding protease and the reverse transcriptase region.Results. In the group (n = 138), most of the patients had sub-subtype A6 (97.4%) common in Russia, though a few patients had subtype B and a recombinant containing circulating recombinant form CRF_03AB and sub-subtype A1. The tests showed that 95.79% of patients had at least one significant drug-resistance mutation; in most cases (73%) the virus was resistant to 2 classes of antiretroviral drugs and in some cases (8%) — to 3 classes. A total of 105 different drug-resistance mutations were found at 35 positions of the virus genome.Conclusions. The high prevalence of HIV-1 drug-resistance mutations among ART patients with virological failure calls attention to surveillance of drug resistance of the virus both among ART-experienced patients and ARTnaïve individuals.

HIV-1 subtype diversity, phylogenetic analysis and study of drug resistance in strains circulating in the Ural Federal District

Introduction. Ural Federal District (UFD) has been one of the most HIV-affected areas in the Russian Federation during past 20 years. The total number of people living with HIV/AIDS (PLWH) and receiving antiretroviral therapy (ART) exceeds 100,000 (61.7% of all PLWH in the UFD), which creates opportunities for the wide spread of resistant HIV strains.Research aim was to determine the distribution of HIV-1 subtypes, evaluate the genetic heterogeneity of HIV-1 strains, and analyze the prevalence of HIV-1 drug resistance mutations (DRM) and the incidence of acquired resistance to antiretroviral drugs (ARVDs) in PLWH receiving ART in the UFD.Materials and methods. 223 patients receiving ART at stage III–IV of HIV infection living in the UFD were examined. To determine the subtypes and the DRM in the HIV-1 pol gene, molecular genetic studies were performed using the AmpliSense® HIV-Resist-Seq kit by Sanger sequencing on the Applied Biosystems 3500 Genetic Analyzer. The genetic heterogeneity was evaluated by calculating the identity of the genome region of the isolated strains in comparison with the genomes of foreign HIV strains, as well as using phylogenetic analysis.Results. In the studied group of patients, 5 subtypes of HIV-1 were identified: subtype A6 prevalence was 91.03%, that of subtype B was 2.69%, 3 recombinant subtypes (CRF03_A6B, CRF02_AG, CRF63_02A6) accounted for 6.28%. Among analyzed HIV-1 strains, 43.9% had a significant genetic similarity (identity of at least 97%) with the strains isolated from patients from neighboring countries (Belarus, Kazakhstan, Kyrgyzstan, Uzbekistan, Lithuania), 35.9% were similar to the strains isolated from patients from far-abroad countries (USA, China, South Korea, Australia, Sweden, Germany). A high heterogeneity of the circulating genetic variants of HIV-1 strains in the territory of the UFD region was established, which is an unfavorable factor for the diagnosis and treatment of HIV. The most common DRMs to both nucleoside reverse transcriptase inhibitors (NRTI) and non-nucleoside reverse transcriptase inhibitors (NNRTI) were detected in 81 specimens (36.3%). NRTI resistance-forming M184V DRM was more common than any other DRM with statistical significance (p = 0,0008) and was detected in 88 specimens (39.5%).Conclusion. In the subtype structure of HIV-1, the dominant subtype was subtype A6, the most common in the countries that were formerly part of the USSR. The heterogeneity of the HIV-1 strains circulating in the UFD suggests that HIV-1 infection continues to be introduced into the UFD from populations outside the Russian Federation. The findings confirm the high prevalence of DRMs (62.8%) and secondary drug resistance of HIV-1 (60.1%) among PLWH in the territory of the UFD. At the same time, high-level resistance was detected in 56.5% of patients, which requires increasing the coverage of HIV resistance testing, including the introduction of monitoring for primary resistance, in order to optimize first-line ART regimens.

Next generation sequencing reveals low-abundance HIV-1 drug resistance mutations among patients experiencing virological failure at the time of therapy switching in Uganda

Next generation sequencing reveals low-abundance HIV-1 drug resistance mutations among patients experiencing virological failure at the time of therapy switching in Uganda

Effects of cytochrome P450 2B6 and constitutive androstane receptor genetic variation on Efavirenz plasma concentrations among HIV patients in Kenya.

