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Tao K, Osman ZA, Tzou PL, Rhee SY, Ahluwalia V, Shafer RW. GPT-4 performance on querying scientific publications: reproducibility, accuracy, and impact of an instruction sheet. BMC Med Res Methodol 2024; 24:139. [PMID: 38918736 PMCID: PMC11197181 DOI: 10.1186/s12874-024-02253-y] [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: 01/09/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024] Open
Abstract
BACKGROUND Large language models (LLMs) that can efficiently screen and identify studies meeting specific criteria would streamline literature reviews. Additionally, those capable of extracting data from publications would enhance knowledge discovery by reducing the burden on human reviewers. METHODS We created an automated pipeline utilizing OpenAI GPT-4 32 K API version "2023-05-15" to evaluate the accuracy of the LLM GPT-4 responses to queries about published papers on HIV drug resistance (HIVDR) with and without an instruction sheet. The instruction sheet contained specialized knowledge designed to assist a person trying to answer questions about an HIVDR paper. We designed 60 questions pertaining to HIVDR and created markdown versions of 60 published HIVDR papers in PubMed. We presented the 60 papers to GPT-4 in four configurations: (1) all 60 questions simultaneously; (2) all 60 questions simultaneously with the instruction sheet; (3) each of the 60 questions individually; and (4) each of the 60 questions individually with the instruction sheet. RESULTS GPT-4 achieved a mean accuracy of 86.9% - 24.0% higher than when the answers to papers were permuted. The overall recall and precision were 72.5% and 87.4%, respectively. The standard deviation of three replicates for the 60 questions ranged from 0 to 5.3% with a median of 1.2%. The instruction sheet did not significantly increase GPT-4's accuracy, recall, or precision. GPT-4 was more likely to provide false positive answers when the 60 questions were submitted individually compared to when they were submitted together. CONCLUSIONS GPT-4 reproducibly answered 3600 questions about 60 papers on HIVDR with moderately high accuracy, recall, and precision. The instruction sheet's failure to improve these metrics suggests that more sophisticated approaches are necessary. Either enhanced prompt engineering or finetuning an open-source model could further improve an LLM's ability to answer questions about highly specialized HIVDR papers.
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Affiliation(s)
- Kaiming Tao
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Zachary A Osman
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Philip L Tzou
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Soo-Yon Rhee
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | | | - Robert W Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA.
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Chen H, Hao J, Hu J, Song C, Zhou Y, Li M, Chen J, Liu X, Wang D, Xu X, Xin P, Zhang J, Liao L, Feng Y, Li D, Pan SW, Shao Y, Ruan Y, Xing H. Pretreatment HIV Drug Resistance and the Molecular Transmission Network Among HIV-Positive Individuals in China in 2022: Multicenter Observational Study. JMIR Public Health Surveill 2023; 9:e50894. [PMID: 37976080 PMCID: PMC10692882 DOI: 10.2196/50894] [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: 07/17/2023] [Revised: 09/10/2023] [Accepted: 10/06/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Emerging HIV drug resistance caused by increased usage of antiretroviral drugs (ARV) could jeopardize the success of standardized HIV management protocols in resource-limited settings. OBJECTIVE We aimed to characterize pretreatment HIV drug resistance (PDR) among HIV-positive individuals and risk factors in China in 2022. METHODS This cross-sectional study was conducted using 2-stage systematic sampling according to the World Health Organization's surveillance guidelines in 8 provincial-level administrative divisions in 2022. Demographic information and plasma samples were obtained from study participants. PDR was analyzed using the Stanford HIV drug resistance database, and the Tamura-Nei 93 model in HIV-TRACE was used to calculate pairwise matches with a genetic distance of 0.01 substitutions per site. Logistic regression was used to identify and estimate factors associated with PDR. RESULTS PDR testing was conducted on 2568 participants in 2022. Of the participants, 34.8% (n=893) were aged 30-49 years, 81.4% (n=2091) were male, and 3.2% (n=81) had prior ARV exposure. The prevalence of PDR to protease and reverse transcriptase regions, nonnucleoside reverse transcriptase inhibitors, nucleoside reverse transcriptase inhibitors, and protease inhibitors were 7.4% (n=190), 6.3% (n=163), 1.2% (n=32), and 0.2% (n=5), respectively. Yunnan, Jilin, and Zhejiang had much higher PDR incidence than did Sichuan. The prevalence of nonnucleoside reverse transcriptase inhibitor-related drug resistance was 6.1% (n=157) for efavirenz and 6.3% (n=163) for nevirapine. Multivariable logistic regression models indicated that participants who had prior ARV exposure (odds ratio [OR] 7.45, 95% CI 4.50-12.34) and the CRF55_01B HIV subtype (OR 2.61, 95% CI 1.41-4.83) were significantly associated with PDR. Among 618 (24.2%) sequences (nodes) associated with 253 molecular transmission clusters (size range 2-13), drug resistance mutation sites included K103, E138, V179, P225, V106, V108, L210, T215, P225, K238, and A98. CONCLUSIONS The overall prevalence of PDR in China in 2022 was modest. Targeted genotypic PDR testing and medication compliance interventions must be urgently expanded to address PDR among newly diagnosed people living with HIV in China.
