Transmitted Drug Resistance in Antiretroviral Therapy-Naive Persons With Acute/Early/Primary HIV Infection: A Systematic Review and Meta-Analysis

Prevalence of Doravirine Resistance Mutations in a Large-Scale HIV-1 Transmitted Drug Resistance Survey in Buenos Aires, Argentina

BACKGROUND

Argentina has reported moderate to high levels of transmitted drug resistance in people living with HIV/AIDS (PLWHA), mostly to non-nucleoside reverse transcriptase inhibitors (NNRTIs). Doravirine (DOR) has a unique resistance profile and retains potent antiviral activity in the presence of the most prevalent NNRTI-associated resistant viruses. Scarce data exist regarding the frequency of DOR resistance-associated mutations (RAMs) in Latin America. We describe the prevalence of DOR RAMs in samples from adults PLWHA in Buenos Aires, Argentina, in the context of a survey of transmitted drug resistance (TDR).

MATERIAL AND METHODS

A cross-sectional study was undertaken utilizing samples collected between 2017 and 2021 at two reference HIV clinics. Samples were analyzed for RAMs using the World Health Organization (WHO) mutation list. Mutations to DOR were assessed with the Stanford and Agence Nationale de Recherches sur le SIDA (ANRS) algorithms. Rilpivirine (RPV) RAMs were assessed using the Stanford algorithm. Susceptibility to NNRTIs was evaluated using the HIVdb Program with Stanford and ANRS criteria.

RESULTS

Samples from 1667 PLWHA were analyzed: 81.2% were male, with 52.6% identifying as men who have sex with men. According to the WHO list, the overall TDR was 12.1% (n = 203). The prevalence of RAMs was 10.1% (170/1667) for NNRTIs, 4% (67/1667) for nucleoside reverse-transcriptase inhibitors (NRTIs), and 1.7% (30/1667) for protease inhibitors (PIs). The most frequent NNRTI mutations were K103N (5.6%), G190A (0.89%), and K103S (0.77%). The prevalence of DOR RAMs was <2%, with the most common being Y188L (0.53%). Rilpivirine RAM prevalence was 6%. Susceptibility to DOR, RPV, efavirenz, and nevirapine as given by the Stanford algorithm was 97.4%, 92%, 91.4%, and 90.4%, respectively. The ANRS criteria yielded susceptibility rates of 98.3%, 93.3%, 92.3%, and 90.8%, respectively. Regarding NRTIs, thymidine analog mutations (including T215 revertants) were the most frequent RAMs. Among PIs, the most prevalent RAMs were M46L (0.47%) and V82A (0.35%).

CONCLUSIONS

Our study shows the persistence of moderate to high levels of resistance to first-generation NNRTIs. Despite this, prevalence was low for DOR. Surveillance of TDR remains critical for recommendations of ART initiation.

Distinct region-specific neutralization profiles of contemporary HIV-1 clade C against best-in-class broadly neutralizing antibodies

While broadly neutralizing antibodies (bnAbs) have been clinically shown to prevent HIV-1 acquisition, their relative effectiveness against regionally relevant HIV-1 forms is not clear. In the present study, we examined the extent of neutralization susceptibility of contemporary HIV-1 Indian clade C at a population level along with a head-to-head comparison with that from South Africa against a panel of clinically relevant best-in-class bnAbs. Env-pseudotyped viruses encoding HIV-1 India clade C env were found to be best neutralized by the V3 glycan-directed bnAbs (10-1074 and BG18) and select CD4 binding site (CD4bs)-directed bnAbs (VRC07, N6, and 1-18); however, they demonstrated significant resistance to V1/V2 apex-directed bnAbs. Interestingly, the magnitude of the neutralization sensitivity differed between contemporary India and South Africa clade C. Neutralization resistance to key bnAbs was observed to be associated with differences in residues on Env that form bnAb contact sites, gp120 loop lengths, and potential N-linked glycans. Notably, the second generation CD4bs bnAbs (VRC07, N6, 1-18) showed neutralization of VRC01- and 3BNC117-resistant viruses but with two- to sevenfold reduced potency compared to the VRC01-sensitive counterparts, likely due to the enrichment of resistance-associated residues observed in loop D. Predictive analysis indicated that the combination of BG18, N6, and PGDM1400 can provide over 95% neutralization coverage of contemporary India clade C at 1 µg/mL (IC80), an observation distinct from that observed with Africa clade C. Our study clearly highlights that both the complementarity of bnAb classes and the regionally relevant HIV-1 forms are important in achieving clinical effectiveness.IMPORTANCEWhile the development of vaccines to prevent HIV infection remains a global priority, their potential effectiveness is limited by the extraordinarily diversified circulating forms of HIV-1. The prospect of best-in-class broadly neutralizing antibodies (bnAbs) as a potential prevention option has been demonstrated in several studies, including the phase 2b Antibody-Mediated Prevention trials; however, to be broadly applicable, bnAbs will need to overcome the substantial variability of HIV env circulating globally, beyond the regions where efficacy trials are conducted. The present study highlights that the region-specific contemporary HIV-1 clade C viruses not only vary in their degree of susceptibility to the best-in-class clinically relevant bnAbs, but also are evolving at a population level to become increasingly resistant to the best-in-class bnAbs. Overall, the outcome of this study highlights the need for periodic assessment of sequence and neutralization profiles of the circulating regionally relevant HIV-1 forms toward prioritizing the bnAb combination suitable for effective intervention.

