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Ouyang F, Yuan D, Zhai W, Liu S, Zhou Y, Yang H. HIV-1 Drug Resistance Detected by Next-Generation Sequencing among ART-Naïve Individuals: A Systematic Review and Meta-Analysis. Viruses 2024; 16:239. [PMID: 38400015 PMCID: PMC10893194 DOI: 10.3390/v16020239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/31/2023] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND There are an increasing number of articles focused on the prevalence and clinical impact of pretreatment HIV drug resistance (PDR) detected by Sanger sequencing (SGS). PDR may contribute to the increased likelihood of virologic failure and the emergence of new resistance mutations. As SGS is gradually replaced by next-generation sequencing (NGS), it is necessary to assess the levels of PDR using NGS in ART-naïve patients systematically. NGS can detect the viral variants (low-abundance drug-resistant HIV-1 variants (LA-DRVs)) of virus quasi-species at levels below 20% that SGS may fail to detect. NGS has the potential to optimize current HIV drug resistance surveillance methods and inform future research directions. As the NGS technique has high sensitivity, it is highly likely that the level of pretreatment resistance would be underestimated using conventional techniques. METHODS For the systematic review and meta-analysis, we searched for original studies published in PubMed, Web of Science, Scopus, and Embase before 30 March 2023 that focused exclusively on the application of NGS in the detection of HIV drug resistance. Pooled prevalence estimates were calculated using a random effects model using the 'meta' package in R (version 4.2.3). We described drug resistance detected at five thresholds (>1%, 2%, 5%, 10%, and 20% of virus quasi-species). Chi-squared tests were used to analyze differences between the overall prevalence of PDR reported by SGS and NGS. RESULTS A total of 39 eligible studies were selected. The studies included a total of 15,242 ART-naïve individuals living with HIV. The prevalence of PDR was inversely correlated with the mutation detection threshold. The overall prevalence of PDR was 29.74% at the 1% threshold, 22.43% at the 2% threshold, 15.47% at the 5% threshold, 12.95% at the 10% threshold, and 11.08% at the 20% threshold. The prevalence of PDR to INSTIs was 1.22% (95%CI: 0.58-2.57), which is the lowest among the values for all antiretroviral drugs. The prevalence of LA-DRVs was 9.45%. At the 2% and 20% detection threshold, the prevalence of PDR was 22.43% and 11.08%, respectively. Resistance to PIs and INSTIs increased 5.52-fold and 7.08-fold, respectively, in those with a PDR threshold of 2% compared with those with PDR at 20%. However, resistance to NRTIs and NNRTIs increased 2.50-fold and 2.37-fold, respectively. There was a significant difference between the 2% and 5% threshold for detecting HIV drug resistance. There was no statistically significant difference between the results reported by SGS and NGS when using the 20% threshold for reporting resistance mutations. CONCLUSION In this study, we found that next-generation sequencing facilitates a more sensitive detection of HIV-1 drug resistance than SGS. The high prevalence of PDR emphasizes the importance of baseline resistance and assessing the threshold for optimal clinical detection using NGS.
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Affiliation(s)
- Fei Ouyang
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China; (F.O.); (D.Y.); (W.Z.); (S.L.)
| | - Defu Yuan
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China; (F.O.); (D.Y.); (W.Z.); (S.L.)
| | - Wenjing Zhai
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China; (F.O.); (D.Y.); (W.Z.); (S.L.)
| | - Shanshan Liu
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China; (F.O.); (D.Y.); (W.Z.); (S.L.)
| | - Ying Zhou
- Department of HIV/STD Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Haitao Yang
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China; (F.O.); (D.Y.); (W.Z.); (S.L.)