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Affiliation(s)
- Hongli Chen
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
- Sichuan Nursing Vocational College, Chengdu, China
| | - Jingjing Hao
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Jing Hu
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Chang Song
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Yesheng Zhou
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Miaomiao Li
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Jin Chen
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Xiu Liu
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Dong Wang
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Xiaoshan Xu
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Peixian Xin
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Jiaxin Zhang
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Lingjie Liao
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Yi Feng
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Dan Li
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Stephen W Pan
- Department of Public Health, The University of Texas at San Antonio, San Antonio, TX, United States
| | - Yiming Shao
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Yuhua Ruan
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Hui Xing
- National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
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Kassaye SG, Grossman Z, Vengurlekar P, Chai W, Wallace M, Rhee SY, Meyer WA, Kaufman HW, Castel A, Jordan J, Crandall KA, Kang A, Kumar P, Katzenstein DA, Shafer RW, Maldarelli F. Insights into HIV-1 Transmission Dynamics Using Routinely Collected Data in the Mid-Atlantic United States. Viruses 2022; 15:68. [PMID: 36680108 PMCID: PMC9863702 DOI: 10.3390/v15010068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Background: Molecular epidemiological approaches provide opportunities to characterize HIV transmission dynamics. We analyzed HIV sequences and virus load (VL) results obtained during routine clinical care, and individual’s zip-code location to determine utility of this approach. Methods: HIV-1 pol sequences aligned using ClustalW were subtyped using REGA. A maximum likelihood (ML) tree was generated using IQTree. Transmission clusters with ≤3% genetic distance (GD) and ≥90% bootstrap support were identified using ClusterPicker. We conducted Bayesian analysis using BEAST to confirm transmission clusters. The proportion of nucleotides with ambiguity ≤0.5% was considered indicative of early infection. Descriptive statistics were applied to characterize clusters and group comparisons were performed using chi-square or t-test. Results: Among 2775 adults with data from 2014−2015, 2589 (93%) had subtype B HIV-1, mean age was 44 years (SD 12.7), 66.4% were male, and 25% had nucleotide ambiguity ≤0.5. There were 456 individuals in 193 clusters: 149 dyads, 32 triads, and 12 groups with ≥ four individuals per cluster. More commonly in clusters were males than females, 349 (76.5%) vs. 107 (23.5%), p < 0.0001; younger individuals, 35.3 years (SD 12.1) vs. 44.7 (SD 12.3), p < 0.0001; and those with early HIV-1 infection by nucleotide ambiguity, 202/456 (44.3%) vs. 442/2133 (20.7%), p < 0.0001. Members of 43/193 (22.3%) of clusters included individuals in different jurisdictions. Clusters ≥ four individuals were similarly found using BEAST. HIV-1 viral load (VL) ≥3.0 log10 c/mL was most common among individuals in clusters ≥ four, 18/21, (85.7%) compared to 137/208 (65.8%) in clusters sized 2−3, and 927/1169 (79.3%) who were not in a cluster (p < 0.0001). Discussion: HIV sequence data obtained for HIV clinical management provide insights into regional transmission dynamics. Our findings demonstrate the additional utility of HIV-1 VL data in combination with phylogenetic inferences as an enhanced contact tracing tool to direct HIV treatment and prevention services. Trans-jurisdictional approaches are needed to optimize efforts to end the HIV epidemic.
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Affiliation(s)
- Seble G. Kassaye
- Department of Medicine, Georgetown University, Washington, DC 20057, USA
| | - Zehava Grossman
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA
- School of Public Health, Tel Aviv University, Tel Aviv 69978, Israel
| | | | - William Chai
- Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
| | - Megan Wallace
- Department of Medicine, Georgetown University, Washington, DC 20057, USA
| | - Soo-Yon Rhee
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | | | | | - Amanda Castel
- Department of Epidemiology, George Washington University, Washington, DC 20052, USA
| | - Jeanne Jordan
- Department of Epidemiology, George Washington University, Washington, DC 20052, USA
| | - Keith A. Crandall
- Computational Biology Institute, George Washington University, Ashburn, VA 20147, USA
| | - Alisa Kang
- Department of Medicine, Georgetown University, Washington, DC 20057, USA
| | - Princy Kumar
- Department of Medicine, Georgetown University, Washington, DC 20057, USA
| | | | - Robert W. Shafer
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA
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4
