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Hehe Z, Minna Z, Qin F, Tielin N, Yi F, Liping F, Fangfang C, Houlin T, Shi W, Maohe Y, Fan L. Application of molecular epidemiology in revealing HIV-1 transmission network and recombination patterns in Tianjin, China. J Med Virol 2024; 96:e29824. [PMID: 39072805 DOI: 10.1002/jmv.29824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/24/2024] [Accepted: 07/16/2024] [Indexed: 07/30/2024]
Abstract
Using a comprehensive molecular epidemiological approach, we characterized the transmission dynamics of HIV-1 among the MSM population in Tianjin, China. Our findings revealed that 38.56% (386/1001) of individuals clustered across 109 molecular transmission clusters (TCs), with MSM aged 50 and below being the group most commonly transmitting HIV-1. Among the identified TCs, CRF01_AE predominated, followed by CRF07_BC. Notably, CRF07_BC demonstrated a higher propensity for forming large clusters compared to CRF01_AE. Birth-death skyline analyses of the two largest clusters indicated that the HIV/AIDS transmission may be at a critical point, nearly all had Re approximately 1 by now. A retrospective analysis revealed that the rapid expansion of these large clusters was primarily driven by the introduction of viruses in 2021, highlighting the crucial importance of continuous molecular surveillance in identifying newly emerging high-risk transmission chains and adapting measures to address evolving epidemic dynamics. Furthermore, we detected the transmission of drug-resistant mutations (DRMs) within the TCs, particularly in the CRF07_BC clusters (K103N, Y181C, and K101E) and CRF01_AE clusters (P225H and K219R), emphasizing the importance of monitoring to support the continued efficacy of first-line therapies and pre-exposure prophylaxis (PrEP). Recombination analyses indicated that complex recombinant patterns, associated with increased amino acid variability, could confer adaptive traits to the viruses, potentially providing a competitive advantage in certain host populations or regions. Our study highlights the potential of integrating molecular epidemiological and phylodynamic approaches to inform targeted interventions.
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Affiliation(s)
- Zhao Hehe
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zheng Minna
- Department of HIV/AIDS and STDs Control and Prevention, Tianjin Provincial Center for Disease Control and Prevention, Tianjin, China
- Tianjin Key Laboratory of Pathogenic Microbiology of Infectious Disease, Tianjin, China
| | - Fan Qin
- Department of HIV/AIDS and STDs Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Ning Tielin
- Department of HIV/AIDS and STDs Control and Prevention, Tianjin Provincial Center for Disease Control and Prevention, Tianjin, China
- Tianjin Key Laboratory of Pathogenic Microbiology of Infectious Disease, Tianjin, China
| | - Feng Yi
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- State Key Laboratory for Infectious Disease Prevention and Control, Beijing, China
| | - Fei Liping
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Chen Fangfang
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Tang Houlin
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wang Shi
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yu Maohe
- Department of HIV/AIDS and STDs Control and Prevention, Tianjin Provincial Center for Disease Control and Prevention, Tianjin, China
- Tianjin Key Laboratory of Pathogenic Microbiology of Infectious Disease, Tianjin, China
| | - Lyu Fan
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
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Wang Z, Zhang H, Gao Z, Sang Z, De Clercq E, Pannecouque C, Kang D, Zhan P, Liu X. Structure-based design and optimization lead to the identification of novel dihydrothiopyrano[3,2- d]pyrimidine derivatives as potent HIV-1 inhibitors against drug-resistant variants. Acta Pharm Sin B 2024; 14:1257-1282. [PMID: 38486991 PMCID: PMC10935503 DOI: 10.1016/j.apsb.2023.11.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/03/2023] [Accepted: 11/14/2023] [Indexed: 03/17/2024] Open