- Jiangsu Health Development Research Center, Nanjing 210029, China
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Dong Z, Xu Z, Zhou Y, Tian R, Zhou K, Wang D, Ya X, Shen Q. Genetic characterization of HIV-1 viruses among cases with antiretroviral therapy failure in Suzhou City, China. AIDS Res Ther 2023; 20:41. [PMID: 37381002 PMCID: PMC10303762 DOI: 10.1186/s12981-023-00540-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 06/21/2023] [Indexed: 06/30/2023] Open
Abstract
BACKGROUND This retrospective study aimed to characterize the distribution of HIV-1 genotypes and the prevalence of drug resistance mutations in people with antiretroviral treatment (ART) failure in Suzhou City, China. METHODS Pol gene of HIV-1 viruses in blood samples of EDTA anticoagulants from 398 patients with failed antiviral treatment was successfully amplified by using an in-house assay. Drug resistance mutations were analyzed by using the Stanford HIV Drug Resistance Database system ( https://hivdb.stanford.edu/hivdb/by-mutations/ ). HIV-1 genotypes were determined by the REGA HIV subtyping tool (version 3.46, https://www.genomedetective.com/app/typingtool/hiv ). Near full-length genomes (NFLG) of HIV-1 viruses were obtained by next generation sequencing method. RESULTS Sequences analysis of the pol gene revealed that CRF 01_AE (57.29%, 228/398) was the dominant subtype circulating in Suzhou City, followed by CRF 07_BC (17.34%, 69/398), subtype B (7.54%, 30/398), CRF 08_BC (6.53%, 26/398), CRF 67_01B (3.02%, 12/398) and CRF55_01B (2.51%, 10/398). The overall prevalence of drug-resistant mutations in cases with ART failure was 64.57% (257/398), including 45.48% (181/398) for nucleotide reverse transcriptase inhibitors (NRTIs) mutations, 63.32% (252/398) for non-nucleoside reverse transcriptase inhibitors (NNRTIs) mutations, and 3.02% (12/398) for protease inhibitors (PIs) mutations. Ten near full-length genomes (NFLG) of HIV-1 viruses were identified, including six recombinants of CRF 01_AE and subtype B, two recombinants of CRF 01_AE, subtype B and subtype C sequences, one recombinant of CRF 01_AE and subtype C and one recombinant of CRF 01_AE, subtype A1 and subtype C. CONCLUSIONS The high prevalence of drug-resistant HIV-1 viruses was a serious challenge for HIV prevention and treatment of people with HIV infection. Treatment regimens for ART failure patients should be adjusted over time based on the outcome of drug resistance tests. NFLG sequencing facilitates the identification of new recombinants of HIV-1.
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Affiliation(s)
- Zefeng Dong
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Zhihui Xu
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Ying Zhou
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210003, China
| | - Runfang Tian
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Kai Zhou
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Di Wang
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Xuerong Ya
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China.
| | - Qiang Shen
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China.
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Reepalu A, Arimide DA, Balcha TT, Yeba H, Zewdu A, Medstrand P, Björkman P. Drug Resistance in HIV-Positive Adults During the Initial Year of Antiretroviral Treatment at Ethiopian Health Centers. Open Forum Infect Dis 2021; 8:ofab106. [PMID: 34805444 PMCID: PMC8597620 DOI: 10.1093/ofid/ofab106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/03/2021] [Indexed: 11/30/2022] Open
Abstract
Background The increasing prevalence of antiretroviral drug resistance in Sub-Saharan
Africa threatens the success of HIV programs. We have characterized patterns
of drug resistance mutations (DRMs) during the initial year of
antiretroviral treatment (ART) in HIV-positive adults receiving care at
Ethiopian health centers and investigated the impact of tuberculosis on DRM
acquisition. Methods Participants were identified from a cohort of ART-naïve individuals aged
≥18 years, all of whom had been investigated for active tuberculosis
at inclusion. Individuals with viral load (VL) data at 6 and/or 12 months
after ART initiation were selected for this study. Genotypic testing was
performed on samples with VLs ≥500 copies/mL obtained on these
occasions and on pre-ART samples from those with detectable DRMs during ART.
Logistic regression analysis was used to investigate the association between
DRM acquisition and tuberculosis. Results Among 621 included individuals (110 [17.5%] with concomitant tuberculosis),
101/621 (16.3%) had a VL ≥500 copies/mL at 6 and/or 12 months. DRMs
were detected in 64/98 cases with successful genotyping (65.3%). DRMs were
detected in 7/56 (12.5%) pre-ART samples from these individuals. High
pre-ART VL and low mid-upper arm circumference were associated with
increased risk of DRM acquisition, whereas no such association was found for
concomitant tuberculosis. Conclusions Among adults receiving health center–based ART in Ethiopia, most
patients without virological suppression during the first year of ART had
detectable DRM. Acquisition of DRM during this period was the dominant cause
of antiretroviral drug resistance in this setting. Tuberculosis did not
increase the risk of DRM acquisition.
