HIV Drug Resistance Research Articles

Adaptive evaluation of mHealth and conventional adherence support interventions to optimize outcomes with new treatment regimens for drug-resistant tuberculosis and HIV in South Africa (ADAP-TIV): study protocol for an adaptive randomized controlled trial

BackgroundHighly effective, short-course, bedaquiline-containing treatment regimens for multidrug-resistant tuberculosis (MDR-TB) and integrase strand transfer inhibitor (INSTI)-containing fixed dose combination antiretroviral therapy (ART) have radically transformed treatment for MDR-TB and HIV. However, without advances in adherence support, we may not realize the full potential of these therapeutics. The primary objective of this study is to compare the effect of adherence support interventions on clinical and biological endpoints using an adaptive randomized platform.MethodsThis is a prospective, adaptive, randomized controlled trial comparing the effectiveness of four adherence support strategies on a composite clinical outcome in adults with MDR-TB and HIV initiating bedaquiline-containing MDR-TB treatment regimens and receiving ART in KwaZulu-Natal, South Africa. Trial arms include (1) enhanced standard of care, (2) psychosocial support, (3) mHealth using cellular-enabled electronic dose monitoring, and (4) combined mHealth and psychosocial support. The level of support will be titrated using a differentiated service delivery (DSD)-informed assessment of treatment support needs. The composite primary outcome will include survival, negative TB culture, retention in care, and undetectable HIV viral load at month 12. Secondary outcomes will include individual components of the primary outcome and quantitative evaluation of adherence on TB and HIV treatment outcomes.DiscussionThis trial will evaluate the contribution of different modes of adherence support on MDR-TB and HIV outcomes with WHO-recommended all-oral MDR-TB regimens and ART in a high-burden operational setting. We will also assess the utility of a DSD framework to pragmatically adjust levels of MDR-TB and HIV treatment support.Trial registrationClinicalTrials.gov NCT05633056. Registered on 1 December 2022

Prevalence of HIV-1 drug resistance among patients with high viral loads while on second-line antiretroviral treatment in Butha-Buthe and Mokhotlong, Lesotho

Prevalence of HIV-1 drug resistance among patients with high viral loads while on second-line antiretroviral treatment in Butha-Buthe and Mokhotlong, Lesotho

The Enlightenment of Evolutionary Medicine

Darwin’s evolution theory serves as the basis to understand biology and medicine. In addition to fossil evidence used by Darwin and his contemporaries, advances in genomics allowed the tracing of gene sequences. Understanding human evolution further allowed us to re-evaluate our body’s maladaptation due to rapid environmental and cultural changes, including anxiety, fever, pain, vomiting as well as menstrual blood loss, increases in reproductive tissue cancers, and dystocia in human females. The talk will discuss the relationship between evolution and acute infectious diseases, including HIV resistance, and why the new coronavirus is not man-made. We will further discuss the relationship between evolution and chronic diseases, including why many modern people are obese and our increased risk of diabetes. Cancer development can be explained as somatic cell evolution, starting from cancer stem cell mutations to developing resistance against cancer therapies. Applying evolutionary concepts in medical research, one can discover new hormones and receptors based on their co-evolution, and the development of bionics based on unique characteristics evolved in diverse organisms. Beyond biology, Darwin’s theory explains the evolution of languages and memes such as currencies and religions. During future evolution, the application of artificial intelligence and big data algorithms could guide our “free will”.

HIV Type-1 Genotyping in the Context of the COVID-19 Pandemic: A Critical Tool for Identifying Antiretroviral Drug Resistance and Optimizing Treatment Strategies

Abstract Introduction/Objective The COVID-19 pandemic strained the healthcare system and the WHO recently reported increased rates of antibiotic resistance. Meanwhile, antiretroviral resistance can also lead to treatment failure and disease progression, especially in HIV patients. Here, we investigated the rates of HIV drug resistance (HIVDR) in our HIV population between pre and post-COVID-19 eras. Methods/Case Report The post-COVID-19 era began on 03/11/2020. Patients positive for HIV-1 between 01/2019- 08/2021 were included (total: 94 patients, 46 pre-COVID-19; 48 post-COVID-19). Patients’ charts were reviewed for demographics, laboratory results (including HIV-1 sequencing/genotyping (e.g., Genosure)), clinical presentation and management. Student t-test and Fisher exact test were calculated. Results (if a Case Study enter NA) Most patients were male (70%) and had a mean age of 49 years. 70% of patients had sufficient viral loads in samples reflexed to HIV genotyping. Post-COVID-19 patients harbored lower viral loads (1.8x105 vs. 3.4x105 copies/mL, p=0.05), CD4 counts (174 vs. 196 cells/mcL, p=0.7), CD8 counts (555 vs. 800 cells/mcL, p=0.04), and higher CD4/CD8 ratio (0.312 vs. 0.266, p=0.57). Overall, 20% of patients had HIVDR. Following COVID-19 pandemic, there was a 9% increase in HIVDR, predominantly seen in non-nucleotide reverse transcriptase inhibitors (NNRTI), although insignificant. Specifically, high resistance was documented for drugs Efavirenz (16%), Nevirapine (16%), and Rilpivirine (13%). We observed an increased prevalence of G190A, K101, K103, and E138 mutations conferring resistance to NNRTIs. Changes to therapy were observed in 47.8% (42/88) of total cases, with an increase of 12.5% in patients from post-COVID-19 era. Additionally, changes to therapy were observed more in patients with infectious diseases consultation (16% increase). Conclusion Increasing HIVDR was seen in our patient population post-COVID-19. Continued surveillance is critical to managing HIVDR and improving patient outcomes. The clinical utility of sequencing tests can outweigh the cost if results are appropriately acted upon which may involve the participation of other clinical teams and the antimicrobial stewardship committee.

1601. Transmitted Drug Resistance in Treatment-Naïve People Living with HIV in Costa Rica

Abstract Background Transmitted drug resistance (TDR) occurs in people living with HIV infection (PLWH) who are not exposed to antiretroviral drugs but who are infected with a virus with mutations associated with resistance. In Costa Rica, HIV genotyping is performed in PLWH failing their first-line ART regimen, but it is not routinely done for all treatment-naïve PLWH before ART initiation, therefore, little is known about TDR prevalence. Methods The aim of this study was to determine the prevalence of TDR and the HIV mutation patterns. During 2020, 162 cases of newly diagnosed treatment-naïve PLWH from all of the country’s HIV clinics were included for a genotyping study. Viral ARN was extracted from plasma samples obtained from the HIV National Reference Laboratory and protease (PR), reverse transcriptase (RT), and integrase (IN) regions were amplified and sequenced. The HIV database Program (Stanford University) and the World Health Organization (WHO) 2009 TDR surveillance mutation list were used for interpretation of resistance-associated mutations. Results The overall prevalence of TDR was 36% (N=59/162). According to ART class, TDR was 22% in the nucleoside reverse transcriptase inhibitors (NRTI), followed by 13% in the non-nucleoside reverse transcriptase inhibitors (NNRTI); for the protease inhibitors (PI) and the integrase inhibitors (INI), TDR was 8% and 3%, respectively. (Figures 1-3). Most common mutations were: in NRTI, M41L (9.9%), and M184I (6.8%); in NNRTI, K103N (7.4%); in PI, M46I (4.3%); in INI, T97A (1.9%). (Table 1). The median age was 32 years-old (range: 16-71), and 91% were male. Median CD4 count was 420 cells/uL (range: 11-1670) and median viral load was 588337 copies/mL (range: 1220-10000000). According to CDC classification, 20% were stage C-3. Source: local database Source: local database Source: local database Conclusion This study population has a moderate level of HIV drug resistance (HIVDR) in ART-naïve PLWH and strongly implies the need to introduce HIVDR surveillance in Costa Rica. These findings confirm the TDR and highlight the need for systematic viral load monitoring and drug resistance testing at diagnosis. Continuous surveillance of newly infected individuals is required to help strategize the best ART regimen for these patients, and should prompt a change in current local recommendations for starting ART. Source: local database Disclosures All Authors: No reported disclosures

633. Nanopore Sequencing and In-house Bioinformatic Pipeline for Rapid and Accurate Detection of NRTI, NNRTI, PI, and INSTI Drug Resistance Mutations

Abstract Background Sanger-based sequencing (SBS) remains the gold standard for HIV-1 drug resistance testing (DRT). However, SBS output is still limited to an approximately 800-1000 bp read length. This is inadequate for amplifying the pol gene region that contains most of the clinically significant drug resistance mutation (DRM) positions, requiring separate steps for the protease (PR) and reverse transcriptase (RT) regions as is available in most commercial genotyping kits. Integrase (IN) gene is typically not sequenced, a major drawback since the WHO-recommended first-line treatment is now IN strand transfer inhibitor-based. We explore an alternative workflow for HIV-1 genotyping and DRT using the MinION sequencer to sequence a ∼2,800 bp amplicon covering PR and RT, and the first 224 codons of the IN region. This workflow also aims to reduce the turnaround time and cost of DRT. Methods Thirty samples (VL 3,160-3,520,000 copies/mL) previously tested for drug resistance underwent PCR amplification using customized primers targeting the pol gene. Agarose gel electrophoresis and library preparation (SQK-RBK110.96 kit, Oxford Nanopore Technologies) were then performed, followed by MinION sequencing. An in-house bioinformatic pipeline was used to analyze the sequencing data. Results MinION sequencing was able to detect all DRMs detected by SBS in all 27 samples and did not detect any DRMs in the ones without DRMs on SBS. A few additional DRMs undetected by SBS were detected by MinION sequencing which is expected since MinION is known to have higher minority variant sensitivity. Comparison of the resistance profiles showed that SBS and MinION sequencing are concordant with a kappa value of 95.8 interpreted as having perfect agreement (Landis & Koch, 1977). DRMs from IN could not be properly evaluated due to lack of positive SBS controls but will be assessed at a later time using deep-sequenced controls. The entire workflow from RNA extraction to data analysis for all samples was completed within 22 hours, significantly shorter than that of the WHO protocol for HIV-1 DRT. The projected cost per run is comparable with that of SBS with a more rapid turnaround time. Conclusion Our findings show that MinION sequencing and our in-house analysis pipeline can rapidly and accurately detect DRMs in HIV-1 positive patients. Disclosures Edsel Maurice Salvaña, MD, MSD: Advisor/Consultant|Pfizer: Advisor/Consultant

1596. Efficacy and Safety of Long-Acting Subcutaneous Lenacapavir in Heavily Treatment-Experienced People with Multi-Drug Resistant HIV: Week 104 Results

Abstract Background Lenacapavir (LEN) is a highly potent, long-acting, first-in-class inhibitor of HIV-1 capsid protein for the treatment of HIV-1 infection in adults with multidrug resistance (MDR) in combination with other antiretrovirals. Methods CAPELLA is an ongoing, phase 2/3 study in heavily treatment-experienced people with HIV-1 with multidrug-resistance. Participants received oral LEN for loading followed by subcutaneous LEN Q6M in addition to an investigator-selected optimized background regimen (OBR). After reporting the efficacy and safety data through 52 weeks (W), the protocol was amended to allow longer follow up; we report W104 results. Results Of 72 participants enrolled (36 in each cohort), 25% were female, 38% were Black, median age was 52 years, 64% had CD4 <200 cells/µL, and 46% had HIV-1 resistant to all 4 major classes (NRTI, NNRTI, PI, INSTI). One participant (of 72) decided not to continue in the post-W52 extension. At W104, 62% (44/71) had HIV-1 RNA <50 c/mL via FDA Snapshot algorithm, and 14% (10/71) had HIV-1 RNA >50 c/mL; 24% discontinued for reasons other than lack of efficacy (13/71) or had missing data but were on study drug (4/71). When analyzed as missing=excluded, 81% (44/54) had HIV-1 RNA <50 c/mL. CD4 count increased by a median 97 cells/µL (Q1 to Q3: 18 to 224) and the proportion of participants with CD4 count ≥200 cells/µL increased from 36% (26/72) at baseline to 71% (39/55) at W104. Fourteen participants had emergent LEN resistance (9 previously reported), 6 of whom subsequently suppressed while continuing LEN. The median (Q1–Q3) duration of follow-up on LEN was 125 (111–140) weeks. One participant discontinued due to injection site nodule at W52 (Grade 1, previously reported); no participant discontinued due to an AE after W52. Most common AEs (excluding injection site reactions [ISRs] and COVID-19) were diarrhea and nausea (19% each, +5% each since W52, respectively). LEN-related ISRs were mostly mild-to-moderate. Conclusion In people with MDR HIV-1 and limited treatment options, LEN in combination with an OBR was well tolerated and maintained virologic suppression at W104. These data support the use of LEN for treatment of people with MDR HIV-1. Disclosures Onyema Ogbuagu, MD, Gilead Sciences, Inc: Advisor/Consultant|Gilead Sciences, Inc: Honoraria|Janssen: Advisor/Consultant|Viiv: Advisor/Consultant Edwin DeJesus, MD, Gilead Sciences, Inc: Advisor/Consultant|Theratechnology: Advisor/Consultant|Theratechnology: Honoraria Mezgebe Berhe, MD, MPH, Gilead Sciences, Inc: Clinical Trial Investigator Gary J Richmond, MD, Gilead Sciences, Inc: Grant/Research Support|Glaxo Smith Kline: Grant/Research Support|Insmed: Grant/Research Support|TaiMed: Grant/Research Support Peter J Ruane, MD, Gilead Sciences, Inc: Advisor/Consultant|Viiv: Advisor/Consultant|Viiv: Honoraria Gary I. Sinclair, MD, Abbvie: Grant/Research Support|Gilead: Advisor/Consultant|Gilead: Grant/Research Support|Janssen: Advisor/Consultant|Janssen: Grant/Research Support|Janssen: Honoraria|Merck: Advisor/Consultant|Merck: Grant/Research Support|Merck: Honoraria|Thera: Advisor/Consultant|Thera: Grant/Research Support|Thera: Honoraria|ViiV: Advisor/Consultant|ViiV: Grant/Research Support|ViiV: Honoraria Moti N Ramgopal, MD, Abbvie: Honoraria|Gilead Sciences, Inc: Advisor/Consultant|Gilead Sciences, Inc: Honoraria|Janssen: Advisor/Consultant|Janssen: Honoraria|Merck: Advisor/Consultant|Viiv: Advisor/Consultant|Viiv: Honoraria William Sanchez, MD, Gilead Sciences, Inc: Grant/Research Support|GSK: Grant/Research Support|Merck: Advisor/Consultant|Merck: Grant/Research Support Gordon E Crofoot, MD, Gilead Sciences, Inc: Clinical Trial Investigator Nicolas A Margot, MA, Gilead Sciences, Inc: Employee|Gilead Sciences, Inc: Stocks/Bonds Hui Wang, PhD, Gilead Sciences, Inc: Employee|Gilead Sciences, Inc: Stocks/Bonds Hadas Dvory-Sobol, PhD, Gilead Sciences, Inc: Employee|Gilead Sciences, Inc: Stocks/Bonds Martin Rhee, MD, Gilead Sciences, Inc: Employee|Gilead Sciences, Inc: Stocks/Bonds Jared Baeten, MD, PhD, Gilead Sciences, Inc: Employee|Gilead Sciences, Inc: Stocks/Bonds Sorana Segal-Maurer, MD, Gilead Sciences, Inc: Advisor/Consultant|Gilead Sciences, Inc: Honoraria|Janssen: Advisor/Consultant|Janssen: Honoraria|Theratechnologies: Advisor/Consultant|Theratechnologies: Honoraria|Viiv: Advisor/Consultant|Viiv: Honoraria