Abstract
With our continuous endeavors in seeking potent anti-HIV-1 agents, we reported here the discovery, biological characterization, and druggability evaluation of a class of nonnucleoside reverse transcriptase inhibitors. To fully explore the chemical space of the NNRTI-binding pocket, novel series of dihydrothiopyrano [3,2-d]pyrimidines were developed by employing the structure-based design strategy. Most of the derivatives were endowed with prominent antiviral activities against HIV-1 wild-type and resistant strains at nanomolar levels. Among them, compound 23h featuring the aminopiperidine moiety was identified as the most potent inhibitor, with EC50 values ranging from 3.43 to 21.4 nmol/L. Especially, for the challenging double-mutants F227L + V106A and K103N + Y181C, 23h exhibited 2.3- to 14.5-fold more potent activity than the first-line drugs efavirenz and etravirine. Besides, the resistance profiles of 23h achieved remarkable improvement compared to efavirenz and etravirine. The binding target of 23h was further confirmed to be HIV-1 reverse transcriptase. Molecular modeling studies were also performed to elucidate the biological evaluation results and give guidance for the optimization campaign. Furthermore, no apparent inhibition of the major CYP450 enzymes and hERG channel was observed for 23h. Most importantly, 23h was characterized by good pharmacokinetic properties and excellent safety in vivo. Collectively, 23h holds great promise as a potential candidate for its effective antiviral efficacy and favorable drug-like profiles.
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Affiliation(s)
- Zhao Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, Jinan 250012, China
- Suzhou Research Institute, Shandong University, Suzhou 215123, China
| | - Heng Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Zhen Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Zihao Sang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Leuven B-3000, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Leuven B-3000, Belgium
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, Jinan 250012, China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, Jinan 250012, China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, Jinan 250012, China
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3
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Załęski A, Lembas A, Dyda T, Siwak E, Osińska J, Suchacz M, Stempkowska-Rejek J, Strycharz M, Orzechowska J, Wiercińska-Drapało A. Changes in Primary HIV-1 Drug Resistance Due to War Migration from Eastern Europe. J Immigr Minor Health 2024; 26:15-22. [PMID: 37973713 PMCID: PMC10771373 DOI: 10.1007/s10903-023-01559-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2023] [Indexed: 11/19/2023]
Abstract
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.
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Affiliation(s)
- Andrzej Załęski
- Hospital for Infectious Diseases in Warsaw, Warsaw, Poland
- Department of Infectious Diseases, Tropical Diseases and Hepatology, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Lembas
- Hospital for Infectious Diseases in Warsaw, Warsaw, Poland.
- Department of Infectious Diseases, Tropical Diseases and Hepatology, Medical University of Warsaw, Warsaw, Poland.
| | - Tomasz Dyda
- Hospital for Infectious Diseases in Warsaw, Warsaw, Poland
- Molecular Diagnostics Laboratory, Hospital for Infectious Diseases in Warsaw, Warsaw, Poland
| | - Ewa Siwak
- Hospital for Infectious Diseases in Warsaw, Warsaw, Poland
- Department of Infectious Diseases, Tropical Diseases and Hepatology, Medical University of Warsaw, Warsaw, Poland
- HIV Out-Patient Clinic, Hospital for Infectious Diseases in Warsaw, Warsaw, Poland
| | - Joanna Osińska
- Infectious Diseases Clinical Ward in Ostróda, Department of Family Medicine and Infectious Diseases, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Magdalena Suchacz
- Hospital for Infectious Diseases in Warsaw, Warsaw, Poland
- Department of Infectious Diseases, Tropical Diseases and Hepatology, Medical University of Warsaw, Warsaw, Poland
| | | | - Marta Strycharz
- Clinical Department of Infectious Diseases and Hepatology, Medical University of Lodz, Lodz, Poland
| | - Justyna Orzechowska
- Clinical Department of Infectious Diseases, College of Medical Sciences, Medical Center in Łańcut, University of Rzeszów, Rzeszów, Poland
| | - Alicja Wiercińska-Drapało
- Hospital for Infectious Diseases in Warsaw, Warsaw, Poland
- Department of Infectious Diseases, Tropical Diseases and Hepatology, Medical University of Warsaw, Warsaw, Poland
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Branda F, Giovanetti M, Sernicola L, Farcomeni S, Ciccozzi M, Borsetti A. Comprehensive Analysis of HIV-1 Integrase Resistance-Related Mutations in African Countries. Pathogens 2024; 13:102. [PMID: 38392840 PMCID: PMC10892843 DOI: 10.3390/pathogens13020102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
The growing emergence of non-nucleoside reverse transcriptase inhibitor (NNRTI) HIV drug resistance in sub-Saharan Africa (SSA) led to the World Health Organization (WHO) recommending, in 2018, a transition to dolutegravir (DTG) as a first-line antiretroviral therapy (ART) in SSA. The broad HIV-1 genetic diversity in SSA could shape DTG effectiveness and the pattern of drug resistance mutations (DRMs) in this region. This study evaluated HIV-1 integrase (IN) DRMs and conserved regions among published groups M, N, O, and P HIV-1 sequences spanning forty years of the HIV epidemic during the transition of DTG-based ART. Overall, we found low levels of integrase strand transfer inhibitor (INSTI)-DRMs (<1%) across HIV groups between the years 1983 and 2023; however, it was unexpected to detect DRMs at statistically significantly higher frequencies in pre-INSTI (1983-2007) than in the INSTI (2008-2023) era. The variability of accessory INSTI-DRMs depended on the HIV subtypes, with implications for susceptibility to DTG. Our findings provide new perspectives on the molecular epidemiology and drug resistance profiles of INSTIs in SSA, emphasizing the need for ongoing surveillance and customized treatment approaches to address the continent's varied HIV subtypes and changing resistance patterns.
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Affiliation(s)
- Francesco Branda
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy; (F.B.); (M.C.)
| | - Marta Giovanetti
- Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, 00128 Rome, Italy;
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-002, Brazil
- Climate Amplified Diseases and Epidemics (CLIMADE), Brasilia 70070-130, Brazil
| | - Leonardo Sernicola
- National HIV/AIDS Research Center (CNAIDS), Istituto Superiore di Sanità, 00161 Rome, Italy; (L.S.); (S.F.)
| | - Stefania Farcomeni
- National HIV/AIDS Research Center (CNAIDS), Istituto Superiore di Sanità, 00161 Rome, Italy; (L.S.); (S.F.)
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy; (F.B.); (M.C.)
| | - Alessandra Borsetti
- National HIV/AIDS Research Center (CNAIDS), Istituto Superiore di Sanità, 00161 Rome, Italy; (L.S.); (S.F.)
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Viñuela L, de Salazar A, Fuentes A, Serrano-Conde E, Falces-Romero I, Pinto A, Portilla I, Masiá M, Peraire J, Gómez-Sirvent JL, Sanchiz M, Iborra A, Baza B, Aguilera A, Olalla J, Espinosa N, Iribarren JA, Martínez-Velasco M, Imaz A, Montero M, Rivero M, Suarez-García I, Maciá MD, Galán JC, Perez-Elias MJ, García-Fraile LJ, Moreno C, Garcia F. Transmitted drug resistance to antiretroviral drugs in Spain during the period 2019-2021. J Med Virol 2023; 95:e29287. [PMID: 38084763 DOI: 10.1002/jmv.29287] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 10/17/2023] [Accepted: 11/18/2023] [Indexed: 12/18/2023]
Abstract
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.
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Affiliation(s)
- Laura Viñuela
- Clinical Microbiology Unit, Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Ibs, Granada, Spain
- Ciber de Enfermedades Infecciosas, CIBERINFEC, ISCIII, Madrid, Spain
| | - Adolfo de Salazar
- Clinical Microbiology Unit, Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Ibs, Granada, Spain
- Ciber de Enfermedades Infecciosas, CIBERINFEC, ISCIII, Madrid, Spain
| | - Ana Fuentes
- Clinical Microbiology Unit, Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Ibs, Granada, Spain
- Ciber de Enfermedades Infecciosas, CIBERINFEC, ISCIII, Madrid, Spain
| | - Esther Serrano-Conde
- Clinical Microbiology Unit, Hospital Universitario Clínico San Cecilio, Granada, Spain
| | | | - Adriana Pinto
- Infectious Diseases Unit, Hospital 12 de Octubre, Madrid, Spain
| | - Irene Portilla
- Infectious Diseases Unit, Hospital General Universitario de Alicante, Alicante, Spain
| | - Mar Masiá
- Ciber de Enfermedades Infecciosas, CIBERINFEC, ISCIII, Madrid, Spain
- Infectious Diseases Unit, Hospital General Universitario de Elche, Elche, Spain
| | - Joaquim Peraire
- Ciber de Enfermedades Infecciosas, CIBERINFEC, ISCIII, Madrid, Spain
- Infectious Diseases Unit, Hospital Universitari de Tarragona Joan XXIII, IISPV, Universitat Rovira i Virgili, Tarragona, Spain
| | - Juan Luis Gómez-Sirvent
- Infectious Diseases Unit, Hospital Universitario de Canarias, Las Palmas de Gran Canaria, Spain
| | - Marta Sanchiz
- Infectious Diseases Unit, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Asunción Iborra
- Clinical Microbiology Unit, Hospital Virgen de la Arrixaca, Murcia, Spain
| | - Begoña Baza
- Centro Sanitario Sandoval, Hospital Clínico San Carlos, Madrid, Spain
- Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
- Instituto de Medicina de Laboratorio (IML), Madrid, Spain
| | - Antonio Aguilera
- Clinical Microbiology Unit, Complejo Hospitalario Universitario de Santiago, Santiago, Spain
| | - Julián Olalla
- Infectious Diseases Unit, Hospital Costa del Sol, Marbella, Spain
| | - Nuria Espinosa
- Infectious Diseases Unit, Hospital Virgen del Rocío, Seville, Spain
| | | | | | - Arkaitz Imaz
- Infectious Diseases Unit, Hospital Universitario de Bellvitge, Barcelona, Spain
| | - Marta Montero
- Infectious Diseases Unit, Hospital Universitario La Fe, Valencia, Spain
| | - María Rivero
- Infectious Diseases Unit, Hospital de Navarra, Pamplona, Spain
| | | | | | - Juan Carlos Galán
- Infectious Diseases Unit, Hospital Ramón y Cajal, Madrid, Spain
- Ciber de Epidemiologia y Salud Publica, CIBERESP, Madrid, Spain
- Insituto Ramón y Cajal de Investigación Sanitaria (IRYSCIS), Madrid, Spain
| | - Maria Jesus Perez-Elias
- Ciber de Enfermedades Infecciosas, CIBERINFEC, ISCIII, Madrid, Spain
- Infectious Diseases Unit, Hospital Ramón y Cajal, Madrid, Spain
| | | | - Cristina Moreno
- Ciber de Enfermedades Infecciosas, CIBERINFEC, ISCIII, Madrid, Spain
- Instituto de Salud Carlos III, Madrid, Spain
| | - Federico Garcia
- Clinical Microbiology Unit, Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Ibs, Granada, Spain
- Ciber de Enfermedades Infecciosas, CIBERINFEC, ISCIII, Madrid, Spain
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6
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Kim MJ, Yu KL, Han R, Lee Y, Oh K, You JC. Identification of a Non-Nucleoside Reverse Transcriptase Inhibitor against Human Immunodeficiency Virus-1. ACS Infect Dis 2023; 9:1582-1592. [PMID: 37415514 DOI: 10.1021/acsinfecdis.3c00166] [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] [Indexed: 07/08/2023]
Abstract
The HIV-1 infection epidemic remains a global health problem. Current antiretroviral treatments are effective in controlling the progression of a severe infection. However, the emergence of drug resistance requires an urgent identification of new treatment regimes. HIV-1 reverse transcriptase (RTs) has been a successful therapeutic target owing to its high specificity and potent antiviral properties; therefore, it has become an essential component of current HIV-1 standard treatments. This study identified a new HIV-1 RTs inhibitor (Compound #8) that is structurally unique and greatly effective against HIV-1 through chemical library screening and a medicinal chemistry program by analyzing the structure-activity relationship (SAR). Further analysis of molecular docking and mechanisms of action demonstrated that Compound #8 is a novel type of HIV-1 non-nucleoside reverse transcriptase inhibitor (NNRTI) with a flexible binding mode. Therefore, it exhibits great therapeutic potential when combined with other existing HIV-1 drugs. Our current studies suggest that Compound #8 is a promising novel scaffold for the development of new HIV-1 treatments.
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Affiliation(s)
- Min-Jung Kim
- Avixgen Inc., 2477 Nambusunhwan-ro, Seocho, Seoul 06725, Republic of Korea
| | - Kyung Lee Yu
- National Research Laboratory of Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho, Seoul 06591, Republic of Korea
| | - Ri Han
- College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak, Seoul 06974, Republic of Korea
| | - Yoonji Lee
- College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak, Seoul 06974, Republic of Korea
| | - Kyungsoo Oh
- College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak, Seoul 06974, Republic of Korea
- Center for Metareceptome Research, Graduate School of Pharmaceutical Sciences, Chung-Ang University, 84 Heukseok-ro, Dongjak, Seoul 06974, Republic of Korea
| | - Ji Chang You
- Avixgen Inc., 2477 Nambusunhwan-ro, Seocho, Seoul 06725, Republic of Korea
- National Research Laboratory of Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho, Seoul 06591, Republic of Korea
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7
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Alexiev I, Shankar A, Pan Y, Grigorova L, Partsuneva A, Dimitrova R, Gancheva A, Kostadinova A, Elenkov I, Yancheva N, Grozdeva R, Strashimirov D, Stoycheva M, Baltadzhiev I, Doichinova T, Pekova L, Kosmidis M, Emilova R, Nikolova M, Switzer WM. Transmitted HIV Drug Resistance in Bulgaria Occurs in Clusters of Individuals from Different Transmission Groups and Various Subtypes (2012-2020). Viruses 2023; 15:v15040941. [PMID: 37112921 PMCID: PMC10146724 DOI: 10.3390/v15040941] [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: 02/12/2023] [Revised: 04/04/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Transmitted HIV drug resistance in Bulgaria was first reported in 2015 using data from 1988-2011. We determined the prevalence of surveillance drug resistance mutations (SDRMs) and HIV-1 genetic diversity in Bulgaria during 2012-2020 using polymerase sequences from 1053 of 2010 (52.4%) antiretroviral therapy (ART)-naive individuals. Sequences were analyzed for DRM using the WHO HIV SDRM list implemented in the calculated population resistance tool at Stanford University. Genetic diversity was inferred using automated subtyping tools and phylogenetics. Cluster detection and characterization was performed using MicrobeTrace. The overall rate of SDRMs was 5.7% (60/1053), with 2.2% having resistance to nucleoside reverse transcriptase inhibitors (NRTIs), 1.8% to non-nucleoside reverse transcriptase inhibitors (NNRTIs), 2.1% to protease inhibitors (PIs), and 0.4% with dual-class SDRMs. We found high HIV-1 diversity, with the majority being subtype B (60.4%), followed by F1 (6.9%), CRF02_AG (5.2%), A1 (3.7%), CRF12_BF (0.8%), and other subtypes and recombinant forms (23%). Most (34/60, 56.7%) of the SDRMs were present in transmission clusters of different subtypes composed mostly of male-to-male sexual contact (MMSC), including a 14-member cluster of subtype B sequences from 12 MMSC and two males reporting heterosexual contact; 13 had the L90M PI mutation and one had the T215S NRTI SDRM. We found a low SDRM prevalence amid high HIV-1 diversity among ART-naive patients in Bulgaria during 2012-2020. The majority of SDRMs were found in transmission clusters containing MMSC, indicative of onward spread of SDRM in drug-naive individuals. Our study provides valuable information on the transmission dynamics of HIV drug resistance in the context of high genetic diversity in Bulgaria, for the development of enhanced prevention strategies to end the epidemic.
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Affiliation(s)
- Ivailo Alexiev
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Anupama Shankar
- Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Yi Pan
- Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Lyubomira Grigorova
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Alexandra Partsuneva
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Reneta Dimitrova
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Anna Gancheva
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Asya Kostadinova
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Ivaylo Elenkov
- Specialized Hospital for Active Treatment of Infectious & Parasitic Diseases, 1606 Sofia, Bulgaria
| | - Nina Yancheva
- Specialized Hospital for Active Treatment of Infectious & Parasitic Diseases, 1606 Sofia, Bulgaria
| | - Rusina Grozdeva
- Specialized Hospital for Active Treatment of Infectious & Parasitic Diseases, 1606 Sofia, Bulgaria
| | - Dimitar Strashimirov
- Specialized Hospital for Active Treatment of Infectious & Parasitic Diseases, 1606 Sofia, Bulgaria
| | - Mariana Stoycheva
- Department of Infectious Diseases, Medical University, 4002 Plovdiv, Bulgaria
| | - Ivan Baltadzhiev
- Department of Infectious Diseases, Medical University, 4002 Plovdiv, Bulgaria
| | - Tsetsa Doichinova
- Department of Infectious Diseases, Medical University, 5800 Pleven, Bulgaria
| | - Lilia Pekova
- Clinic of Infectious Diseases, Medical University, 6000 Stara Zagora, Bulgaria
| | - Minas Kosmidis
- Clinic of Infectious Diseases, Medical University, 9002 Varna, Bulgaria
| | - Radoslava Emilova
- National Reference Laboratory of Immunology, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Maria Nikolova
- National Reference Laboratory of Immunology, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - William M Switzer
- Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
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Fofana DB, Diarra H, Guindo I, Savadogo MK, d’Almeida M, Diallo FI, Baldé A, Soulié C, Kone A, Marcelin AG, Maiga AI, Lambert-Niclot S, Maiga M, McFall S, Hawkins CA, Murphy RL, Sylla M, Katlama C, Holl JL, Calvez V, Morand-Joubert L. Prevalence of HIV-1 Natural Polymorphisms and Integrase-Resistance-Associated Mutations in African Children. Viruses 2023; 15:v15020546. [PMID: 36851760 PMCID: PMC9964382 DOI: 10.3390/v15020546] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/05/2023] [Accepted: 02/12/2023] [Indexed: 02/18/2023] Open
Abstract
Integrase inhibitors (INIs) are a potent option for HIV treatment. Limited data exist on INI resistance in West Africa, particularly in children living with HIV/AIDS. We determined the prevalence of integrase gene polymorphisms and the frequency of naturally occurring amino acid (aa) substitutions at positions associated with INI resistance. Dried blood spot (DBS) samples were obtained from one hundred and seven (107) HIV-1-infected children aged less than 15 years old in two West African countries, Benin and Mali. All children were naïve to INI treatment, 56 were naïve to anti-retroviral therapy (ART), and 51 had received ART. Genetic sequencing of HIV integrase was successful in 75 samples. The aa changes at integrase positions associated with INI resistance were examined according to the Stanford HIV Genotypic Resistance database. The median ages were 2.6 and 10 years for ART-naïve and -treated children, respectively. The most common subtypes observed were CRF02_AG (74.7%) followed by CRF06_cpx (20%). No major INI-resistance mutations at positions 66, 92, 121, 143, 147, 148, 155, and 263 were detected. The most prevalent INI accessory resistance mutations were: L74I/M (14/75, 18.6%) followed by E157Q (8/75, 10.6%), G163E/N/T/Q (5/75, 6.6%), Q95A/H/P (2/75, 2.6%), and T97A (4/75, 5.3%). Other substitutions observed were M50I/L/P, H51E/P/S/Q, I72V, T112V, V201I, and T206S. Polymorphisms at positions which may influence the genetic barrier and/or drive the selection of specific INI-resistance pathways were detected. However, no transmitted drug resistance (TDR) to INI was detected among samples of INI-naïve patients. These findings support the use of this treatment class for children with HIV-1, particularly in West Africa.
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Affiliation(s)
- Djeneba B. Fofana
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-Hôpitaux de Paris (AP-HP), Saint-Antoine Hospital, F-75012 Paris, France
- Correspondence:
| | - Houdou Diarra
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | - Ibrahima Guindo
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | | | - Marceline d’Almeida
- Département Mère Enfant, Faculté Des Sciences De La Santé, Université Abomey-Calavi, CNHU—HKM, Cotonou 229, Benin
| | - Fatoumata I. Diallo
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | - Aliou Baldé
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
| | - Cathia Soulié
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-HÔpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, F-75013 Paris, France
| | - Amadou Kone
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-HÔpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, F-75013 Paris, France
| | - Almoustapha I. Maiga
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | - Sidonie Lambert-Niclot
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-Hôpitaux de Paris (AP-HP), Saint-Antoine Hospital, F-75012 Paris, France
| | - Mamoudou Maiga
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
- Institute for Global Health, Northwestern University, Chicago, IL 60208, USA
| | - Sally McFall
- Institute for Global Health, Northwestern University, Chicago, IL 60208, USA
| | - Claudia A. Hawkins
- Institute for Global Health, Northwestern University, Chicago, IL 60208, USA
| | - Robert L. Murphy
- Institute for Global Health, Northwestern University, Chicago, IL 60208, USA
| | - Mariam Sylla
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | - Christine Katlama
- Service des Maladies Infectieuses, Hôpital Pitié-Salpêtrière APHP, F-75013 Paris, France
| | - Jane L. Holl
- Biological Sciences Division, University of Chicago, Chicago, IL 60637, USA
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-HÔpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, F-75013 Paris, France
| | - Laurence Morand-Joubert
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-Hôpitaux de Paris (AP-HP), Saint-Antoine Hospital, F-75012 Paris, France
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Novitsky V, Steingrimsson J, Gillani FS, Howison M, Aung S, Solomon M, Won CY, Brotherton A, Shah R, Dunn C, Fulton J, Bertrand T, Civitarese A, Howe K, Marak T, Chan P, Bandy U, Alexander-Scott N, Hogan J, Kantor R. Statewide Longitudinal Trends in Transmitted HIV-1 Drug Resistance in Rhode Island, USA. Open Forum Infect Dis 2022; 9:ofab587. [PMID: 34988256 PMCID: PMC8709897 DOI: 10.1093/ofid/ofab587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/06/2021] [Indexed: 11/14/2022] Open
Abstract
Background HIV-1 transmitted drug resistance (TDR) remains a global challenge that can impact care, yet its comprehensive assessment is limited and heterogenous. We longitudinally characterized statewide TDR in Rhode Island. Methods Demographic and clinical data from treatment-naïve individuals were linked to protease, reverse transcriptase, and integrase sequences routinely obtained over 2004-2020. TDR extent, trends, impact on first-line regimens, and association with transmission networks were assessed using the Stanford Database, Mann-Kendall statistic, and phylogenetic tools. Results In 1123 individuals, TDR to any antiretroviral increased from 8% (2004) to 26% (2020), driven by non-nucleotide reverse transcriptase inhibitor (NNRTI; 5%-18%) and, to a lesser extent, nucleotide reverse transcriptase inhibitor (NRTI; 2%-8%) TDR. Dual- and triple-class TDR rates were low, and major integrase strand transfer inhibitor resistance was absent. Predicted intermediate to high resistance was in 77% of those with TDR, with differential suppression patterns. Among all individuals, 34% were in molecular clusters, some only with members with TDR who shared mutations. Among clustered individuals, people with TDR were more likely in small clusters. Conclusions In a unique (statewide) assessment over 2004-2020, TDR increased; this was primarily, but not solely, driven by NNRTIs, impacting antiretroviral regimens. Limited TDR to multiclass regimens and pre-exposure prophylaxis are encouraging; however, surveillance and its integration with molecular epidemiology should continue in order to potentially improve care and prevention interventions.
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Affiliation(s)
| | | | | | - Mark Howison
- Research Improving People's Life, Providence, Rhode Island, USA
| | - Su Aung
- Brown University, Providence, Rhode Island, USA
| | | | - Cindy Y Won
- Brown University, Providence, Rhode Island, USA
| | | | - Rajeev Shah
- Brown University, Providence, Rhode Island, USA
| | - Casey Dunn
- Yale University, New Haven, Connecticut, USA
| | - John Fulton
- Brown University, Providence, Rhode Island, USA
| | - Thomas Bertrand
- Rhode Island Department of Health, Providence, Rhode Island, USA
| | - Anna Civitarese
- Rhode Island Department of Health, Providence, Rhode Island, USA
| | - Katharine Howe
- Rhode Island Department of Health, Providence, Rhode Island, USA
| | - Theodore Marak
- Rhode Island Department of Health, Providence, Rhode Island, USA
| | - Philip Chan
- Brown University, Providence, Rhode Island, USA.,Rhode Island Department of Health, Providence, Rhode Island, USA
| | - Utpala Bandy
- Rhode Island Department of Health, Providence, Rhode Island, USA
| | | | | | - Rami Kantor
- Brown University, Providence, Rhode Island, USA
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Impact of HIV-1 Resistance-Associated Mutations on Susceptibility to Doravirine: Analysis of Real-World Clinical Isolates. Antimicrob Agents Chemother 2021; 65:e0121621. [PMID: 34570651 PMCID: PMC8597775 DOI: 10.1128/aac.01216-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Clinical management of human immunodeficiency virus type-1 (HIV-1) infection may be negatively impacted by either acquired or transmitted drug resistance. Here, we aim to extend our understanding of the impact of resistance-associated mutations (RAMs) on the susceptibility of clinical isolates to the nonnucleoside reverse transcriptase inhibitor (NNRTI) doravirine. Clinical isolates from people living with HIV-1 undergoing routine testing for susceptibility to doravirine and other approved NNRTIs (etravirine, rilpivirine, efavirenz, and nevirapine) were collected from August 2018 to August 2019. Susceptibility in the presence/absence of NNRTI and nucleos(t)ide reverse transcriptase inhibitor (NRTI) mutations was determined using cutoffs for relative fold change in inhibition (ratio of the 50% inhibitory concentration [IC50] of patient virus compared with the IC50 of a wild-type reference strain). Biological cutoffs of 3- to 15-fold change were investigated for doravirine, with preestablished cutoffs used for the other NNRTIs. Of 4,070 clinical isolates, 42.9% had ≥1 NNRTI RAM. More isolates were susceptible to doravirine (92.5-96.7%) than to etravirine (91.5%), rilpivirine (89.5%), efavirenz (81.5%), or nevirapine (77.5%). Based on a 3-fold cutoff, doravirine susceptibility was retained in 44.7-65.8% of isolates resistant to another NNRTI and 28.5% of isolates resistant to all other tested NNRTIs. The presence of NRTI RAMs, including thymidine analog mutations, was associated with doravirine hypersusceptibility in some isolates, particularly in the absence of NNRTI RAMs. These results support the favorable resistance profile of doravirine and are of particular importance given the challenge posed by both acquired and transmitted resistance.
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