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Affiliation(s)
- Anton Reepalu
- Clinical Infection Medicine, Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Dawit A Arimide
- Clinical Virology, Department of Translational Medicine, Lund University, Malmö, Sweden.,Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Taye T Balcha
- Clinical Infection Medicine, Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Habtamu Yeba
- Adama Public Health Research and Referral Laboratory Center, Adama, Ethiopia
| | - Adinew Zewdu
- Adama Public Health Research and Referral Laboratory Center, Adama, Ethiopia
| | - Patrik Medstrand
- Clinical Virology, Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Per Björkman
- Clinical Infection Medicine, Department of Translational Medicine, Lund University, Malmö, Sweden
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Nyamaruze P, Cowden RG, Padgett RN, Govender K. Body image and antiretroviral therapy adherence among people living with HIV: a protocol for a systematic review and meta-analysis. BMJ Open 2021; 11:e045700. [PMID: 34233973 PMCID: PMC8264875 DOI: 10.1136/bmjopen-2020-045700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 06/18/2021] [Indexed: 11/29/2022] Open
Abstract
INTRODUCTION Adherence to antiretroviral therapy (ART) remains a key challenge to achieving the fast-track goal of ending the HIV epidemic by 2030. To provide a more comprehensive indication of whether interventions designed to promote ART adherence might benefit from targeting body image perceptions, we aim to conduct a systematic review to synthesise existing evidence on the association between body image and ART adherence. METHODS AND ANALYSIS A systematic review of peer-reviewed observational studies and randomised controlled trials that have investigated the association between body image and adherence to ART will be performed. JSTOR, PsycARTICLES, PsycINFO, PubMed, ScienceDirect and Web of Science databases will be searched from 1 January 2000 to 31 March 2021. Eligible records will consider body image as either an independent variable or a mediator, whereas ART adherence will be assessed as an outcome variable. Study selection will follow the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines and study quality will be assessed using relevant tools developed by the National Institute of Health. If sufficient data are available, a meta-analysis will be conducted. Effect size estimates will be aggregated using a random effects meta-analysis approach. Publication bias and its impact will be evaluated through the use of a funnel plot and the trim-and-fill method. The Grading of Recommendations Assessment, Development and Evaluation approach will be used to report on the overall quality of evidence. ETHICS AND DISSEMINATION Ethical approval is not required for a systematic review protocol. Findings of the proposed systematic review will be disseminated through conference presentations and publication in a peer-reviewed journal. PROSPERO REGISTRATION NUMBER CRD42020212597.
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Affiliation(s)
- Patrick Nyamaruze
- Psychology, University of KwaZulu-Natal College of Humanities, Durban, Kwazulu Natal, South Africa
| | - Richard Gregory Cowden
- Human Flourishing Program, Institute for Quantitative Social Science, Harvard University, Cambridge, Massachusetts, USA
| | - R Noah Padgett
- Department of Educational Psychology, Baylor University, Waco, Texas, USA
| | - Kaymarlin Govender
- Health Economics and HIV and AIDS Research Division, University of KwaZulu Natal, Durban, KwaZulu-Natal, South Africa
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Monaco DC, Zapata L, Hunter E, Salomon H, Dilernia DA. Resistance profile of HIV-1 quasispecies in patients under treatment failure using single molecule, real-time sequencing. AIDS 2020; 34:2201-2210. [PMID: 33196493 DOI: 10.1097/qad.0000000000002697] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Short-read next-generation sequencing (NGS) has been implemented to study the resistance profile of HIV as it provides a higher sensitivity than Sanger sequencing. However, short-reads only generates a consensus view of the viral population rather than a reconstruction of the viral haplotypes. In this study, we evaluated the resistance profile of HIV quasispecies in patients undergoing treatment failure using SMRT sequencing. DESIGN Whole-pol RT-PCR was performed on viral RNA extracted from plasma samples of 38 HIV-positive individuals undergoing treatment failure, and sequenced in the RSII instrument. Error correction and viral haplotype phasing was performed with the Multilayer Directed Phasing and Sequencing (MDPSeq) algorithm. Presence of resistance mutations reported by the IAS-USA in 2017 was assessed using an in-house script. RESULTS The SMRT sequencing-based test detected 131/134 resistance mutations previously detected using a Sanger sequencing-based test. However, the SMRT test also identified seven additional mutations present at an estimated frequency lower than 30%. The intra-host phylogenetic analysis showed that seven samples harbored at least one resistance variant at 20--80% frequency. The haplotype-resolved sequencing revealed viral diversification and selection of new resistance during suboptimal treatment, an overall trend toward selection and accumulation of new resistance mutations, as well as the co-existence of resistant and susceptible variants. CONCLUSION Our results validate the SMRT sequencing-based test for detection of HIV drug resistance. In addition, this method unraveled the complex dynamic of HIV quasispecies during treatment failure, which might have several implications on clinical management.
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Affiliation(s)
| | - Lucas Zapata
- Institute of Biomedical Investigations in Retrovirus and AIDS (INBIRS), School of Medicine, University of Buenos Aires, Buenos Aires, Argentina
| | - Eric Hunter
- Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Horacio Salomon
- Institute of Biomedical Investigations in Retrovirus and AIDS (INBIRS), School of Medicine, University of Buenos Aires, Buenos Aires, Argentina
| | - Dario A Dilernia
- Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology, School of Medicine, Emory University, Atlanta, Georgia, USA
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Yan L, Yu F, Zhang H, Zhao H, Wang L, Liang Z, Zhang X, Wu L, Liang H, Yang S, Tang Y, Zhang F. Transmitted and Acquired HIV-1 Drug Resistance from a Family: A Case Study. Infect Drug Resist 2020; 13:3763-3770. [PMID: 33122923 PMCID: PMC7591230 DOI: 10.2147/idr.s272232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/11/2020] [Indexed: 11/23/2022] Open
Affiliation(s)
- Liting Yan
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
| | - Fengting Yu
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
| | - Huimin Zhang
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Department of Pediatrics, Beijing Ditan Hospital, Beijing, People’s Republic of China
| | - Hongxin Zhao
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
| | - Linghang Wang
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
| | - Zaiyan Liang
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
| | - Xia Zhang
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
| | - Liang Wu
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
| | - Hongyuan Liang
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
| | - Siyuan Yang
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
| | - Yunxia Tang
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
| | - Fujie Zhang
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
- Correspondence: Fujie Zhang Beijing Ditan Hospital, Capital Medical University, Beijing100015, People’s Republic of ChinaTel +86 10 84322581 Email
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Ye M, Chen X, Wang Y, Zhou YH, Pang W, Zhang C, Zheng YT. HIV-1 Drug Resistance in ART-Naïve Individuals in Myanmar. Infect Drug Resist 2020; 13:1123-1132. [PMID: 32368103 PMCID: PMC7182463 DOI: 10.2147/idr.s246462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/31/2020] [Indexed: 01/29/2023] Open
Abstract
Background Estimating the prevalence and characterizing the transmission of HIV-1 drug resistance in treatment-naïve individuals are very important in the prevention and control of HIV/AIDS. As one of the areas most affected by HIV/AIDS, few data are currently available for HIV-1 drug resistance in antiretroviral therapy (ART)-naïve individuals in Myanmar, which borders Yunnan, China. Methods HIV-1 pol sequences from ART-naïve HIV-1-infected individuals during 2008 and 2014 in Myanmar were retrieved from our previous studies. HIV-1 transmitted drug resistance (TDR) and susceptibility to antiretroviral drugs were predicted using the Stanford HIVdb program. HIV-1 transmission cluster (TC) was determined by Cluster Picker. Results A total of 169 partial pol sequences from ART-naïve HIV-1 positive Burmese were analyzed. The prevalence of TDR was 20.1%. CRF01_AE and BC recombinants appeared to have a higher prevalence of TDR than other subtypes. The V179D/T was found to be very common in the China–Myanmar border region and was involved in half of the transmission clusters formed by HIV-1 drug-resistance strains in this region. Comparison showed that drug-resistance mutation profile in Myanmar was very similar to that in Dehong prefecture of Yunnan. By further phylogenetic analysis with all available sequences from the China–Myanmar border region, four HIV-1 drug-resistance-related TCs were identified. Three of them were formed by Burmese long-distance truck drivers and the Burmese staying in Yunnan, and another was formed by Burmese injection drug users staying in Myanmar and Yunnan. These results suggest a potential transmission link of HIV-1 drug resistance between Myanmar and Yunnan. Conclusion Given the high prevalence of TDR in Myanmar, and the potential risk of cross-border transmission of HIV-1 drug-resistant strains between Myanmar and Yunnan, China, ongoing monitoring of HIV-1 drug resistance in ART-naïve individuals will provide a guideline for clinical antiretroviral treatment and benefit the prevention and control of HIV/AIDS in this border region.
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Affiliation(s)
- Mei Ye
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, People's Republic of China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China
| | - Xin Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, People's Republic of China.,Department of Pathogenic Biology, School of Basic Medical Sciences, Gannan Medical University, Ganzhou 341000, People's Republic of China
| | - Yu Wang
- KIZ-SU Joint Laboratory of Animal Model and Drug Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215000, People's Republic of China
| | - Yan-Heng Zhou
- Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, College of Life Sciences, Yan'an University, Yan'an, Shaanxi 716000, People's Republic of China
| | - Wei Pang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, People's Republic of China
| | - Chiyu Zhang
- Pathogen Discovery and Evolution Unit, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200025, People's Republic of China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, People's Republic of China.,KIZ-SU Joint Laboratory of Animal Model and Drug Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215000, People's Republic of China
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Kong W, Biswas A, Zhou D, Fiches G, Fujinaga K, Santoso N, Zhu J. Nucleolar protein NOP2/NSUN1 suppresses HIV-1 transcription and promotes viral latency by competing with Tat for TAR binding and methylation. PLoS Pathog 2020; 16:e1008430. [PMID: 32176734 PMCID: PMC7098636 DOI: 10.1371/journal.ppat.1008430] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 03/26/2020] [Accepted: 02/24/2020] [Indexed: 01/11/2023] Open
Abstract
Recent efforts have been paid to identify previously unrecognized HIV-1 latency-promoting genes (LPGs) that can potentially be targeted for eradication of HIV-1 latent reservoirs. From our earlier orthologous RNAi screens of host factors regulating HIV-1 replication, we identified that the nucleolar protein NOP2/NSUN1, a m5C RNA methyltransferase (MTase), is an HIV-1 restriction factor. Loss- and gain-of-function analyses confirmed that NOP2 restricts HIV-1 replication. Depletion of NOP2 promotes the reactivation of latently infected HIV-1 proviruses in multiple cell lines as well as primary CD4+ T cells, alone or in combination with latency-reversing agents (LRAs). Mechanistically, NOP2 associates with HIV-1 5' LTR, interacts with HIV-1 TAR RNA by competing with HIV-1 Tat protein, as well as contributes to TAR m5C methylation. RNA MTase catalytic domain (MTD) of NOP2 mediates its competition with Tat and binding with TAR. Overall, these findings verified that NOP2 suppresses HIV-1 transcription and promotes viral latency.
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Affiliation(s)
- Weili Kong
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, California, United States of America
| | - Ayan Biswas
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Dawei Zhou
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Guillaume Fiches
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Koh Fujinaga
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Netty Santoso
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Jian Zhu
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
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Bandera A, Gori A, Clerici M, Sironi M. Phylogenies in ART: HIV reservoirs, HIV latency and drug resistance. Curr Opin Pharmacol 2019; 48:24-32. [PMID: 31029861 DOI: 10.1016/j.coph.2019.03.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/07/2019] [Accepted: 03/12/2019] [Indexed: 11/17/2022]
Abstract
Combination antiretroviral therapy (ART) has significantly reduced the morbidity and mortality resulting from HIV infection. ART is, however, unable to eradicate HIV, which persists latently in several cell types and tissues. Phylogenetic analyses suggested that the proliferation of cells infected before ART initiation is mainly responsible for residual viremia, although controversy still exists. Conversely, it is widely accepted that drug resistance mutations (DRMs) do not appear during ART in patients with suppressed viral loads. Studies based on sequence clustering have in fact indicated that, at least in developed countries, HIV-infected ART-naive patients are the major source of drug-resistant viruses. Analysis of longitudinally sampled sequences have also shown that DRMs have variable fitness costs, which are strongly influenced by the viral genetic background.
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Affiliation(s)
- Alessandra Bandera
- Infectious Diseases Unit, Department of Internal Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20090 Milan, Italy; Department of Pathophysiology and Transplantation, School of Medicine and Surgery, University of Milan, 20090 Milan, Italy
| | - Andrea Gori
- Infectious Diseases Unit, Department of Internal Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20090 Milan, Italy; Department of Pathophysiology and Transplantation, School of Medicine and Surgery, University of Milan, 20090 Milan, Italy
| | - Mario Clerici
- Department of Pathophysiology and Transplantation, School of Medicine and Surgery, University of Milan, 20090 Milan, Italy; IRCCS Fondazione Don Carlo Gnocchi, 20148 Milan, Italy
| | - Manuela Sironi
- Bioinformatics, Scientific Institute, IRCCS E. MEDEA, 23842 Bosisio Parini, Lecco, Italy.
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Emu B, Fessel J, Schrader S, Kumar P, Richmond G, Win S, Weinheimer S, Marsolais C, Lewis S. Phase 3 Study of Ibalizumab for Multidrug-Resistant HIV-1. N Engl J Med 2018; 379:645-654. [PMID: 30110589 DOI: 10.1056/nejmoa1711460] [Citation(s) in RCA: 146] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Ibalizumab, a humanized IgG4 monoclonal antibody, blocks the entry of human immunodeficiency virus type 1 (HIV-1) by noncompetitive binding to CD4. METHODS In this single-group, open-label, phase 3 study, we enrolled 40 adults with multidrug-resistant (MDR) HIV-1 infection in whom multiple antiretroviral therapies had failed. All the patients had a viral load of more than 1000 copies of HIV-1 RNA per milliliter. After a 7-day control period in which patients continued to receive their current therapy, a loading dose of 2000 mg of ibalizumab was infused; the viral load was quantified 7 days later. Through week 25 of the study, patients received 800 mg of ibalizumab every 14 days, combined with an individually optimized background regimen including at least one fully active agent. The primary end point was the proportion of patients with a decrease in viral load of at least 0.5 log10 copies per milliliter from baseline (day 7) to day 14. RESULTS A total of 31 patients completed the study. The mean baseline viral load was 4.5 log10 copies per milliliter, and the mean CD4 count was 150 per microliter. Of the 40 patients in the intention-to-treat population, 33 (83%) had a decrease in viral load of at least 0.5 log10 copies per milliliter from baseline (P<0.001 for the comparison with the control period). The mean viral-load decrease was 1.1 log10 copies per milliliter. During the control period, 1 patient, who received the optimized background regimen prematurely, had a decrease in viral load of 0.5 log10 copies per milliliter. At week 25, patients who had received ibalizumab plus an optimized background regimen had a mean decrease of 1.6 log10 copies per milliliter from baseline; 43% of the patients had a viral load of less than 50 copies per milliliter, and 50% had a viral load of less than 200 copies per milliliter. Among 10 patients who had virologic failure or rebound, in vitro testing identified 9 who had a lower degree of susceptibility to ibalizumab than at baseline. The most common adverse event was diarrhea (in 20% of patients). Four patients died from causes related to underlying illnesses; 1 had a serious adverse event (the immune reconstitution inflammatory syndrome) that was deemed to be related to ibalizumab therapy. CONCLUSIONS In patients with MDR HIV-1 infection who had advanced disease and limited treatment options, ibalizumab had significant antiviral activity during a 25-week study. Evidence of the emergence of diminished ibalizumab susceptibility was observed in vitro in patients who had virologic failure. (Funded by the Orphan Products Clinical Trials Grants Program of the Food and Drug Administration and TaiMed Biologics; TMB-301 ClinicalTrials.gov number, NCT02475629 .).
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Affiliation(s)
- Brinda Emu
- From the Yale School of Medicine, New Haven, CT (B.E.); Kaiser Foundation Research Institute (J.F.) and Quest Clinical Research (S. Win), San Francisco; Schrader Clinic, Houston (S.S.); Georgetown University, Washington, DC (P.K.); Nova Southeastern University, Ft. Lauderdale, FL, and Florida International University, Miami (G.R.); TaiMed Biologics, Irvine, CA (S. Weinheimer, S.L.); and Theratechnologies, Montreal (C.M.)
| | - Jeffrey Fessel
- From the Yale School of Medicine, New Haven, CT (B.E.); Kaiser Foundation Research Institute (J.F.) and Quest Clinical Research (S. Win), San Francisco; Schrader Clinic, Houston (S.S.); Georgetown University, Washington, DC (P.K.); Nova Southeastern University, Ft. Lauderdale, FL, and Florida International University, Miami (G.R.); TaiMed Biologics, Irvine, CA (S. Weinheimer, S.L.); and Theratechnologies, Montreal (C.M.)
| | - Shannon Schrader
- From the Yale School of Medicine, New Haven, CT (B.E.); Kaiser Foundation Research Institute (J.F.) and Quest Clinical Research (S. Win), San Francisco; Schrader Clinic, Houston (S.S.); Georgetown University, Washington, DC (P.K.); Nova Southeastern University, Ft. Lauderdale, FL, and Florida International University, Miami (G.R.); TaiMed Biologics, Irvine, CA (S. Weinheimer, S.L.); and Theratechnologies, Montreal (C.M.)
| | - Princy Kumar
- From the Yale School of Medicine, New Haven, CT (B.E.); Kaiser Foundation Research Institute (J.F.) and Quest Clinical Research (S. Win), San Francisco; Schrader Clinic, Houston (S.S.); Georgetown University, Washington, DC (P.K.); Nova Southeastern University, Ft. Lauderdale, FL, and Florida International University, Miami (G.R.); TaiMed Biologics, Irvine, CA (S. Weinheimer, S.L.); and Theratechnologies, Montreal (C.M.)
| | - Gary Richmond
- From the Yale School of Medicine, New Haven, CT (B.E.); Kaiser Foundation Research Institute (J.F.) and Quest Clinical Research (S. Win), San Francisco; Schrader Clinic, Houston (S.S.); Georgetown University, Washington, DC (P.K.); Nova Southeastern University, Ft. Lauderdale, FL, and Florida International University, Miami (G.R.); TaiMed Biologics, Irvine, CA (S. Weinheimer, S.L.); and Theratechnologies, Montreal (C.M.)
| | - Sandra Win
- From the Yale School of Medicine, New Haven, CT (B.E.); Kaiser Foundation Research Institute (J.F.) and Quest Clinical Research (S. Win), San Francisco; Schrader Clinic, Houston (S.S.); Georgetown University, Washington, DC (P.K.); Nova Southeastern University, Ft. Lauderdale, FL, and Florida International University, Miami (G.R.); TaiMed Biologics, Irvine, CA (S. Weinheimer, S.L.); and Theratechnologies, Montreal (C.M.)
| | - Steven Weinheimer
- From the Yale School of Medicine, New Haven, CT (B.E.); Kaiser Foundation Research Institute (J.F.) and Quest Clinical Research (S. Win), San Francisco; Schrader Clinic, Houston (S.S.); Georgetown University, Washington, DC (P.K.); Nova Southeastern University, Ft. Lauderdale, FL, and Florida International University, Miami (G.R.); TaiMed Biologics, Irvine, CA (S. Weinheimer, S.L.); and Theratechnologies, Montreal (C.M.)
| | - Christian Marsolais
- From the Yale School of Medicine, New Haven, CT (B.E.); Kaiser Foundation Research Institute (J.F.) and Quest Clinical Research (S. Win), San Francisco; Schrader Clinic, Houston (S.S.); Georgetown University, Washington, DC (P.K.); Nova Southeastern University, Ft. Lauderdale, FL, and Florida International University, Miami (G.R.); TaiMed Biologics, Irvine, CA (S. Weinheimer, S.L.); and Theratechnologies, Montreal (C.M.)
| | - Stanley Lewis
- From the Yale School of Medicine, New Haven, CT (B.E.); Kaiser Foundation Research Institute (J.F.) and Quest Clinical Research (S. Win), San Francisco; Schrader Clinic, Houston (S.S.); Georgetown University, Washington, DC (P.K.); Nova Southeastern University, Ft. Lauderdale, FL, and Florida International University, Miami (G.R.); TaiMed Biologics, Irvine, CA (S. Weinheimer, S.L.); and Theratechnologies, Montreal (C.M.)
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