High viral suppression and detection of dolutegravir-resistance associated mutations in treatment-experienced Tanzanian adults living with HIV-1 in Dar es Salaam

To curb HIV infection rate in Tanzania, antiretroviral therapy (ART) has been scaled up since 2006, and in 2019, the country shifted to regimen including dolutegravir as a default first line. We assessed the success of ART and the contribution of HIV drug resistance (HIVDR) to unsuppressed viral loads. Between February and May 2023 a cross-sectional survey with random sampling was conducted in the six clinics in an urban cohort in Dar es Salaam. Patients with unsuppresed viral loads (local criteria viral load (VL) ≥ 1000 copies/mL) were tested for HIVDR mutations using the WHO adapted protocol for plasma samples. Mutations were interpreted using the Stanford HIVDR database. In total 600 individuals participated in this survey, the majority were female (76.83%), mean age (pm standard deviation) was 44.0 (pm 11.6) years. The median duration on ART (interquartile range) was 6.5 (3.9–10.2) years. Approximately 99% were receiving tenofovir + lamivudine + dolutegravir as a fixed dose combination. VL testing was successful in 99.67% (598/600) of survey patients and only 33 had VL ≥ 1000 copies/mL, resulting in a viral suppression level of 94.48% (565/598, 95% CI 92.34–96.17%). For 23 samples, protease and reverse transcriptase (RT) genotyping were successful, with 13 sequences containing RT inhibitor surveillance drug resistance mutations (SDRMs) (56.5%). No SDRM against protease inhibitors were detected. Thirty samples were successfully genotyped for integrase with 3 sequences (10.08%) containing integrase strand transfer inhibitor (INSTI) SDRMs. In samples successfully genotyped in the three genetic regions, 68.18% (16/22) had a genotypic susceptibility score (GSS) ≥ 2.5 for the concurrent regimen, implying factors beyond drug resistance caused the unsuppressed viral load. For five patients, GSS indicated that HIVDR may have caused the unsuppressed viral load. All three patients with INSTI resistance mutations were highly resistant to dolutegravir and accumulated nucleoside and non-nucleoside RT inhibitor HIVDR mutations. Although in this cohort the last 95 UNAIDS target was almost achieved, HIVDR mutations, including INSTIs resistance mutations were detected in HIV-positive individuals taking ART for at least one year. We recommend the design and implementation of high-impact interventions to prevent the increase of HIVDR, failure of dolutegravir and address the non-resistance factors in the study area.

Performance characteristics of Allele-Specific PCR (ASPCR) in detecting drug resistance mutations among non-B HIV-1 Variants

Allele-Specific Polymerase Chain Reaction (ASPCR) is an affordable point-mutation assay whose validation could improve the detection of HIV-1 drug resistance mutations (DRMs) in resource-limited settings (RLS). We assessed the performance of ASPCR onforty-four non-B HIV-1 plasma samples from patients who were ARV treated in failure in N’Djamena-Chad. Viral RNA was reverse-transcribed and amplified using LightCycler® FastStart DNA MasterPLUS SYBR Green I. Detection of six major DRMs (K70R, K103N, Y181C, M184V, T215F, T215Y) was evaluated on Roche LightCycler®480 automated system (with dilutions 0.01–100%). ASPCR-results were compared to Sanger-sequencing (gold-standard). Correlations of mutation curves were excellent (R2 >0.97); all DRMs were detected with desirable mutant/wild-type threshold differences (ΔCt≥9) except K70R(ΔCtK70R=6; ΔCtK103N=13; ΔCtM184V=9; ΔCtT215F=12; ΔCtT215Y=12; ΔCtY181C=9) and positive controls were below required thresholds. Also, ASPCR reproducibility on DRMs was assessed by using dilutions of intra-assay and inter-assay coefficient of variations respectively with a threshold of less than 50(i.e.<0.50 variation) which are;: K70R (0.02–0.28 vs. 0.12–0.37), K103N (0.08–0.42 vs. 0.12–0.37), Y181C (0.12–0.39 vs. 0.31–0.37), M184V (0.13–0.39 vs. 0.23–0.42), T215F (0.05–0.43 vs. 0.04–0.45) and T215Y (0.13–0.41 vs. 0.19–0.41). DRM detection-rate by ASPCR vs Sanger was respectively: M184V (63.6% vs. 38.6%); T215F (18.1% vs. 9.1%); T215Y (6.8% vs. 2.3%); K70R (4.5% vs. 2.3%). K103N (22.7% vs. 13.6%); Y181C (13.6% vs. 11.4%). Correlations of mutation curves were excellent (R2 >0.97); all DRMs were detected with desirable mutant/wild-type threshold differences (ΔCt≥9) except K70R(ΔCtK70R=6; ΔCtK103N=13; ΔCtM184V=9; ΔCtT215F=12; ΔCtT215Y=12; ΔCtY181C=9) and positive controls were below required thresholds. Also, ASPCR reproducibility on DRMs was assessed by using dilutions of intra-assay and inter-assay coefficient of variations respectively with a threshold of less than 50(i.e.<0.50 variation) which are;: K70R (0.02–0.28 vs. 0.12–0.37), K103N (0.08–0.42 vs. 0.12–0.37), Y181C (0.12–0.39 vs. 0.31–0.37), M184V (0.13–0.39 vs. 0.23–0.42), T215F (0.05–0.43 vs. 0.04–0.45) and T215Y (0.13–0.41 vs. 0.19–0.41). DRM detection-rate by ASPCR vs Sanger was respectively: M184V (63.6% vs. 38.6%); T215F (18.1% vs. 9.1%); T215Y (6.8% vs. 2.3%); K70R (4.5% vs. 2.3%). K103N (22.7% vs. 13.6%); Y181C (13.6% vs. 11.4%). ASPCR appears more efficient for detecting DRMs on diverse HIV-1 non-B circulating in RLS like Chad.

Antibody-directed evolution reveals a mechanism for enhanced neutralization at the HIV-1 fusion peptide site

The HIV-1 fusion peptide (FP) represents a promising vaccine target, but global FP sequence diversity among circulating strains has limited anti-FP antibodies to ~60% neutralization breadth. Here we evolve the FP-targeting antibody VRC34.01 in vitro to enhance FP-neutralization using site saturation mutagenesis and yeast display. Successive rounds of directed evolution by iterative selection of antibodies for binding to resistant HIV-1 strains establish a variant, VRC34.01_mm28, as a best-in-class antibody with 10-fold enhanced potency compared to the template antibody and ~80% breadth on a cross-clade 208-strain neutralization panel. Structural analyses demonstrate that the improved paratope expands the FP binding groove to accommodate diverse FP sequences of different lengths while also recognizing the HIV-1 Env backbone. These data reveal critical antibody features for enhanced neutralization breadth and potency against the FP site of vulnerability and accelerate clinical development of broad HIV-1 FP-targeting vaccines and therapeutics.

Evolution Driven By A Varying Host Environment Selects For Distinct HIV-1 Entry Phenotypes and Other Informative Variants.

HIV-1 generates remarkable intra- and inter-host viral diversity during infection. In response to dynamic selective pressures of the host environment, HIV-1 will evolve distinct phenotypes - biological features that provide fitness advantages. The transmitted form of HIV-1 has been shown to require a high density of CD4 on the target cell surface (as found on CD4+ T cells) and typically uses CCR5 as a co-receptor during entry. This phenotype is referred to as R5 T cell-tropic (or R5 T-tropic); however, HIV-1 can switch to a secondary co-receptor, CXCR4, resulting in a X4 T cell-tropic phenotype. Macrophage-tropic (or M-tropic) HIV-1 can evolve to efficiently enter cells expressing low densities of CD4 on their surface (such as macrophages/microglia). So far only CCR5-using M-tropic viruses have been found. M-tropic HIV-1 is most frequently found within the central nervous system, and infection of the CNS has been associated with neurological impairment. It has been shown that interferon resistance phenotypes have a selective advantage during transmission, but the underlying mechanism of this is still unclear. During untreated infection, HIV-1 evolves under selective pressure from both the humoral/antibody response and CD8+ T cell killing. Sufficiently potent antiviral therapy will suppress viral replication, but if the antiviral drugs are not sufficiently potent to stop replication then the replicating virus will evolve drug resistance. HIV-1 phenotypes are highly relevant to treatment efforts, clinical outcomes, vaccine studies, and cure strategies. Therefore, it is critical to understand the dynamics of the host environment that drive these phenotypes and how they affect HIV-1 pathogenesis. This review will provide a comprehensive discussion of HIV-1 entry, transmission, and drug resistance phenotypes. Finally, we will assess the methods used in previous and current research to characterize these phenotypes.

Changes in Primary HIV-1 Drug Resistance Due to War Migration from Eastern Europe

In recent years, especially as a result of war in Ukraine, enormous movements of migration to Poland from eastern European countries have been reported, including people living with Human Immunodeficiency Virus (HIV). We have conducted multi-center, prospective study, which aimed to establish HIV-1 subtype and assess the presence of primary drug resistance mutations to nucleoside reverse transcriptase inhibitors, non-nucleoside reverse transcriptase inhibitors and protease inhibitors in antiretroviral treatment naïve patients. The clinical trial recruited 117 individuals during 2 years period (2020–2022). The prevalence of HIV-1 subtype A was statistically significantly more frequent in Ukrainian, and HIV-1 subtype B in Polish patients (p < 0.05). Drug resistance mutations were detected in 44% of all cases and the comparison of presence of mutations in the analyzed groups, as well as in the subgroups of subtype A and B HIV-1 has not revealed any significant differences (p > 0.05), nevertheless Polish patients had multidrug resistance mutations more frequent (p < 0.05). The results from our trial show no increased risk of transmission of multidrug resistant HIV strains in our cohort of Ukrainian migrants.Clinical trials. Gov number NCT04636736; date of registration: November 19, 2020.

Web Service for HIV Drug Resistance Prediction Based on Analysis of Amino Acid Substitutions in Main Drug Targets.

Predicting viral drug resistance is a significant medical concern. The importance of this problem stimulates the continuous development of experimental and new computational approaches. The use of computational approaches allows researchers to increase therapy effectiveness and reduce the time and expenses involved when the prescribed antiretroviral therapy is ineffective in the treatment of infection caused by the human immunodeficiency virus type 1 (HIV-1). We propose two machine learning methods and the appropriate models for predicting HIV drug resistance related to amino acid substitutions in HIV targets: (i) k-mers utilizing the random forest and the support vector machine algorithms of the scikit-learn library, and (ii) multi-n-grams using the Bayesian approach implemented in MultiPASSR software. Both multi-n-grams and k-mers were computed based on the amino acid sequences of HIV enzymes: reverse transcriptase and protease. The performance of the models was estimated by five-fold cross-validation. The resulting classification models have a relatively high reliability (minimum accuracy for the drugs is 0.82, maximum: 0.94) and were used to create a web application, HVR (HIV drug Resistance), for the prediction of HIV drug resistance to protease inhibitors and nucleoside and non-nucleoside reverse transcriptase inhibitors based on the analysis of the amino acid sequences of the appropriate HIV proteins from clinical samples.

Prevalence and analysis of acquired and transmitted integrase strand transfer inhibitor-associated HIV-1 drug resistance in Chongqing, China

ABSTRACT In this study, we examined the occurrence of acquired and transmitted drug resistance to integrase strand transfer inhibitor (INSTI) in HIV-1 strains in Chongqing (China) for guiding for the routine testing of INSTI-associated HIV-1 genotype resistance. Plasma samples were obtained from HIV-1 patients at Chongqing Public Health Medical Center from July 2019 to August 2022. Besides, amplification, sequence, and analysis of the portion of the HIV-1 pol gene that encodes the integrase protein were implemented to identify INSTI resistance. Integrase sequence data was harvested for a comprehensive cohort of 1032 patients infected with HIV-1. This cohort consisted of 564 ART-naive patients, 465 ART-treated patients, and 3 patients with an unknown treatment history. Within the study group, we identified INSTI resistance in 21 patients (2.03%, 21/1032), including 17 ART-treated patients (3.66%, 17/465). Among the ART-treated patients, 12 were INSTI-treated (11.76%, 12/102), 5 were INSTI-naive (1.38%, 5/363), and 4 were ART-ineffective patients (0.71%, 4/564). The prevalent major resistance mutation was Q148R (0.48%, 5/1032), while the most prevalent accessory resistance mutation was E157Q (1.65%, 17/1032). In light of the above, it is recommended that the incidence of accessory genotype analysis should be considered before starting any future INSTI-based therapy, especially in patients with drug resistance to NRTIs and NNRTIs and the reduction of INSTI sensitivity should be carefully monitored and investigated. Regular monitoring for resistance should be implemented after the use of INSTIs, and, importantly, ongoing monitoring of the decreasing susceptibility to INSTIs is crucial following the initiation of treatment with INSTIs.

Incidence and related factors of antiviral drug resistance in HIV-infected pregnant and postpartum women in some areas of three western provinces of China from 2017 to 2019

Objective: To analyze the incidence and related factors of drug resistance in HIV-infected pregnant and postpartum women in some areas of three western provinces of China from 2017 to 2019. Methods: From April 2017 to April 2019, face-to-face questionnaires and blood sample testing were conducted in all health care institutions providing maternal and perinatal care and midwifery-assisted services in 7 prevention of mother-to-child transmissi project areas in Xinjiang, Yunnan and Guangxi provinces/autonomous regions. Information was collected during the perinatal period and viral load, CD4+T lymphocytes and drug resistance genes were detected at the same time. The multivariate logistic regression model was used to analyze the relationship between different factors and drug resistance in HIV-infected pregnant and postpartum women. Results: A total of 655 HIV-infected pregnant and postpartum women were included in this study. The incidence of drug resistance was 3.4% (22/655), all of whom were cross-drug resistant. The rate of low, moderate and high drug resistance was 2.1% (14/655), 1.2% (8/655) and 0.8% (5/655), respectively. The drug resistance rate in the people who had previously used antiviral drugs was 1.9% (8/418), and the drug resistance rate in the people who had not used drugs was 5.9% (14/237). The NNRTI drug resistance accounted for 2.8% (18/655) and the NRTI drug resistance rate was 2.5% (16/655). The multivariate logistic regression model showed that the risk of HIV resistance was lower in pregnant women who had previously used antiviral drugs (OR=0.32, 95%CI: 0.11-0.76). Conclusion: Strengthening the management of antiviral drug use and focusing on pregnant and postpartum women who have not previously used antiviral drugs can help reduce the occurrence of drug-resistant mutations. Personalized antiviral therapy should be considered to achieve viral inhibition effects in clinical practice.

Evaluation of the ABL NGS assay for HIV-1 drug resistance testing

HIV evolution and variability around the world requires special monitoring of the viral strains in infected people. High-throughput HIV sequencing and drug resistance testing techniques have become routinely available over the last few years.We conducted a study to assess the new CE-marked ABL NGS HIV genotyping assay on an Illumina® platform, to compare the results (the detection of resistance associated mutations (RAMs) detected in the three main targets: reverse transcriptase, protease, and integrase) with those produced by three Sanger-based assays, and to compare the assays’ respective costs.For the 10 samples and a 20 % sensitivity threshold for the NGS technology, the percent agreement between the four assays ranged from 99.5 % to 100 %. We detected 4 more and 10 more RAMs of interest when we lowered the NGS assay's threshold to 10 % and 3 %, respectively. At a threshold of 3 %, the antiretroviral sensitivity interpretation algorithm (for protease inhibitors) was modified for only two patients. The NGS assay's unit cost fell rapidly as the number of samples per run increased.Compared with Sanger sequencing, the ABL NGS HIV genotyping assay is just as robust and somewhat more expensive but opens up interesting multiplexing perspectives for virology laboratories.

A National HIV Provider Survey of Antiretroviral Therapy Preferences for Management of Treatment-Naive and Experienced Individuals With Drug Resistance.

HIV clinical practice guidelines outline broad treatment principles but offer less explicit recommendations by permutations of encountered viral resistance. We hypothesize that there is variability in antiretroviral (ARV) regimen decision making among providers when considering HIV drug resistance (HIVDR). US HIV providers provided ARV regimen recommendations for case vignettes in a series of electronic surveys encompassing variations of HIVDR. Responses were characterized by drugs and classes selected and anticipated activity based on genotypic susceptibility. Heterogeneity was defined as the proportion of unique ARV regimens from total responses. An overall 119 providers from the United States participated. Among case vignettes with isolated M184V and viremia, 85.9% selected a regimen with 2 nucleoside reverse transcriptase inhibitors (NRTIs) + integrase strand transfer inhibitor (INSTI); 9.9% selected regimens with >3 ARVs. Alternatively, in scenarios of viremia with moderate to high-level NRTI resistance, >50% of providers selected an NRTI-sparing regimen, while a minority recommended 2 NRTIs + INSTI (21/123, 17%). In moderate to high-level INSTI resistance, there was response heterogeneity, with no common unifying approach to management (127 unique regimens/181 responses, 70% heterogeneity). Providers used cabotegravir/rilpivirine for treatment simplification in suppressed cases, despite a history of treatment failure (37/205, 36%). Our national survey of US HIV providers revealed a consensus to management of HIV resistance with potential alternative options in cases with low heterogeneity. Providers selected cabotegravir/rilpivirine as a viable treatment simplification strategy in suppressed cases with a history of treatment failure. The responses to the case vignettes could be used an education tool for ARV decision making in HIVDR.

Prevalence of HIV drug resistance among adolescents receiving ART in Cameroon with low- or high-level viraemia.

To characterize HIV drug resistance (HIVDR) below and above the WHO threshold of 1000 copies/mL, considered for the definition of HIV ART failure in resource-limited settings. From a cohort of 280 adolescents (aged 10-19 years) receiving ART for at least 6 months, genotypic resistance testing (GRT) was attempted for two groups of participants: participants with low-level viraemia [LLV; viral load (VL) 200-999 copies/mL] and those in virological failure (VF; confirmed VL ≥1000 copies/mL) using an in-house method. The Stanford HIValg Program was used to identify relevant HIVDR mutations and predict the efficacy of the newly introduced tenofovir-lamivudine-dolutegravir combination. GRT was successfully performed in 54/58 (93.1%) eligible participants, of which 28/31 (90.3%) were in VF and 26/27 (96.3%) had LLV. A high level of resistance was found both in adolescents with LLV and those in VF, with respectively 84.6% (22/26) and 75.0% (21/28) of participants harbouring at least one HIVDR mutation. NRTIs and NNRTIs were the most affected drug classes in both population groups. In contrast, PIs were not significantly affected and dolutegravir was expected to be active for all participants tested. However, for the newly introduced dolutegravir-based combination, functional monotherapy (dolutegravir only) was potentially possible for 22.7% (5/22) of the participants with LLV. Our findings show that the 1000 copies/mL threshold is not an indicator of virological success and we call for a revision of the current WHO definition of VF in resource-limited countries.

A Randomized Trial of Dolutegravir Plus Darunavir/Cobicistat as a Switch Strategy in HIV-1-Infected Patients With Resistance to at Least 2 Antiretroviral Classes.

Suppressed patients with drug-resistant HIV-1 require effective and simple antiretroviral therapy to maintain treatment adherence and viral suppression. This randomized, open-label, noninferiority, multicenter pilot study involved HIV-infected adults who met the following criteria: confirmed HIV-1 RNA <50 copies/mL for ≥6 months preceding the study randomization, treatment with at least 3 antiretroviral drugs, and a history of drug resistance mutations against at least 2 antiretroviral classes but remaining fully susceptible to darunavir (DRV) and integrase inhibitors. Participants were randomized 1:1 to switch to dolutegravir (DTG; 50 mg once per day) plus DRV boosted with cobicistat (DRV/c; 800/150 mg once per day; 2D group) or continue with their baseline regimen (standard-of-care [SOC] group). The primary endpoint was the proportion of patients with HIV-1 RNA <50 copies/mL at week 48 relative to time to loss of virologic response, with a noninferiority margin set at -12.5%. Virologic failure was defined as confirmed HIV-1 RNA ≥50 copies/mL or a single determination of HIV-1 RNA >50 copies/mL followed by antiretroviral therapy discontinuation. Forty-five participants were assigned to the 2D group and 44 to the SOC group. Time to loss of virologic response showed no difference in the proportion maintaining HIV-1 RNA <50 copies/mL at week 48: 39 of 45 (86.7%; 95% CI, 73.21%-94.95%) in the 2D group vs 42 of 44 (95.4%; 95% CI, 84.53%-99.44%) in the SOC group (log-rank P = .159) with an estimated difference of -8.7 (95% CI, -22.72 to 5.14). Only 2 (4.5%) in the SOC group experienced virologic failure, and 3 participants from the 2D group experienced adverse events leading to treatment discontinuation. In suppressed patients with at least 2 resistant antiretroviral classes, noninferiority could not be demonstrated by fully active DRV/c plus DTG. Nevertheless, there were no unexpected adverse events or virologic failure. DRV/c plus DTG may be considered a once-daily therapy option only for well-selected patients. Clinical Trials Registration. ClinicalTrials.gov (NCT03683524).

Need assessment for HIV drug resistance testing and landscape of current and future technologies in low- and middle-income countries.

Resistance to antiretroviral drugs used to treat HIV is an important and evolving concern, particularly in low- and middle-income countries (LMICs) which have been impacted to the greatest extent by the HIV pandemic. Efforts to monitor the emergence and transmission of resistance over the past decade have shown that drug resistance-especially to the nucleoside analogue and non-nucleoside reverse transcriptase inhibitors-can (and have) increased to levels that can jeopardize the efficacy of available treatment options at the population level. The global shift to integrase-based regimens as the preferred first-line therapy as well as technological advancements in the methods for detecting resistance have had an impact in broadening and diversifying the landscape of and use case for HIV drug resistance testing. This review estimates the potential demand for HIV drug resistance tests, and surveys current testing methodologies, with a focus on their application in LMICs.