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Chen H, Hu J, Song C, Li M, Zhou Y, Dong A, Kang R, Hao J, Zhang J, Liu X, Li D, Feng Y, Liao L, Ruan Y, Xing H, Shao Y. Molecular transmission network of pretreatment drug resistance among human immunodeficiency virus-positive individuals and the impact of virological failure on those who received antiretroviral therapy in China. Front Med (Lausanne) 2022; 9:965836. [PMID: 36106325 PMCID: PMC9464856 DOI: 10.3389/fmed.2022.965836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/10/2022] [Indexed: 11/14/2022] Open
Abstract
Objectives We investigated the prevalence of pretreatment drug resistance (PDR), the molecular transmission network among HIV-positive individuals, and the impact of virological failure on those who received antiretroviral therapy (ART) in China. Methods Based on the World Health Organization (WHO) surveillance guidelines for PDR, a baseline survey and follow-up were conducted in 2018 and 2021, respectively. Demographic information and plasma samples were obtained from all participants. HIV pol gene region sequences were used to analyze the PDR and molecular transmission networks using the Stanford HIV database algorithm and HIV-TRACE, respectively. This study assessed the odds ratios (OR) of PDR to virological failure (viral load ≥ 50 copies/mL) after 3 years of ART using multivariable logistic regression. Results Of the 4,084 individuals, 370 (9.1%) had PDR. The prevalence of PDR to non-nucleoside reverse transcriptase inhibitors (5.2%) was notably higher than that to nucleoside reverse transcriptase inhibitors (0.7%, p < 0.001), protease inhibitors (3.0%, p < 0.001), and multidrug resistance (0.3%, p < 0.001). A total of 1,339 (32.8%) individuals from 361 clusters were enrolled in the molecular transmission network. Of the 361 clusters, 22 included two or more individuals with PDR. The prevalence of virological failure among HIV-positive individuals after 3 years of ART without PDR, those with PDR to Chinese listed drugs, and those with PDR to other drugs was 7.9, 14.3, and 12.6%, respectively. Compared with that in HIV-positive individuals without PDR, virological failure after 3 years of ART was significantly higher (OR: 2.02, 95% confidence interval (CI): 1.25–3.27) and not significantly different (OR: 1.72, 95% CI: 0.87–3.43) in individuals with PDR to Chinese listed drugs and those with PDR to other drugs, respectively. Missed doses in the past month were significantly associated with virological failure (OR, 2.82; 95% CI: 4.08–5.89). Conclusion The overall prevalence of PDR was close to a high level and had an impact on virological failure after 3 years of ART. Moreover, HIV drug-resistant strains were transmitted in the molecular transmission network. These results illustrate the importance of monitoring PDR and ensuring virological suppression through drug adherence.
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Werbel WA, Brown DM, Kusemiju OT, Doby BL, Seaman SM, Redd AD, Eby Y, Fernandez RE, Desai NM, Miller J, Bismut GA, Kirby CS, Schmidt HA, Clarke WA, Seisa M, Petropoulos CJ, Quinn TC, Florman SS, Huprikar S, Rana MM, Friedman-Moraco RJ, Mehta AK, Stock PG, Price JC, Stosor V, Mehta SG, Gilbert AJ, Elias N, Morris MI, Mehta SA, Small CB, Haidar G, Malinis M, Husson JS, Pereira MR, Gupta G, Hand J, Kirchner VA, Agarwal A, Aslam S, Blumberg EA, Wolfe CR, Myer K, Wood RP, Neidlinger N, Strell S, Shuck M, Wilkins H, Wadsworth M, Motter JD, Odim J, Segev DL, Durand CM, Tobian AAR. National Landscape of Human Immunodeficiency Virus-Positive Deceased Organ Donors in the United States. Clin Infect Dis 2022; 74:2010-2019. [PMID: 34453519 PMCID: PMC9187316 DOI: 10.1093/cid/ciab743] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Organ transplantation from donors with human immunodeficiency virus (HIV) to recipients with HIV (HIV D+/R+) presents risks of donor-derived infections. Understanding clinical, immunologic, and virologic characteristics of HIV-positive donors is critical for safety. METHODS We performed a prospective study of donors with HIV-positive and HIV false-positive (FP) test results within the HIV Organ Policy Equity (HOPE) Act in Action studies of HIV D+/R+ transplantation (ClinicalTrials.gov NCT02602262, NCT03500315, and NCT03734393). We compared clinical characteristics in HIV-positive versus FP donors. We measured CD4 T cells, HIV viral load (VL), drug resistance mutations (DRMs), coreceptor tropism, and serum antiretroviral therapy (ART) detection, using mass spectrometry in HIV-positive donors. RESULTS Between March 2016 and March 2020, 92 donors (58 HIV positive, 34 FP), representing 98.9% of all US HOPE donors during this period, donated 177 organs (131 kidneys and 46 livers). Each year the number of donors increased. The prevalence of hepatitis B (16% vs 0%), syphilis (16% vs 0%), and cytomegalovirus (CMV; 91% vs 58%) was higher in HIV-positive versus FP donors; the prevalences of hepatitis C viremia were similar (2% vs 6%). Most HIV-positive donors (71%) had a known HIV diagnosis, of whom 90% were prescribed ART and 68% had a VL <400 copies/mL. The median CD4 T-cell count (interquartile range) was 194/µL (77-331/µL), and the median CD4 T-cell percentage was 27.0% (16.8%-36.1%). Major HIV DRMs were detected in 42%, including nonnucleoside reverse-transcriptase inhibitors (33%), integrase strand transfer inhibitors (4%), and multiclass (13%). Serum ART was detected in 46% and matched ART by history. CONCLUSION The use of HIV-positive donor organs is increasing. HIV DRMs are common, yet resistance that would compromise integrase strand transfer inhibitor-based regimens is rare, which is reassuring regarding safety.