Assessing the utilization of HIV genotype resistance testing: Insight from Italian Infectious Diseases Units

PURPOSE

We aimed to assess the utilization of genotype resistance testing (GRT) by Infectious Diseases Units across Italy.

METHODS

A cross-sectional study was conducted involving a questionnaire distributed to the Infectious Diseases Unit in Italy. A web-based survey using Google Forms software was utilized and spread via email or cellphone.

RESULTS

Responses were obtained from 101 Infectious Diseases Units. Among these centres, only seven (6.9%) reported not performing GRT at any time. Of the 94 centres performing GRT, 52 (55.3%) sent blood samples to external laboratories. Notably, only 6/35 (17.1%) small centres had internal laboratories, compared to 14/35 (40.0%) medium centres and 22/24 (91.7%) large centres (P < 0.001). Most centres requested GRT for treatment-naïve individuals and all cases of virological failure. Only 24 (25.5%) requested GRT of HIVDNA before treatment changes. Regarding virological failure, most centres (38, 40.4%) requested GRT when HIV-RNA levels exceeded 200 copies/mL, while 26 (27.7%) requested it at levels exceeding 50 copies/mL. Additionally, 18 (19.1%) and 12 (12.8%) centres requested GRT at thresholds of 500 copies/mL and 1000 copies/mL, respectively. Regarding the specific GRT test used, 34 (36.2%) were unsure, while 16 (17.0%) reported using both next-generation sequencing and Sanger methods. Furthermore, 30 (31.9%) and 14 (14.9%) centres exclusively used next-generation sequencing and Sanger, respectively. Most centres reported receiving GRT results within 1 month (n = 72, 76.6%), while 22 (23.4%) centres obtained results within 2 weeks. However, 22 (23.4%) centres typically experienced more than 1-month delays. Finally, most participants (86, 91.5%) regarded GRT as a crucial routine test for the treatment of naïve people living with HIV.

CONCLUSIONS

This study demonstrates that most Infectious Diseases Units in Italy continue to consider GRT an essential test for newly diagnosed people living with HIV in clinical practice. However, the utilization of GRT on HIV-DNA remains limited. Further efforts are required to decrease turnaround time in centres experiencing prolonged delays in obtaining results.

Role of low-frequency integrase strand transfer inhibitor resistance mutations on virological outcomes in antiretroviral therapy-naïve individuals initiating second-generation integrase inhibitors

OBJECTIVES

This study investigated the role of low-frequency integrase strand transfer inhibitor (INSTI) resistance mutations, detectable by next-generation sequencing (NGS), at predicting virological rebound (VR) among people with HIV (PWH) starting second-generation INSTI-based first-line regimens.

METHODS

This case-control study compared PWH (retrieved from the ICONA cohort; www.icona.org) who experienced VR (cases) with those who maintained virological control (controls) under first-line regimens based on dolutegravir or bictegravir. NGS data obtained through the Illumina platform were interpreted using the HIVdb algorithm version 9.7. Major (MRM), accessory (ARM), and other (ORM) INSTI resistance mutations were analysed at 5%, 10%, and 20% NGS cut-offs, respectively. Conditional logistic regression was used to evaluate the association between INSTI resistance and risk of VR.

RESULTS

Among 266 PWH (90 cases, 176 controls), cases experienced VR with a median (interquartile range) viremia of 317 (93-6060) copies/mL after 15 (8-28) months from antiretroviral therapy start. The prevalence of MRM was low (NGS cut-off 5%, 10%, 20%: 1.9%, 0.8%, 0.4%, respectively), while it was moderate for ARM (7.5%, 7.1%, 6.4%) and high for ORM (50.0%, 44.7%, 42.1%). There was no evidence of a difference in prevalence of ≥1 MRM, ARM, or ORM between cases and controls. At 5% NGS cut-off, the prevalence of ≥2 ORM was higher in cases compared with controls. After adjusting for confounders, including HIV-1 subtype, ≥2 ORM detected as minority variants remained associated with VR risk.

CONCLUSION

Our findings suggest that combinations of low-frequency ORM may increase the risk of VR in individuals starting dolutegravir or bictegravir-based regimens. Further studies are needed to better understand these findings.

Genetic Diversity and Antiretroviral Resistance in HIV-1-Infected Patients Newly Diagnosed in Cabo Verde

The high genetic variability of HIV-1 and the emergence of transmitted drug resistance (TDR) can impact treatment efficacy. In this study, we investigated the prevalent HIV-1 genotypes and drug-resistance-associated mutations in drug-naïve HIV-1 individuals in Cabo Verde. The study, conducted between 2018 and 2019, included drug-naïve HIV-1 individuals from the São Vicente, Boa Vista, Fogo, and Santiago islands. The HIV-1 pol gene was sequenced using Sanger sequencing. TDR was identified using the Stanford Calibrated Population Resistance tool, and resistance levels to different drugs were interpreted with the Stanford HIV database. The genetic diversity of HIV-1 was determined through phylogenetic analysis, and epidemiological and behavioural data were collected via questionnaires. Of the 73 participants, the majority were male (52.1%). The CRF02_AG recombinant form predominated (41.1%), followed by subtype G (37.0%). The overall prevalence of TDR was 9.6%. Nucleoside Reverse Transcriptase Inhibitor (NRTI) mutations occurred in 2.7% of individuals, while Non-Nucleoside Reverse Transcriptase Inhibitor (NNRTI) mutations occurred in 9.6%. The most prevalent mutations were K103N (5.5%) and M184V (2.7%). No protease- or integrase-associated mutations were found. The high levels of resistance to NNRTIs found demonstrate the need for surveillance of resistance mutations to ensure the efficacy and durability of the current therapeutic regimen, which includes Dolutegravir.

HIV-1 transmitted drug resistance in newly diagnosed individuals in Italy over the period 2015-21

BACKGROUND

Transmitted drug resistance (TDR) is still a critical aspect for the management of individuals living with HIV-1. Thus, its evaluation is crucial to optimize HIV care.

METHODS

Overall, 2386 HIV-1 protease/reverse transcriptase and 1831 integrase sequences from drug-naïve individuals diagnosed in north and central Italy between 2015 and 2021 were analysed. TDR was evaluated over time. Phylogeny was generated by maximum likelihood. Factors associated with TDR were evaluated by logistic regression.

RESULTS

Individuals were mainly male (79.1%) and Italian (56.2%), with a median (IQR) age of 38 (30-48). Non-B infected individuals accounted for 44.6% (N = 1065) of the overall population and increased over time (2015-2021, from 42.1% to 51.0%, P = 0.002). TDR prevalence to any class was 8.0% (B subtype 9.5% versus non-B subtypes 6.1%, P = 0.002) and remained almost constant over time. Overall, 300 transmission clusters (TCs) involving 1155 (48.4%) individuals were identified, with a similar proportion in B and non-infected individuals (49.7% versus 46.8%, P = 0.148). A similar prevalence of TDR among individuals in TCs and those out of TCs was found (8.2% versus 7.8%, P = 0.707).By multivariable analysis, subtypes A, F, and CFR02_AG were negatively associated with TDR. No other factors, including being part of TCs, were significantly associated with TDR.

CONCLUSIONS

Between 2015 and 2021, TDR prevalence in Italy was 8% and remained almost stable over time. Resistant strains were found circulating regardless of being in TCs, but less likely in non-B subtypes. These results highlight the importance of a continuous surveillance of newly diagnosed individuals for evidence of TDR to inform clinical practice.

Molecular Transmission Network and Drug Resistance in Treatment-Naive HIV-1-Infected Patients in the Liangshan District, China

This study aimed to investigate the molecular transmission network and drug resistance in treatment-naive HIV-1-infected patients in the Liangshan District, China. The research subjects for this study were HIV-1-infected patients who did not receive any antiretroviral therapy (ART) in the Liangshan District between January 2022 and July 2023. Peripheral venous whole-blood samples were collected from the research subjects. Two milliliters of blood was used for CD4+ T lymphocyte counting detection. Ten milliliters of blood was centrifuged to separate the plasma and blood cells for quantitative detection of HIV-1 RNA and DNA and drug resistance testing of HIV-1. A total of 156 participants were included in this study (88 males and 68 females). The median age of the participants was 37 years. The findings revealed a positive correlation between the HIV-1 DNA and the HIV-1 RNA levels (r = 0.478, p < 0.001). However, a negative correlation was observed between the HIV-1 DNA levels and CD4+ T lymphocyte counts (r = -0.186, p = 0.020). Of the 156 participants, 145 were successfully tested for drug resistance of HIV-1 RNA and HIV-1 DNA simultaneously. Four cases failed the HIV-1 RNA drug resistance testing, and another two failed the HIV-1 DNA drug resistance testing. The most common HIV-1 subtype was the CRF07_BC recombinant. In this study, the overall incidence of transmitted drug resistance (TDR) was 8.33%. The resistance rates of non-nucleoside reverse transcriptase inhibitor (NNRTI) and protease inhibitor (PI) were 7.69% and 0.64%, respectively. In addition, 32 participants were found to have drug-resistant mutations. The primary drug-resistant mutations were K103N, V179D, E157Q, and A128T, mainly against efavirenz (EFV) and nevirapine (NVP) resistance. The drug resistance of HIV-1-infected ART-naive patients in the Liangshan District cannot be ignored. HIV-1 drug resistance testing is recommended before initiating ART.

The Use of Broadly Neutralizing Antibodies (bNAbs) in HIV-1 Treatment and Prevention

BACKGROUND

Although antiretroviral therapy (ART) effectively halts disease progression in HIV infection, the complete eradication of the virus remains elusive. Additionally, challenges such as long-term ART toxicity, drug resistance, and the demanding regimen of daily and lifelong adherence required by ART highlight the imperative need for alternative therapeutic and preventative approaches. In recent years, broadly neutralizing antibodies (bNAbs) have emerged as promising candidates, offering potential for therapeutic, preventative, and possibly curative interventions against HIV infection.

OBJECTIVE

This review aims to provide a comprehensive overview of the current state of knowledge regarding the passive immunization of bNAbs in HIV-1-infected individuals.

MAIN FINDINGS

Recent findings from clinical trials have highlighted the potential of bNAbs in the treatment, prevention, and quest for an HIV-1 cure. While monotherapy with a single bNAb is insufficient in maintaining viral suppression and preventing viral escape, ultimately leading to viral rebound, combination therapy with potent, non-overlapping epitope-targeting bNAbs have demonstrated prolonged viral suppression and delayed time to rebound by effectively restricting the emergence of escape mutations, albeit largely in individuals with bNAb-sensitive strains. Additionally, passive immunization with bNAb has provided a "proof of concept" for antibody-mediated prevention against HIV-1 acquisition, although complete prevention has not been obtained. Therefore, further research on the use of bNAbs in HIV-1 treatment and prevention remains imperative.

Trends of pre-treatment drug resistance in antiretroviral-naïve people with HIV-1 in the era of second-generation integrase strand-transfer inhibitors in Taiwan

BACKGROUND

Monitoring the trends of pre-treatment drug resistance (PDR) and resistance-associated mutations (RAMs) among antiretroviral-naïve people with HIV (PWH) is important for the implementation of HIV treatment and control programmes. We analysed the trends of HIV-1 PDR after the introduction of second-generation integrase strand-transfer inhibitors (INSTIs) in 2016 in Taiwan, when single-tablet regimens of non-nucleoside reverse-transcriptase inhibitor (NNRTI-) and INSTI-based antiretroviral therapy became the preferred treatments.

MATERIALS AND METHODS

In this multicentre study, we included newly diagnosed, antiretroviral-naïve PWH who underwent tests for RAMs between 2016 and 2022. Pre-treatment genotypic resistance testing was performed, along with HIV-1 subtyping and determinations of plasma HIV RNA load and CD4 lymphocyte counts. RAMs were analysed using the Stanford University HIV Drug Resistance Database and only RAMs conferring at least low-level resistance were included.

RESULTS

From 2016 to 2022, pre-treatment blood samples from 3001 newly diagnosed PWH, which constituted 24.3% of newly diagnosed PWH in Taiwan during the study period, were tested. Of the PWH with analysable gene sequences, the HIV-1 PDR prevalence to NNRTIs, nucleoside reverse-transcriptase inhibitors (NRTIs), first- and second-generation INSTIs and PIs was 10.0%, 2.1%, 2.5%, 0.6% and 0.4%, respectively. While the trends of PDR remained stable for NRTIs, INSTIs and PIs, there was a significantly increasing trend of PDR to NNRTIs from 6.0% in 2016% to 13.1% in 2022 (P = 0.001).

CONCLUSIONS

After the introduction of second-generation INSTIs in Taiwan, the trends of HIV-1 PDR to NRTIs and INSTIs remained low. Furthermore, there was no significant decrease of the prevalence of PDR toward NNRTIs between 2016 and 2022.

Navigating the Antiretroviral Therapy Switch Conundrum: Unveiling the Dilemma of Drug Resistance and Disease Progression in HIV/AIDS

There is a need to establish consensus for harmonization in antiretroviral (ARV) therapy (ART) switch treatment strategy and address the dilemma that exists in terms of subpar immune response to therapy or an immunologic deterioration while on therapy. The purpose of this review is to identify the factors that contribute to ARV treatment failure, such as insufficient dosage, drug interactions, poor adherence, drug resistance, and poor medication absorption. It is crucial to adopt a more efficient strategy to address this challenging dilemma. After ARV treatment failure, the aim of therapy is virologic suppression, which targets plasma viral load below the limits of detection as assessed by very sensitive tests with lower limits of quantification of 20 to 75 RNA copies/ml. The therapeutic objectives when complete virologic suppression is not possible, should be to maintain or restore immunologic function, stop the progression of the clinical illness, and minimize the emergence of new drug resistance that could further restrict the options for ARV drugs. Treatment history and drug-resistance testing, including the findings of previous and ongoing resistance tests, should be considered while selecting ARV regimens. Hence, the treatment approach post-ARV failure can be personalized based on clinical, immunologic, virologic, or as a mix of the three domains on a case-to-case basis. The evaluation of projected ARV activity should be based on treatment history and previous resistance test findings.

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.

Transmitted drug resistance to antiretroviral drugs in Spain during the period 2019-2021

To evaluate the prevalence of transmitted drug resistance (TDR) to nucleoside and nonnucleoside reverse transcriptase inhibitors (NRTI, NNRTI), protease inhibitors (PI), and integrase strand transfer inhibitors (INSTI) in Spain during the period 2019-2021, as well as to evaluate transmitted clinically relevant resistance (TCRR) to antiretroviral drugs. Reverse transcriptase (RT), protease (Pro), and Integrase (IN) sequences from 1824 PLWH (people living with HIV) were studied. To evaluate TDR we investigated the prevalence of surveillance drug resistance mutations (SDRM). To evaluate TCRR (any resistance level ≥ 3), and for HIV subtyping we used the Stanford v.9.4.1 HIVDB Algorithm and an in-depth phylogenetic analysis. The prevalence of NRTI SDRMs was 3.8% (95% CI, 2.8%-4.6%), 6.1% (95% CI, 5.0%-7.3%) for NNRTI, 0.9% (95% CI, 0.5%-1.4%) for PI, and 0.2% (95% CI, 0.0%-0.9%) for INSTI. The prevalence of TCRR to NRTI was 2.1% (95% CI, 1.5%-2.9%), 11.8% for NNRTI, (95% CI, 10.3%-13.5%), 0.2% (95% CI, 0.1%-0.6%) for PI, and 2.5% (95% CI, 1.5%-4.1%) for INSTI. Most of the patients were infected by subtype B (79.8%), while the majority of non-Bs were CRF02_AG (n = 109, 6%). The prevalence of INSTI and PI resistance in Spain during the period 2019-2021 is low, while NRTI resistance is moderate, and NNRTI resistance is the highest. Our results support the use of integrase inhibitors as first-line treatment in Spain. Our findings highlight the importance of ongoing surveillance of TDR to antiretroviral drugs in PLWH particularly with regard to first-line antiretroviral therapy.

Current ART, determinants for virologic failure and implications for HIV drug resistance: an umbrella review

OBJECTIVE

The purpose of this study is to investigate the incidence of determinants for virologic failure and to identify predisposing factors to enhance treatment efficacy. Tackling this global public health issue is the key to reducing the rate of virological failure and increasing the success of treatment for those living with HIV.

METHODS

This umbrella review delves into various aspects of current anti-retroviral therapy (ART) which is the primary treatment for human immunodeficiency virus (HIV) infection. Comprehensive searches were conducted in online databases including PubMed, Embase, Scopus, and Web of Science, up to May 26, 2023. Following the screening and selection of relevant articles, eligible articles were included in the data extraction. This study adhered to the PRISMA guideline to report the results and employed the NIH quality and bias risk assessment tool to ensure the quality of included studies.

RESULTS

In total, 40 review studies published from 2015 to 2023 were included. The bulk of these studies concurred on several major factors contributing to HIV drug resistance and virological failure. Key among these were medication adherence, baseline and therapeutic CD4 levels, the presence of co-infections, and the advanced clinical stage of the infection.

CONCLUSION

The resistance to HIV drugs and instances of determinants for virologic failure have a profound impact on the life quality of those infected with HIV. Primary contributors to this scenario include insufficient adherence to treatment, decreased CD4 T-cell count, elevated viral levels, and certain treatment regimens. Implementing appropriate interventions could address these issues. Sub-Saharan Africa exhibits elevated rates of determinants for virologic failure, attributed to the delay in HIV testing and diagnosis, and late initiation of antiretroviral therapy (ART). It is essential to undertake further research aimed at enhancing the detection of resistance in HIV patients and mitigating viral failure by addressing these underlying causes.

Nirmatrelvir-resistant SARS-CoV-2 is efficiently transmitted in female Syrian hamsters and retains partial susceptibility to treatment

The SARS-CoV-2 main protease (3CLpro) is one of the promising therapeutic targets for the treatment of COVID-19. Nirmatrelvir is the first 3CLpro inhibitor authorized for treatment of COVID-19 patients at high risk of hospitalization. We recently reported on the in vitro selection of SARS-CoV-2 3CLpro resistant virus (L50F-E166A-L167F; 3CLpro^res) that is cross-resistant with nirmatrelvir and other 3CLpro inhibitors. Here, we demonstrate that the 3CLpro^res virus replicates efficiently in the lungs of intranasally infected female Syrian hamsters and causes lung pathology comparable to that caused by the WT virus. Moreover, hamsters infected with 3CLpro^res virus transmit the virus efficiently to co-housed non-infected contact hamsters. Importantly, at a dose of 200 mg/kg (BID) of nirmatrelvir, the compound was still able to reduce the lung infectious virus titers of 3CLpro^res-infected hamsters by 1.4 log₁₀ with a modest improvement in the lung histopathology as compared to the vehicle control. Fortunately, resistance to Nirmatrelvir does not readily develop in clinical setting. Yet, as we demonstrate, in case drug-resistant viruses emerge, they may spread easily which may thus impact therapeutic options. Therefore, the use of 3CLpro inhibitors in combination with other drugs may be considered, especially in immunodeficient patients, to avoid the development of drug-resistant viruses.

Single-center experience evaluating and initiating people with HIV on long-acting cabotegravir/rilpivirine

OBJECTIVE

To describe our experience evaluating and initiating individuals on long-acting injectable (LAI) cabotegravir/rilpivirine (CAB/RPV) and evaluate factors associated with starting LAI CAB/RPV and reasons for not starting.

DESIGN

We conducted a retrospective single-center study at the UC San Diego Owen Clinic.

METHODS

We included all individuals who expressed interest in treatment with LAI CAB/RPV between April 2021 and June 2022 who had a definitive decision made on starting LAI CAB/RPV.

RESULTS

In total, 383 individuals were included with 201 (52.5%) initiating LAI CAB/RPV. Those who initiated LAI CAB/RPV were younger ( P  = 0.02) and were more likely to be on a two-drug regimen or first-generation integrase inhibitor regimen and less likely to be on a protease inhibitor or multiclass regimen. The most common reasons for not starting LAI CAB/RPV were inconsistent clinic attendance or difficulty being contacted and patient choice not to start. Of those who had a proviral DNA resistance test as workup for LAI CAB/RPV ( n  = 135), 18.5% had a resistance mutation identified that may have impacted the activity of LAI CAB/RPV.

CONCLUSION

Despite novel challenges over half of our cohort initiated LAI CAB/RPV. Evaluating for potential non-nucleoside reverse transcriptase inhibitor resistance is an important part of the workup for LAI CAB/RPV and proviral DNA resistance testing can be an additional tool to identify potential resistance.

The Substitutions L50F, E166A, and L167F in SARS-CoV-2 3CLpro Are Selected by a Protease Inhibitor In Vitro and Confer Resistance To Nirmatrelvir

The SARS-CoV-2 main protease (3CLpro) has an indispensable role in the viral life cycle and is a therapeutic target for the treatment of COVID-19. The potential of 3CLpro-inhibitors to select for drug-resistant variants needs to be established. Therefore, SARS-CoV-2 was passaged in vitro in the presence of increasing concentrations of ALG-097161, a probe compound designed in the context of a 3CLpro drug discovery program. We identified a combination of amino acid substitutions in 3CLpro (L50F E166A L167F) that is associated with a >20× increase in 50% effective concentration (EC₅₀) values for ALG-097161, nirmatrelvir (PF-07321332), PF-00835231, and ensitrelvir. While two of the single substitutions (E166A and L167F) provide low-level resistance to the inhibitors in a biochemical assay, the triple mutant results in the highest levels of resistance (6× to 72×). All substitutions are associated with a significant loss of enzymatic 3CLpro activity, suggesting a reduction in viral fitness. Structural biology analysis indicates that the different substitutions reduce the number of inhibitor/enzyme interactions while the binding of the substrate is maintained. These observations will be important for the interpretation of resistance development to 3CLpro inhibitors in the clinical setting. IMPORTANCE Paxlovid is the first oral antiviral approved for treatment of SARS-CoV-2 infection. Antiviral treatments are often associated with the development of drug-resistant viruses. In order to guide the use of novel antivirals, it is essential to understand the risk of resistance development and to characterize the associated changes in the viral genes and proteins. In this work, we describe for the first time a pathway that allows SARS-CoV-2 to develop resistance against Paxlovid in vitro. The characteristics of in vitro antiviral resistance development may be predictive for the clinical situation. Therefore, our work will be important for the management of COVID-19 with Paxlovid and next-generation SARS-CoV-2 3CLpro inhibitors.

The Substitutions L50F, E166A, and L167F in SARS-CoV-2 3CLpro Are Selected by a Protease Inhibitor In Vitro and Confer Resistance To Nirmatrelvir

The SARS-CoV-2 main protease (3CLpro) has an indispensable role in the viral life cycle and is a therapeutic target for the treatment of COVID-19. The potential of 3CLpro-inhibitors to select for drug-resistant variants needs to be established. Therefore, SARS-CoV-2 was passaged in vitro in the presence of increasing concentrations of ALG-097161, a probe compound designed in the context of a 3CLpro drug discovery program. We identified a combination of amino acid substitutions in 3CLpro (L50F E166A L167F) that is associated with a >20× increase in 50% effective concentration (EC₅₀) values for ALG-097161, nirmatrelvir (PF-07321332), PF-00835231, and ensitrelvir. While two of the single substitutions (E166A and L167F) provide low-level resistance to the inhibitors in a biochemical assay, the triple mutant results in the highest levels of resistance (6× to 72×). All substitutions are associated with a significant loss of enzymatic 3CLpro activity, suggesting a reduction in viral fitness. Structural biology analysis indicates that the different substitutions reduce the number of inhibitor/enzyme interactions while the binding of the substrate is maintained. These observations will be important for the interpretation of resistance development to 3CLpro inhibitors in the clinical setting. IMPORTANCE Paxlovid is the first oral antiviral approved for treatment of SARS-CoV-2 infection. Antiviral treatments are often associated with the development of drug-resistant viruses. In order to guide the use of novel antivirals, it is essential to understand the risk of resistance development and to characterize the associated changes in the viral genes and proteins. In this work, we describe for the first time a pathway that allows SARS-CoV-2 to develop resistance against Paxlovid in vitro. The characteristics of in vitro antiviral resistance development may be predictive for the clinical situation. Therefore, our work will be important for the management of COVID-19 with Paxlovid and next-generation SARS-CoV-2 3CLpro inhibitors.

The Effect of Treatment-Associated Mutations on HIV Replication and Transmission Cycles

HIV/AIDS mortality has been decreasing over the last decade. While promising, this decrease correlated directly with increased use of antiretroviral drugs. As a natural consequence of its high mutation rate, treatments provide selection pressure that promotes the natural selection of escape mutants. Individuals may acquire drug-naive strains, or those that have already mutated due to treatment. Even within a host, mutation affects HIV tropism, where initial infection begins with R5-tropic virus, but the clinical transition to AIDS correlates with mutations that lead to an X4-tropic switch. Furthermore, the high mutation rate of HIV has spelled failure for all attempts at an effective vaccine. Pre-exposure drugs are currently the most effective drug-based preventatives, but their effectiveness is also threatened by viral mutation. From attachment and entry to assembly and release, the steps in the replication cycle are also discussed to describe the drug mechanisms and mutations that arise due to those drugs. Revealing the patterns of HIV-1 mutations, their effects, and the coordinated attempt to understand and control them will lead to effective use of current preventative measures and treatment options, as well as the development of new ones.

Men who have sex with men is the high-risk drug resistance population: A meta-analysis of HIV-1 drug resistance profiles and trends in China

WHAT IS KNOWN AND OBJECTIVE

Except for the transmitted drug resistance (TDR)'s standard sampling and monitoring protocol, China's HIV-1 pretreatment drug resistance (PDR) and acquired drug resistance (ADR) results vary widely due to the studies' diverse background. This meta-analysis was conducted to comprehensively understand the drug resistance profiles of Chinese HIV/AIDS patients and compare the drug resistance differences among groups to provide a reference for the further improvement of treatment protocols.

METHODS

Data sources for this study were WANFANG, VIP, CNKI, SinoMed, PubMed and Web of Science databases from January 1, 2010 to January 13, 2022. Data extracted from the literature were analyzed by R and Stata to evaluate the profile and changing trend of drug resistance in Chinese HIV/AIDS patients.

RESULTS AND DISCUSSION

One hundred twenty-one literature were included. The combined PDR and ADR in the Chinese HIV/AIDS patients was 5.56% (95% CI: 4.77%-6.41%) and 51.33% (95% CI: 47.57%-55.38%), respectively. The time trend analysis shows the upward trend of PDR. There were significate differences in ADR among different sample sources, the ADR in the central region were higher than those in all other regions. The PDR in men who have sex with men (MSM) was lower the whole population, while the MSM's ADR was much higher than whole population.

WHAT IS NEW AND CONCLUSION

PDR in China showed an upward trend and exceeded the 5% warning line but is still at a low level worldwide. ADR is stable and below the middle level globally; the comprehensively promoted free ART in China still has lasting effects. MSM is the high-risk drug resistance population, targeted treatment strategies should be used.

Epidemiology of HIV drug resistance in low- and middle-income countries and WHO global strategy to monitor its emergence

PURPOSE OF REVIEW

This review summarises the latest information of the epidemiology of HIV drug resistance (HIVDR) in low- and middle-income countries and the updated WHO global strategy for HIVDR surveillance and monitoring.

RECENT FINDINGS

Finding from recent national-representative surveys show a rise in pretreatment drug resistance (PDR) to reverse transcriptase inhibitors and especially to the class of nonnucleoside reverse transcriptase inhibitors. Levels of PDR are especially high in infants <18 months and adults reporting prior exposure to antiretrovirals. Although viral suppression rates are generally high and increasing among adults on antiretroviral therapy, those with unsuppressed viremia have high levels of acquired drug resistance (ADR). Programmatic data on HIVDR to integrase-transfer-inhibitor resistance is scarce, highlighting the need to increase integrase-inhibitors resistance surveillance. As the landscape of HIV prevention, treatment and monitoring evolves, WHO has also adapted its strategy to effectively support countries in preventing and monitoring the emergence of HIVDR. This includes new survey methods for monitoring resistance emerging from patients diagnosed with HIV while on preexposure prophylaxis, and a laboratory-based ADR survey leveraging on remnant viral load specimens which are expected to strengthen dolutegravir-resistance surveillance.

SUMMARY

Monitoring HIVDR remains pivotal to ensure countries attain and sustain the global goals for ending HIV as a public health threat by 2030.

Factors Associated With Newly HIV Infection and Transmitted Drug Resistance Among Men Who Have Sex With Men in Harbin, P.R. China

Background

This study aimed to evaluate HIV incidence, factors associated with HIV incidence and transmitted drug resistance (TDR) among newly infected men who have sex with men (MSM) in Harbin, P.R. China.

Methods

A cohort study was conducted among MSM in Harbin during 2013 and 2018, with a follow-up frequency of every 6 months. Blood samples from MSM were tested for HIV antibodies, RNA was extracted from plasma, and the pol gene was sequenced, and genotypic drug-resistance analyses were performed.

Results

From 2013 to 2018, the overall rate of HIV incidence was 3.55/100 PY. Syphilis infection, unprotected sex with men in the past 6 months, and unawareness of HIV/AIDS knowledge were risk factors for HIV seroconversion. The distribution of HIV genotypes was as follows: CRF01_AE, 57.1%; CRF07_BC, 28.5%; CRF55_01B, 2.0%; B, 8.2%. The prevalence of transmitted drug resistance was 4.08%.

Conclusion

HIV incidence in MSM in Harbin is moderately high, and transmitted drug resistance exists in the population.