The effects of genetic variation of cytochrome P450 2B6 (CYP2B6) and constitutive androstane receptor (CAR) on efavirenz (EFV) plasma concentration was evaluated among 312 HIV patients in Nairobi Kenya. The EFV plasma concentration at steady-state were determined using ultra-high-performance liquid chromatography with a tandem quadruple mass spectrometer (LC-MS/MS). Thirteen CYP2B6 (329G>T, 341T>C, 444 G>T/C, 15582C>T, 516G>T, 548T>G, 637T>C, 785A>G, 18492C>T, 835G>C, 1459C>T and 21563C>T) and one CAR (540C>T) single nucleotide polymorphisms (SNPs) were genotyped using real-time polymerase chain reaction. HIV drug resistance mutations were detected using an in-house genotypic assay. The EFV concentration of patients ranged from 4 ng/mL to 332697 ng/mL (median 2739.5 ng/mL, IQR 1878-4891.5 ng/mL). Overall, 22% patients had EFV concentrations beyond therapeutic range of 1000-4000 ng/mL (4.5%% < 1000 ng/mL and 31.7% > 4000 ng/mL). Five SNPs (15582C>T, 516G>T, 785A>G, 983T>C and 21563C>T) were associated with higher EFV plasma concentration while 18492C>T with lower EFV plasma concentration (p<0.05). Strong linkage disequilibrium (LD) was observed for 15582C>T, 516G>T, 785A>G, 18492C>T, 983T>C, 21563C>T, 1459C>T and CAR 540C>T. Sixteen haplotypes were observed and CTGCTTCC, CTGCTTCT, TTGCTTCT and CGACCCCT were associated with high EFV plasma concentration. In multivariate analysis, factors significantly associated with EFV plasma concentration included; the presence of skin rash (β = 1379, 95% confidence interval (CI) = 3216.9-3416.3; p < 0.039), T allele of CYP2B6 516G>T (β = 1868.9, 95% CI 3216.9-3416.3; p < 0.018), the C allele of CYP2B6 983T>C (β = 2638.3, 95% CI = 1348-3929; p < 0.0001), T allele of CYP2B6 21563C>T (β = 1737, 95% CI = 972.2-2681.9; p < 0.0001) and the presence of 5 to 7 numbers of SNPs per patient (β = 570, 95% CI = 362-778; p < 0.0001) and HIV viral load ≤1000 cells/mL (β = -4199.3, 95% CI = -7914.9 --483.6; p = 0.027). About 36.2% of the patients had EFV plasma concentrations beyond therapeutic window, posing high risk of treatment failure or toxicity. The SNPs of CYP2B6 516G>T, CYP2B6 983T>C, 21563C>T, presence of higher numbers of SNPs per patient and haplotypes CTGCTTCC, CTGCTTCT, TTGCTTCT and CGACCCCT could efficiently serves as genetic markers for EFV plasma concentration and could guide personalization of EFV based ART treatment in Kenya.

HIV-1 drug resistance mutations among individuals with low-level viraemia while taking combination ART in Botswana.

To assess whether a single instance of low-level viraemia (LLV) is associated with the presence of drug resistance mutations (DRMs) and predicts subsequent virological failure (VF) in adults receiving ART in 30 communities participating in the Botswana Combination Prevention Project. A total of 6078 HIV-1 C pol sequences were generated and analysed using the Stanford HIV drug resistance database. LLV was defined as plasma VL = 51-999 copies/mL and VF was defined as plasma VL ≥ 1000 copies/mL. Among 6078 people with HIV (PWH), 4443 (73%) were on ART for at least 6 months. Of the 332 persons on ART with VL > 50 copies/mL, 175 (4%) had VL ≥ 1000 copies/mL and 157 (4%) had LLV at baseline. The prevalence of any DRM was 57 (36%) and 78 (45%) in persons with LLV and VL ≥ 1000 copies/mL, respectively. Major DRMs were found in 31 (20%) with LLV and 53 (30%) with VL ≥ 1000 copies/mL (P = 0.04). Among the 135 PWH with at least one DRM, 17% had NRTI-, 35% NNRTI-, 6% PI- and 3% INSTI-associated mutations. Among the 3596 participants who were followed up, 1709 (48%) were on ART for ≥6 months at entry and had at least one subsequent VL measurement (median 29 months), 43 (3%) of whom had LLV. The OR of experiencing VF in persons with LLV at entry was 36-fold higher than in the virally suppressed group. A single LLV measurement while on ART strongly predicted the risk of future VF, suggesting the use of VL > 50 copies/mL as an indication for more intensive adherence support with more frequent VL monitoring.

Pre-treatment and acquired antiretroviral drug resistance among people living with HIV in Tianjin, China.

This study investigated the prevalence and patterns of pre-treatment and acquired HIV drug resistance mutations among people living with HIV (PLWH) on antiretroviral therapy (ART) for 12 (±3) months in Tianjin, China. From Jan 2018 to Dec 2020, PLWH with HIV-1 RNA greater than 1000 copies/mL visiting the ART clinic in the Tianjin Second People's Hospital were enrolled. Viral RNA isolated from blood samples were taken for genotypic resistance testing using an in-house method. Major drug resistance mutations were analyzed for reverse transcriptase and protease Sanger sequences using the Stanford University HIV Drug Resistance Database. Multivariable Poisson regressions were used to evaluate the factors associated with drug resistance mutations. HIV drug resistance testing was successfully performed on 584 ART-naive and 71 ART-experienced participants. Pre-treatment drug resistance mutation prevalence was 13.5% (79/584) to any antiretroviral drug, 12.5% (73/584) to non-nucleoside reverse transcriptase inhibitors (NNRTIs), 1.5% (9/584) to nucleoside reverse-transcriptase inhibitors (NRTIs), and 0.3% (2/584) to protease inhibitors (PIs). Acquired drug resistance to any antiretroviral drug among PLWH on ART with viral load >1000 copies/mL was 88.7% (63/71). The prevalence of mutation for NNRTIs, NRTIs, and PIs were 93.7% (59/63), 82.5% (52/63), and 3.2% (2/63), respectively. Pre-treatment and acquired drug resistance mutations were highly prevalent among PLWH in Tianjin; therefore, routine baseline genotypic resistance testing and adequate intervals of viral load surveillance are urgently needed for the long-term treatment success. Our findings provide important evidence for first- and second-line regimen drugs for PLWH, especially in China.