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Affiliation(s)
- William A Werbel
- Correspondence: W. A. Werbel, Department of Medicine, Johns Hopkins School of Medicine, 725 N Wolfe St, PCTB/Second Floor, Baltimore, MD 21205 ()
| | - Diane M Brown
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Oyinkansola T Kusemiju
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Brianna L Doby
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Shanti M Seaman
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Andrew D Redd
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Yolanda Eby
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Reinaldo E Fernandez
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Niraj M Desai
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jernelle Miller
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Gilad A Bismut
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Charles S Kirby
- Department of Biochemistry, Cellular, and Molecular Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Haley A Schmidt
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - William A Clarke
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael Seisa
- Laboratory Corporation of America (LabCorp), South San Francisco, California, USA
| | | | - Thomas C Quinn
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Sander S Florman
- Recanati/Miller Transplantation Institute, The Mount Sinai Hospital, New York City, New York, USA
| | - Shirish Huprikar
- Department of Medicine, Division of Infectious Diseases, The Mount Sinai Hospital, New York City, New York, USA
| | - Meenakshi M Rana
- Department of Medicine, Division of Infectious Diseases, The Mount Sinai Hospital, New York City, New York, USA
| | - Rachel J Friedman-Moraco
- Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, Georgia, USA
| | - Aneesh K Mehta
- Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, Georgia, USA
| | - Peter G Stock
- Department of Surgery, University of California San Francisco, San Francisco, California, USA
| | - Jennifer C Price
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Valentina Stosor
- Division of Infectious Disease and Organ Transplantation, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Shikha G Mehta
- Section of Transplant Nephrology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Alexander J Gilbert
- MedStar Georgetown Transplant Institute, Georgetown University School of Medicine, Washington, DC, USA
| | - Nahel Elias
- Department of Surgery, Division of Transplant Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Michele I Morris
- Department of Medicine, Division of Infectious Diseases, University of Miami, Miami, Florida, USA
| | - Sapna A Mehta
- New York University Langone Transplant Institute, New York University Grossman School of Medicine, New York, New York, USA
| | - Catherine B Small
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medical College, New York, New York, USA
| | - Ghady Haidar
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Maricar Malinis
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jennifer S Husson
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Marcus R Pereira
- Department of Medicine, Division of Infectious Diseases, Columbia University Medical Center, New York, New York, USA
| | - Gaurav Gupta
- Department of Medicine, Division of Nephrology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Jonathan Hand
- Department of Infectious Diseases, Ochsner Clinic Foundation, New Orleans, Louisiana, USA
| | - Varvara A Kirchner
- Department of Surgery, University of Minnesota, Minneapolis, Minnesota, USA
| | - Avinash Agarwal
- Department of Surgery, Division of Transplantation, University of Virginia, Charlottesville, Virginia, USA
| | - Saima Aslam
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, California, USA
| | - Emily A Blumberg
- Department of Medicine, Division of Infectious Diseases, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Cameron R Wolfe
- Department of Medicine, Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
| | | | - R Patrick Wood
- Department of Surgery, Division of Transplantation, University of Wisconsin, Madison, Wisconsin, USA
| | - Nikole Neidlinger
- Department of Surgery, Division of Transplantation, University of Wisconsin, Madison, Wisconsin, USA
- UW Health Organ Procurement Organization, Madison, Wisconsin, USA
| | - Sara Strell
- UW Health Organ Procurement Organization, Madison, Wisconsin, USA
| | | | | | | | - Jennifer D Motter
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jonah Odim
- Division of Allergy, Immunology and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Dorry L Segev
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - HOPE in Action Investigators
PiquantDominqueLinkKatherineRNHemmersbach-MillerMarionMD, PhDPearsonThomasMDTurgeonNicoleMDLyonG MarshallMD, MMScKitchensWilliamMD PhDHuckabyJerylMSCRA, CCRCLasseterA FrancieRNElbeinRivkaRN, BSNRobersonAprilRNFerryElizabethRNKlockEthanBSCochranWilla VCRNPMorrisonMichelleBSNRasmussenSarahBABollingerJuliMSSugarmanJeremyMDSmithAngela RMBAThomasMargaretBSCoakleyMargaretRNTimponeJosephMDStuckeAlyssaBSHaydelBrandyDieterRebeccaPharmDKleinElizabeth JBANeumannHenryMDGallonLorenzoMDGoudyLeahRNCallegariMichelleMarrazzoIliseRN, BSN, MPHJacksonTowandaPruettTimothyMDFarnsworthMaryCCRCLockeJayme EMD, MPH, FACS, FASTMompoint-WilliamsDarnellCRNP, DNPBasingerKatherineRN, CCRPMekeelKristinMDNguyenPhirumBSKwanJoanneSrisengfaTabChin-HongPeterMDRogersRodneySimkinsJacquesMDMunozCarlosCRCDunnTyMDSawinskiDierdreMDSilveiraFernandaMDHughesKaileyMPHPakstisDiana LynnRN, BSN, MBANagyJamieBABaldecchiMaryMuthukumarThangamaniMDEddieMelissa DMS, RNRobbKatharineRNSalsgiverElizabethMPHWittingBrittaBSAzarMarwan MVillanuevaMerceditasFormicaRichardTomlinRicardaBS, CCRP
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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6
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Liu M, He XQ, Deng RN, Tang SQ, Harypursat V, Lu YQ, He K, Huo Q, Yang HH, Liu Q, Chen YK. Pretreatment drug resistance in people living with HIV: A large retrospective cohort study in Chongqing, China. HIV Med 2022; 23 Suppl 1:95-105. [PMID: 35293098 PMCID: PMC9311700 DOI: 10.1111/hiv.13253] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2022] [Indexed: 12/24/2022]
Abstract
Objectives The emergence of pretreatment drug resistance (PDR) caused by increased usage of antiretroviral therapy (ART) represents a significant challenge to HIV management. In this study, we evaluated the prevalence of PDR in people living with HIV (PLWH) in Chongqing, China. Methods We retrospectively collected the data of 1110 ART‐naïve PLWH in Chongqing from January 1, 2018 to June 30, 2021. HIV‐1 genotypes and drug resistance were analyzed using the HIV‐1 pol sequence. Risk factors associated with PDR were evaluated via the logistic regression model. Results Nine genotypes were detected among 1110 participants, with CRF07_BC (55.68%) being the dominant genotype, followed by CRF01_AE (21.44%), CRF08_BC (14.14%), and other genotypes (8.74%). Of all the participants, 24.14% exhibited drug resistance mutations (DRMs). The predominant DRMs for non‐nucleoside reverse transcriptase inhibitors (NNRTIs) and nucleoside reverse transcriptase inhibitors (NRTIs) were V179D/E/A/DIN (13.60%) and M184V/I (1.44%), respectively, whereas only two major DRMs (M46L and I54L) were identified for protease inhibitors (PIs). The total prevalence of PDR was 10.54%, with 2.43%, 7.66%, and 1.71% participants exhibiting PDR to NRTIs, NNRTIs, and PIs, respectively. Furthermore, female PLWH, delays in ART initiation, and the CRF08_BC genotype were associated with a higher risk of PDR. Conclusions Our study provides the first large cohort data on the prevalence of PDR in Chongqing, China. HIV‐1 genotypes are diverse and complex, with a moderate level of PDR, which does not reach the threshold for the initiation of a public health response. Nevertheless, continuous surveillance of PDR is both useful and advisable.
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Affiliation(s)
- Min Liu
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Xiao-Qing He
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Ren-Ni Deng
- Department of Clinical Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Sheng-Quan Tang
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Vijay Harypursat
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Yan-Qiu Lu
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Kun He
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Qin Huo
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Hong-Hong Yang
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Qian Liu
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Yao-Kai Chen
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China.,Department of Clinical Laboratory, Chongqing Public Health Medical Center, Chongqing, China
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7
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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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8
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Li R, Song C, Chen D, Li C, Hao Y, Zeng H, Han J, Zhao H. Prevalence of Transmitted Drug Resistance among ART-Naïve HIV-Infected Individuals, Beijing, 2015-2018. J Glob Antimicrob Resist 2022; 28:241-248. [DOI: 10.1016/j.jgar.2022.01.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 12/02/2021] [Accepted: 01/20/2022] [Indexed: 11/16/2022] Open
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9
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Serumula W, Fernandez G, Gonzalez VM, Parboosing R. Anti-HIV Aptamers: Challenges and Prospects. Curr HIV Res 2022; 20:7-19. [PMID: 34503417 DOI: 10.2174/1570162x19666210908114825] [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: 02/19/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 02/08/2023]
Abstract
Human Immunodeficiency Virus (HIV) infection continues to be a significant health burden in many countries around the world. Current HIV treatment through a combination of different antiretroviral drugs (cART) effectively suppresses viral replication, but drug resistance and crossresistance are significant challenges. This has prompted the search for novel targets and agents, such as nucleic acid aptamers. Nucleic acid aptamers are oligonucleotides that attach to the target sites with high affinity and specificity. This review provides a target-by-target account of research into anti-HIV aptamers and summarises the challenges and prospects of this therapeutic strategy, specifically in the unique context of HIV infection.
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Affiliation(s)
- William Serumula
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, c/o Inkosi Albert Luthuli Central Hospital, 5th Floor Laboratory Building, 800 Bellair Road, Mayville, Durban 4091, South Africa
| | - Geronimo Fernandez
- Departamento de Bioquímica-Investigación, Aptus Biotech SL, Avda. Cardenal Herrera Oria, 298-28035 Madrid. Spain
| | - Victor M Gonzalez
- Departamento de Bioquímica-Investigación, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS)-Hospital Ramón y Cajal, 28034 Madrid, Spain
| | - Raveen Parboosing
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, c/o Inkosi Albert Luthuli Central Hospital, 5th Floor Laboratory Building, 800 Bellair Road, Mayville, Durban 4091, South Africa
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10
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Scheibe K, Urbańska A, Jakubowski P, Hlebowicz M, Bociąga-Jasik M, Raczyńska A, Szymczak A, Szetela B, Łojewski W, Parczewski M. Low prevalence of doravirine-associated resistance mutations among polish human immunodeficiency-1 (HIV-1)–infected patients. Antivir Ther 2021; 26:69-78. [DOI: 10.1177/13596535211043044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Introduction Doravirine (DOR) is a novel non-nucleoside reverse transcriptase inhibitor (NNRTI) that retains activity against common NNRTI resistance mutations. In this study, we aimed to investigate the prevalence of DOR resistance mutations compared with that of resistance mutations for other NNRTIs among HIV-1-infected treatment‐experienced and -naïve patients from Poland. Methods Resistance to DOR and other NNRTIs was assessed in two datasets: 1760 antiretroviral treatment-naïve HIV-1 patients and 200 treatment‐experienced patients. All 1960 sequences were derived from the patients using bulk sequencing. For resistance analyses, Stanford HIV drug resistance database scores were used. Results Overall, DOR resistance was present in 32 patients (1.62%), of whom 13 (0.74%) were naïve and 19 (9.50%) were treatment-experienced. The most common DOR resistance mutations observed among the naïve patients were A98G and K101E (0.2% each), and those among cART-experienced patients were L100I (2.0%), K101E, V108I, H221Y, and P225H (1.5% each). Furthermore, among the naïve patients, less common resistance to DOR (0.7%) compared with that to nevirapine (NVP) (2.1%; p = 0.0013) and rilpivirine (5.40%; p < 0.0001) was observed. For sequences obtained from treatment-experienced patients, the frequency of resistance to DOR (9.5%) was lower than that for efavirenz (25.5%; p < 0.0001) and NVP (26.0%; p < 0.0001). Conclusions The frequency of transmitted drug resistance to DOR is low, allowing for effective treatment of antiretroviral treatment-naïve patients and rapid treatment initiation. In cART-experienced patients, this agent remains an attractive NNRTI option with a higher genetic barrier to resistance.
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Affiliation(s)
- Kaja Scheibe
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Anna Urbańska
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | | | - Maria Hlebowicz
- Department of Infectious Diseases, Medical University of Gdansk, Gdańsk, Poland
| | - Monika Bociąga-Jasik
- Department of Infectious and Tropical Diseases, Jagiellonian University Medical College, Kraków, Poland
| | - Aleksandra Raczyńska
- Department of Infectious and Tropical Diseases, Jagiellonian University Medical College, Kraków, Poland
| | - Aleksandra Szymczak
- Department of Infectious Diseases, Liver Diseases and Acquired Immune Deficiencies, Wroclaw Medical University, Wrocław, Poland
| | - Bartosz Szetela
- Department of Infectious Diseases, Liver Diseases and Acquired Immune Deficiencies, Wroclaw Medical University, Wrocław, Poland
| | - Władysław Łojewski
- Department of Infectious Diseases, Regional Hospital in Zielona Gora, Zielona Góra, Poland
| | - Miłosz Parczewski
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
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11
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Rich SN, Poschman K, Hu H, Mavian C, Cook RL, Salemi M, Spencer EC, Prosperi M. Sociodemographic, Ecological, and Spatiotemporal Factors Associated with Human Immunodeficiency Virus Drug Resistance in Florida: A Retrospective Analysis. J Infect Dis 2020; 223:866-875. [PMID: 32644119 DOI: 10.1093/infdis/jiaa413] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/06/2020] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Persons living with human immunodeficiency virus (HIV) with resistance to antiretroviral therapy are vulnerable to adverse HIV-related health outcomes and can contribute to transmission of HIV drug resistance (HIVDR) when nonvirally suppressed. The degree to which HIVDR contributes to disease burden in Florida-the US state with the highest HIV incidence- is unknown. METHODS We explored sociodemographic, ecological, and spatiotemporal associations of HIVDR. HIV-1 sequences (n = 34 447) collected during 2012-2017 were obtained from the Florida Department of Health. HIVDR was categorized by resistance class, including resistance to nucleoside reverse-transcriptase , nonnucleoside reverse-transcriptase , protease , and integrase inhibitors. Multidrug resistance and transmitted drug resistance were also evaluated. Multivariable fixed-effects logistic regression models were fitted to associate individual- and county-level sociodemographic and ecological health indicators with HIVDR. RESULTS The HIVDR prevalence was 19.2% (nucleoside reverse-transcriptase inhibitor resistance), 29.7% (nonnucleoside reverse-transcriptase inhibitor resistance), 6.6% (protease inhibitor resistance), 23.5% (transmitted drug resistance), 13.2% (multidrug resistance), and 8.2% (integrase strand transfer inhibitor resistance), with significant variation by Florida county. Individuals who were older, black, or acquired HIV through mother-to-child transmission had significantly higher odds of HIVDR. HIVDR was linked to counties with lower socioeconomic status, higher rates of unemployment, and poor mental health. CONCLUSIONS Our findings indicate that HIVDR prevalence is higher in Florida than aggregate North American estimates with significant geographic and socioecological heterogeneity.
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Affiliation(s)
- Shannan N Rich
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, Florida, USA.,Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Karalee Poschman
- Florida Department of Health, Division of Disease Control and Health Protection, Bureau of Communicable Diseases, HIV/AIDS Section, Tallahassee, Florida, USA.,Centers for Disease Control and Prevention, Division of HIV/AIDS Prevention, HIV Incidence and Case Surveillance Branch, Atlanta, Georgia, USA
| | - Hui Hu
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Carla Mavian
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA.,Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Robert L Cook
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, Florida, USA.,Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Marco Salemi
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA.,Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Emma C Spencer
- Florida Department of Health, Division of Disease Control and Health Protection, Bureau of Communicable Diseases, HIV/AIDS Section, Tallahassee, Florida, USA
| | - Mattia Prosperi
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, Florida, USA
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12
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Gibson KM, Jair K, Castel AD, Bendall ML, Wilbourn B, Jordan JA, Crandall KA, Pérez-Losada M. A cross-sectional study to characterize local HIV-1 dynamics in Washington, DC using next-generation sequencing. Sci Rep 2020; 10:1989. [PMID: 32029767 PMCID: PMC7004982 DOI: 10.1038/s41598-020-58410-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 12/31/2019] [Indexed: 11/08/2022] Open
Abstract
Washington, DC continues to experience a generalized HIV-1 epidemic. We characterized the local phylodynamics of HIV-1 in DC using next-generation sequencing (NGS) data. Viral samples from 68 participants from 2016 through 2017 were sequenced and paired with epidemiological data. Phylogenetic and network inferences, drug resistant mutations (DRMs), subtypes and HIV-1 diversity estimations were completed. Haplotypes were reconstructed to infer transmission clusters. Phylodynamic inferences based on the HIV-1 polymerase (pol) and envelope genes (env) were compared. Higher HIV-1 diversity (n.s.) was seen in men who have sex with men, heterosexual, and male participants in DC. 54.0% of the participants contained at least one DRM. The 40-49 year-olds showed the highest prevalence of DRMs (22.9%). Phylogenetic analysis of pol and env sequences grouped 31.9-33.8% of the participants into clusters. HIV-TRACE grouped 2.9-12.8% of participants when using consensus sequences and 9.0-64.2% when using haplotypes. NGS allowed us to characterize the local phylodynamics of HIV-1 in DC more broadly and accurately, given a better representation of its diversity and dynamics. Reconstructed haplotypes provided novel and deeper phylodynamic insights, which led to networks linking a higher number of participants. Our understanding of the HIV-1 epidemic was expanded with the powerful coupling of HIV-1 NGS data with epidemiological data.
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Grants
- P30 AI117970 NIAID NIH HHS
- U01 AI069503 NIAID NIH HHS
- UM1 AI069503 NIAID NIH HHS
- This study was supported by the DC Cohort Study (U01 AI69503-03S2), a supplement from the Women’s Interagency Study for HIV-1 (410722_GR410708), a DC D-CFAR pilot award, and a 2015 HIV-1 Phylodynamics Supplement award from the District of Columbia for AIDS Research, an NIH funded program (AI117970), which is supported by the following NIH Co-Funding and Participating Institutes and Centers: NIAID, NCI, NICHD, NHLBI, NIDA, NIMH, NIA, FIC, NIGMS, NIDDK and OAR. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.
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Affiliation(s)
- Keylie M Gibson
- Computational Biology Institute, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA.
| | - Kamwing Jair
- Department of Epidemiology, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Amanda D Castel
- Department of Epidemiology, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Matthew L Bendall
- Computational Biology Institute, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Brittany Wilbourn
- Department of Epidemiology, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Jeanne A Jordan
- Department of Epidemiology, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Keith A Crandall
- Computational Biology Institute, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
- Department of Biostatistics and Bioinformatics, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Marcos Pérez-Losada
- Computational Biology Institute, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
- Department of Biostatistics and Bioinformatics, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
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13
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Rhee SY, Clutter D, Fessel WJ, Klein D, Slome S, Pinsky BA, Marcus JL, Hurley L, Silverberg MJ, Kosakovsky Pond SL, Shafer RW. Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted Human Immunodeficiency Virus Type 1 Drug Resistance in a Large US Clinic Population. Clin Infect Dis 2020; 68:213-221. [PMID: 29846534 PMCID: PMC6321854 DOI: 10.1093/cid/ciy453] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 05/25/2018] [Indexed: 12/20/2022] Open
Abstract
Background There are few large studies of transmitted drug resistance (TDR) prevalence and the drug resistance mutations (DRMs) responsible for TDR in the United States. Methods Human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) and protease sequences were obtained from 4253 antiretroviral therapy (ART)–naive individuals in a California clinic population from 2003 to 2016. Phylogenetic analyses were performed to study linkages between TDR strains and selection pressure on TDR-associated DRMs. Results From 2003 to 2016, there was a significant increase in overall (odds ratio [OR], 1.05 per year [95% confidence interval {CI}, 1.03–1.08]; P < .001) and nonnucleoside RT inhibitor (NNRTI)–associated TDR (OR, 1.11 per year [95% CI, 1.08–1.15]; P < .001). Between 2012 and 2016, TDR rates to any drug class ranged from 15.7% to 19.2%, and class-specific rates ranged from 10.0% to 12.8% for NNRTIs, 4.1% to 8.1% for nucleoside RT inhibitors (NRTIs), and 3.6% to 5.2% for protease inhibitors. The thymidine analogue mutations, M184V/I and the tenofovir-associated DRMs K65R and K70E/Q/G/N/T accounted for 82.9%, 7.3%, and 1.4% of NRTI-associated TDR, respectively. Thirty-seven percent of TDR strains clustered with other TDR strains sharing the same DRMs. Conclusions Although TDR has increased significantly in this large cohort, many TDR strains are unlikely to influence the activity of currently preferred first-line ART regimens. The high proportion of DRMs associated with infrequently used regimens combined with the clustering of TDR strains suggest that some TDR strains are being transmitted between ART-naive individuals.
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Affiliation(s)
- Soo-Yon Rhee
- Division of Infectious Diseases, Department of Medicine, Stanford University
| | - Dana Clutter
- Division of Infectious Diseases, Department of Medicine, Stanford University
| | - W Jeffrey Fessel
- Department of Internal Medicine, Kaiser Permanente Northern California, San Francisco
| | - Daniel Klein
- Department of Infectious Diseases, Kaiser Permanente Northern California, San Leandro
| | - Sally Slome
- Department of Infectious Diseases, Kaiser Permanente Northern California, Oakland
| | | | - Julia L Marcus
- Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts
| | - Leo Hurley
- Division of Research, Kaiser Permanente Northern California, Oakland
| | | | | | - Robert W Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University
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14
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Kagan RM, Dunn KJ, Snell GP, Nettles RE, Kaufman HW. Trends in HIV-1 Drug Resistance Mutations from a U.S. Reference Laboratory from 2006 to 2017. AIDS Res Hum Retroviruses 2019; 35:698-709. [PMID: 31169022 DOI: 10.1089/aid.2019.0063] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Trends in resistance to antiretroviral drugs for HIV-1 may inform clinical support and drug development. We evaluated drug resistance mutation (DRM) trends for nucleoside reverse transcriptase inhibitor (NRTI), non-nucleoside reverse transcriptase inhibitor (NNRTI), protease inhibitor (PI), and integrase strand transfer inhibitor (INSTI) in a large U.S. reference laboratory database. DRMs with a Stanford HIV Drug Resistance Database mutation score ≥10 from deidentified subtype B NRTI/NNRTI/PI specimens (2006-2017; >10,000/year) and INSTI specimens (2010-2017; >1,000/year) were evaluated. Sequences with NRTI, NNRTI, or PI single- or multiclass DRMs declined from 48.9% to 39.3%. High-level dual- and triple-class resistance declined from 43.3% (2006) to 17.1% (2017), while sequences with only single-class DRMs increased from 40.0% to 52.9%. The prevalence of DRMs associated with earlier treatment regimens declined, while prevalence of some DRMs associated with newer regimens increased. M184V/I decreased from 48.3% to 29.4%. K103N/S/T declined from 42.5% in 2012 to 36.4% in 2017. Rilpivirine and etravirine DRMs E138A/Q/R and E138K increased from 4.9% and 0.4% to 9.7% and 1.7%, respectively. Sequences with ≥1 darunavir DRM declined from 18.1% to 4.8% by 2017. INSTI DRM Q148H/K/R declined from 39.3% (2010) to 13.8% (2017). Prevalence of elvitegravir-associated DRMs T66A/I/K, E92Q, S147G, and the dolutegravir-associated DRM R263K increased. For a subset of patients with serial testing, 50% (2,646/5,290) of those who initially had no reportable DRM subsequently developed ≥1 DRM for NRTI/NNRTI/PI and 49.7% (159/320) for INSTI. These trends may inform the need for baseline genotypic resistance testing. The detection of treatment-emergent DRMs in serially tested patients confirms the value of genotypic testing following virologic failure.
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Affiliation(s)
- Ron M. Kagan
- Quest Diagnostics Infectious Disease, San Juan Capistrano, California
| | - Keith J. Dunn
- Janssen Scientific Affairs, LLC, Titusville, New Jersey
| | - Gregg P. Snell
- Quest Diagnostics Medical Informatics, Needham, Massachusetts
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15
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D'Costa J, Gooey M, Richards N, Sameer R, Lee E, Chibo D. Analysis of transmitted HIV drug resistance from 2005 to 2015 in Victoria, Australia: a comparison of the old and the new. Sex Health 2019. [PMID: 28641707 DOI: 10.1071/sh16190] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Background Baseline genotyping is part of standard-of-care treatment. It reveals that transmitted drug resistance (TDR) continues to be important for the management of HIV infection. Attention is typically focused on determining whether resistance to the protease inhibitors (PI) and reverse transcriptase inhibitors (RTI) occurs. However, the increasing use of integrase inhibitors (INIs) raises a concern that TDR to this class of antiretroviral drug may also occur. METHODS PI and RTI drug resistance genotyping was performed on blood samples collected between 2005 and 2015 from 772 treatment-naïve Victorian patients infected with HIV within the previous 12 months. Integrase genotyping was performed on 461 of the 485 patient samples collected between 2010 and 2015. RESULTS In the period 2005-10, 39 of 343 patients (11.4%) had at least one PI- or RTI-associated mutation, compared with 34 of 429 (7.9%) during the period 2011-15. Compared with 2005-10, during 2011-15 there was a significant decline in the prevalence of the non-nucleoside-associated mutation K103N and the nucleoside-associated mutations at codons M41 and T215. One patient was detected with a major INI resistance mutation, namely G118R. However, this mutation is rare and its effect on susceptibility is unclear. A small number of patients (n=12) was infected with HIV containing accessory resistance mutations in the integrase gene. CONCLUSIONS The lack of transmitted resistance to INIs is consistent with a low level of resistance to this class of drugs in the treated population. However, continued surveillance in the newly infected population is warranted as the use of INIs increases.
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Affiliation(s)
- Jodie D'Costa
- Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute, Locked Bag 815, Carlton South, Vic. 3053, Australia
| | - Megan Gooey
- Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute, Locked Bag 815, Carlton South, Vic. 3053, Australia
| | - Nicole Richards
- Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute, Locked Bag 815, Carlton South, Vic. 3053, Australia
| | - Rizmina Sameer
- Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute, