The development of drug resistance mutations K103N Y181C and G190A in long term Nevirapine-containing antiviral therapy

PAM-free diagnostics with diverse type V CRISPR-Cas systems

Type V CRISPR-Cas effectors have revolutionized molecular diagnostics by facilitating the detection of nucleic acid biomarkers. However, their dependence on the presence of protospacer adjacent motif (PAM) sites on the target double-stranded DNA (dsDNA) greatly limits their flexibility as diagnostic tools. Here we present a novel method named PICNIC that solves the PAM problem for CRISPR-based diagnostics with just a simple ∼10-min modification to contemporary CRISPR-detection protocols. Our method involves the separation of dsDNA into individual single-stranded DNA (ssDNA) strands through a high- temperature and high-pH treatment. We then detect the released ssDNA strands with diverse Cas12 enzymes in a PAM-free manner. We show the utility of PICNIC by successfully applying it for PAM-free detection with three different subtypes of the Cas12 family- Cas12a, Cas12b, and Cas12i. Notably, by combining PICNIC with a truncated 15-nucleotide spacer containing crRNA, we demonstrate PAM-independent detection of clinically important single- nucleotide polymorphisms with CRISPR. We apply this approach to detect the presence of a drug-resistant variant of HIV-1, specifically the K103N mutant, that lacks a PAM site in the vicinity of the mutation. Additionally, we successfully translate our approach to clinical samples by detecting and genotyping HCV-1a and HCV-1b variants with 100% specificity at a PAM-less site within the HCV genome. In summary, PICNIC is a simple yet groundbreaking method that enhances the flexibility and precision of CRISPR-Cas12-based diagnostics by eliminating the restriction of the PAM sequence.

Pretreatment and Acquired Drug Resistance in Children With Human Immunodeficiency Virus Type 1 in Jos, Nigeria

We determined pretreatment and acquired human immunodeficiency virus (HIV) drug resistance among children with HIV type 1 (HIV-1) in Jos, Nigeria. The majority (71%) of those who failed first-line antiretroviral therapy were on a nevirapine-containing regimen. The prevalence of pretreatment (48%) and acquired (76%) HIV drug resistance mutations was high in our study. Wider access to HIV drug resistance testing after treatment failure is necessary to optimize second-line treatment options among children with HIV in Nigeria.

Evaluation of Circulating and Archived HIV-1 Integrase Drug-Resistance Variants among Patients on Third-Line ART in Cameroon: Implications for Dolutegravir-Containing Regimens in Resource-Limited Settings

To ensure the long-term efficacy of dolutegravir (DTG), we evaluated the genotypic profile in viral reservoirs among patients on third-line (3L) antiretroviral therapy (ART) in Cameroon, according to prior exposure to raltegravir (RAL). A facility-based study was conducted from May through December 2021 among patients on 3L ART from HIV treatment centers in Yaoundé and Douala. Viral load was measured, and genotyping was performed on plasma RNA and proviral DNA. HIV-1 drug resistance mutations were interpreted using HIVdb.v9.1 and phylogeny analysis was performed using MEGA.v7, with P < 0.05 considered significant. Of the 12,093 patients on ART, 53 fully met our inclusion criteria. The median (IQR) age was 51 years (40 to 55 years), and the male/female ratio was 4/5. The median duration on integrase strand-transfer inhibitors (INSTI)-containing regimens was 18 months (12 to 32 months), and 15.09% (8/53) were exposed to RAL. The most administered 3L ART was TDF+3TC+DTG+DRV/r (33.96%, 18/53). Only 5.66% (3/53) had unsuppressed viremia (>1000 copies/mL). Resistance testing in proviral DNA was successful for 18/22 participants and revealed 1/18 patients (5.56%, in the RAL-arm) with archived mutations at major resistance positions (G140R and G163R). Five subtypes were identified, CRF02_AG (12/18), CRF22_01AE (3/18), A1 (1/18), G (1/18), and F2 (1/18). In Cameroon, 3L-experienced patients had a good virological response with a low level of archived mutations in the integrase. This finding underscored the use of DTG-containing ART for heavily treated patients in similar programmatic settings. However, patients with prior exposure to RAL should be closely monitored following a stratified or personalized approach to mitigate risks of INSTI-resistance, alongside pharmacovigilance. IMPORTANCE We described the analysis of the genotypes of the population within third-line antiviral therapy in Cameroon, with a focus on defining the effects of prior raltegravir (RAL) treatment and resistance mutations for current dolutegravir (DTG) treatment. While supporting the current transition to DTG-containing ART in resource-limited settings toward the achievement of the UNAIDS' goal of HIV elimination by 2030, our findings suggested that RAL-exposed patients may need a specific monitoring approach either in a stratified or personalized model of third-line ART to ensure the long-term success of DTG-containing regimens.

Nevirapine plasma concentration is associated with virologic failure and the emergence of drug-resistant mutations among HIV patients in Kenya: A cross sectional study

This study aimed to determine the association between the plasma concentration of nevirapine (NVP) and clinical outcomes. In this cross-sectional study, sociodemographic and clinical data were collected from 233 HIV patients receiving NVP-based first-line antiretroviral therapy (ART) regimens in Nairobi, Kenya. The mean age was 41.2 (SD ± 11.9) years. Fifty-four (23.2%) patients had virological failure (>1000 copies/mL), whereas 23 (9.9%) were infected with drug-resistant HIV strains. Eleven patients had nucleoside reverse transcriptase inhibitor resistance mutations, including M184V and T215Y, whereas 22 had non-nucleoside reverse transcriptase inhibitor resistance mutations, including G190A, K103N, V106A, Y181C, A98G, and Y188L. The median NVP plasma concentration was 6180 ng/mL (IQR 4444-8843 ng/mL), with 38 (16.3%) patients having suboptimal NVP plasma levels of <3400 ng/mL. The majority 23 of the 38 (60.5%) patients with NVP Cmin < 3400 ng/mL were significantly infected with drug-resistant HIV virus (P = .001). In the multivariate analysis, the time taken to arrive at the ART clinic (β -11.1, 95% CI -21.2 to -1.1; P = .031), higher HIV viral load (β -2008, 95% CI -3370.7 to -645.3; P = .004), and the presence of HIV drug resistance mutation (β 3559, 95% CI 2580.8-4537.2; P = .0001) were associated with NVP plasma concentration. A significant proportion of patients receiving the NVP-based regimen had supra- and sub-therapeutic plasma concentrations. Higher HIV viral load and the presence of HIV drug-resistant mutations are important factors associated with NVP plasma concentrations.

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.

Mutation patterns, cross resistance and virological failure among HIV type-1 patients in Alexandria, Egypt

Aim: The main purpose of this cross-sectional study was to detect the prevalence of drug resistance mutations related to nonnucleoside/nucleoside reverse transcriptase inhibitors (NNRTIs/NRTIs) and protease inhibitors (PIs). Patients & methods: Patients (n = 45) with HIV type-1 were recruited, 30 of whom were treatment naive and 15 treatment experienced. A partial pol gene covering the protease/reverse transcriptase (PRRT) region was amplified and then sequenced by the Sanger method. Results & conclusion: The most common NNRTI/NRTI-related mutations were ‘V179I (24%) and K103N (14.3%)’ and ‘M41L and V75M’ (14.3% each). M36I and H69K were the most prevalent PI-related mutations (86% each). The results of the current study serve as an initial crucial step in defining the overall prevalence of HIV type-1 drug resistance in Egypt.

Biophysical Characterization of Novel DNA Aptamers against K103N/Y181C Double Mutant HIV-1 Reverse Transcriptase

The human immunodeficiency virus type-1 Reverse Transcriptase (HIV-1 RT) plays a pivotal role in essential viral replication and is the main target for antiviral therapy. The anti-HIV-1 RT drugs address resistance-associated mutations. This research focused on isolating the potential specific DNA aptamers against K103N/Y181C double mutant HIV-1 RT. Five DNA aptamers showed low IC50 values against both the KY-mutant HIV-1 RT and wildtype (WT) HIV-1 RT. The kinetic binding affinity forms surface plasmon resonance of both KY-mutant and WT HIV-1 RTs in the range of 0.06–2 μM and 0.15–2 μM, respectively. Among these aptamers, the KY44 aptamer was chosen to study the interaction of HIV-1 RTs-DNA aptamer complex by NMR experiments. The NMR results indicate that the aptamer could interact with both WT and KY-mutant HIV-1 RT at the NNRTI drug binding pocket by inducing a chemical shift at methionine residues. Furthermore, KY44 could inhibit pseudo-HIV particle infection in HEK293 cells with nearly 80% inhibition and showed low cytotoxicity on HEK293 cells. These together indicated that the KY44 aptamer could be a potential inhibitor of both WT and KY-mutant HIV-RT.

The Fellowship of Privileged Scaffolds-One Structure to Inhibit Them All

Over the past few years, the application of privileged structure has emerged as a powerful approach to the discovery of new biologically active molecules. Privileged structures are molecular scaffolds with binding properties to the range of different biological targets. Moreover, privileged structures typically exhibit good drug-like properties, thus assuring more drug-like properties of modified compound. Our main objective is to discuss the privileged structures used for the development of antiviral agents.

Prevalence of HIV-1 Drug-Resistance Genotypes Among Unique Recombinant Forms from Yunnan Province, China in 2016-2017

To investigate the prevalence and characteristics of drug-resistance genotypes among unique recombinant forms (URFs) in HIV-1 infected people under long-term antiretroviral treatment failure from Yunnan Province. The plasma samples were collected from antiretroviral therapy (ART)-failure experienced individuals from 2016 to 2017 in Yunnan Province, China. The genotyping drug resistance of HIV-1 pol gene fragments was implemented using in-house assay. According to the analysis of RIP and MEGA 7.0, the HIV-1 strains related to URFs were screened for recombinant identification and drug resistance analysis. A total of 130 pol sequences of HIV-1 URF strains were obtained from 1,121 samples. The proportion of HIV-1 URF strains was 11.6% among the ART-failure individuals from 2016 to 2017 in Yunnan. The overall drug-resistance rate of HIV-1 URF strains was 56.9%. Meanwhile, the percentage of protease inhibitors, nucleoside reverse transcriptase inhibitors (NRTIs), and non-nucleoside reverse transcriptase inhibitors (NNRTIs) resistance was 3.8% (5/130), 36.2% (47/130), and 53.8% (70/130), respectively. Mutations such as M184V/I (35.4%) in NRTIs and K103N/R/S/T (25.4%), V179D/E/T/Y (18.9%), G190A/E/R/S (13.8%), and Y181C (9.2%) in NNRTIs were common among the HIV-1 URF strains relative to other mutations. Factors such as male, sexual transmission pathway, and source of the year 2017 were significantly correlated with the development of HIV-1 URF drug resistance. The emergence of the multiple recombinant forms identified in Yunnan indicates active transmission networks of HIV-1 of different HIV-1 subtype/circulating recombinant forms cross-infection in this region. Therefore, it is necessary to further monitor the molecular epidemiology and drug resistance of HIV-1 in Yunnan.

The Journey of HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs) from Lab to Clinic

Human immunodeficiency virus (HIV) infection is now pandemic. Targeting HIV-1 reverse transcriptase (HIV-1 RT) has been considered as one of the most successful targets for the development of anti-HIV treatment. Among the HIV-1 RT inhibitors, non-nucleoside reverse transcriptase inhibitors (NNRTIs) have gained a definitive place due to their unique antiviral potency, high specificity, and low toxicity in antiretroviral combination therapies used to treat HIV. Until now, >50 structurally diverse classes of compounds have been reported as NNRTIs. Among them, six NNRTIs were approved for HIV-1 treatment, namely, nevirapine (NVP), delavirdine (DLV), efavirenz (EFV), etravirine (ETR), rilpivirine (RPV), and doravirine (DOR). In this perspective, we focus on the six NNRTIs and lessons learned from their journey through development to clinical studies. It demonstrates the obligatory need of understanding the physicochemical and biological principles (lead optimization), resistance mutations, synthesis, and clinical requirements for drugs.

Surveillance of HIV-1 drug resistance in Xinjiang: high prevalence of K103N in treatment-naïve individuals

To identify transmitted and acquired HIV-1 drug resistance mutations in Xinjiang, China, we collected the peripheral blood of 50 treated and 50 treatment-naïve HIV-1-infected individuals in this region. We successfully amplified 36 reverse transcriptase and 42 protease gene sequences of HIV-1 from 51 individuals and identified mutations associated with resistance to reverse transcriptase (RT) and protease (PR) inhibitors (RTIs and PIs) according to Stanford Drug Resistance Database. Among the drug-treated individuals, the results showed that K103N in the RT region was the most frequent mutation, found in 67% (6/9) of the cases, followed by M184V with 56% (5/9). Five individuals had both nucleoside and non-nucleoside reverse transcriptase inhibitor resistance mutations after more than 12 months of treatment. Among the untreated individuals, 33% (9/27) were found to harbor drug resistance mutations in the RT gene. K103N occurred at the highest rate, accounting for 22% (6/27), followed by P225H (7%) and Y188L (4%). Neither of the two groups showed any major resistance mutations to PIs. Our study revealed that the prevalence of drug resistance was relatively high in Xinjiang and that K103N occurred at the highest rate. These results suggest that it is important to carry out HIV drug resistance testing, especially for the K103N mutation in the RT region, before and during the treatment process. This study may help to guide ART strategies in the Xinjiang region.

K. HK, Ramachandran G, Shet A. Sub-therapeutic nevirapine concentration during antiretroviral treatment initiation among children living with HIV: Implications for therapeutic drug monitoring

Nevirapine, a component of antiretroviral therapy (ART) in resource-limited settings, known for auto-induction of metabolism, is initiated at half therapeutic dose until day 14 (‘lead-in period’), and subsequently escalated to full dose. However, studies have shown that this dosing strategy based on adult studies may not be appropriate in children, given that younger children have higher drug clearance rates. In this prospective cohort study, we studied trough plasma nevirapine levels by high performance liquid chromatography (HPLC) at days 7, 14 (lead-in period) and 28 (full dose period) after ART initiation amongst HIV-1 infected children initiating nevirapine-based ART in southern India. Among the 20 children (50% male, median age 9 years) included in the study, sub-therapeutic trough plasma nevirapine concentration (<4μg/ml) was seen in 65% (13/20) of children during the lead-in period within two weeks of ART initiation and among 10% of children at 4 weeks during full-dose nevirapine. Adherence was documented as ≥95% in all children by both caregiver self-report and pill count. Median nevirapine concentrations achieved at week 1 was 4.8 μg/ml, significantly lower than 8 μg/ml, the concentration achieved at week 4 (p = 0.034). Virological failure at one year of ART was observed in six children, and was not associated with median nevirapine concentration achieved during week 1, 2 or 4. We conclude that the dose escalation strategy currently practiced among young children living with HIV-1 resulted in significant subtherapeutic nevirapine concentration (≤4μg/ml) during the lead-in period. We call for a closer look at pediatric-focused dosing strategies for nevirapine initiation in young children. Further studies to establish age-appropriate threshold nevirapine concentration are warranted in young children to corroborate the role of therapeutic drug monitoring in predicting virological outcome.

Use of Proviral DNA to Investigate Virus Resistance Mutations in HIV-infected Zimbabweans

Background:

Antiretroviral therapy (ART) to suppress HIV replication has reduced morbidity and mortality yet effectiveness of current HIV drugs is threatened by HIV drug resistance (HIVDR) mutations.

Objective:

To determine HIVDR mutations using proviral DNA from specimens of patients presenting to an HIV treatment clinic.

Methods:

DNA from 103 patients, 86 treatment-experienced, 17 treatment-naïve, were genotyped for the HIV-1C reverse transcriptase gene (RT; codons 21-304) using Sanger sequencing and sequences analyzed using Sequencher software. Resistance mutations were interpreted using Stanford HIVDR reference database.

Results:

Median age was 39 (IQR, 33-46) years and 80% of patients were female. Six-percent (n=6) had at least one HIVDR mutation, comprising NRTI-associated mutations, (M184V, T69D, T69N and V75I); NNRTI-associated mutations (G190A, K103N, V106M, Y181C) and thymidine analogue associated mutations (D67N, K70R, K219Q, L210W, M41L, T215Y). Of the six participants, with at least one HIVDR mutation, all were treatment experienced, five were on tenofovir, lamivudine and nevirapine and one was on tenofovir, lamivudine and atazanavir. There was no difference in median CD4 count and viral loads when patients were compared by presence of HIVDR mutations.

Conclusion:

We demonstrated the use of proviral DNA in HIVDR testing in adult patients and present that all the patients with various kinds of HIVDR mutations were treatment experienced, pointing to the role of drug regimens in driving viral mutations. Thus, the use of proviral DNA has potential to help provide surveillance on risk of HIVDR in HIV-infected individuals who are on treatment, which may assist in corrective treatment.

Analysis of reverse transcriptase and protease genes of HIV for antiretroviral drug resistance in treatment-exposed Jamaican pediatrics

This study reports on the drug resistance profiles for HIV-infected pediatrics in Jamaica who have been exposed to antiretroviral therapy (ART). The genetic diversity of HIV-1 found in these patients was also determined using phylogenetic analysis. The protease-reverse transcriptase (Pro-RT) region of the genome was amplified from 40 samples, sequenced, and analyzed for the identification of antiretroviral resistance-associated mutations (RAMs). All isolates belonged to subtype B and 39 possessed multiple RAMs in the reverse transcriptase genes that would compromise the efficacy of drugs being used to treat these patients. Four isolates possessed RAMs in the protease genes. The overall frequency of HIV drug resistance was 95%. The high frequency of drug resistance is supported by epidemiological data that revealed an equally high frequency of treatment failure (98%) among the study participants. The results of this study indicate the urgent need for greater access to drug resistance testing in Jamaica.

Change in the Prevalence of HIV-1 and the Rate of Transmitted Drug-Resistant HIV-1 in Haiphong, Northern Vietnam

We previously reported a significant decrease in HIV-1 prevalence, with no increase in drug-resistant HIV-1 among injecting drug users (IDU), female sex workers (FSW), and blood donors (BD), in Haiphong, Vietnam, from 2007 to 2009. In 2012, 388 IDU, 51 FSW, and 200 BD were recruited for further analysis. None had a history of antiretroviral treatment. From 2007 to 2012, HIV-1 prevalence was reduced from 35.9% to 18.6% (p<0.001), 23.1% to 9.8% (p<0.05), and 2.9% to 1% (p=0.29) in IDU, FSW, and BD, respectively. Of 79 anti-HIV-1 antibody-positive samples, 61 were successfully analyzed for the pol-reverse transcriptase (RT) region. All HIV-1 strains were CRF01_AE. Nonnucleoside RT inhibitor-resistant mutations, Y181C/I, were detected in three subjects; one had the nucleoside RT inhibitor-resistant mutations L74V and M184V and one had E138K. The prevalence of transmitted drug-resistant HIV-1 in Haiphong increased slightly from 1.8% in 2007 to 6.6% in 2012 (p=0.06).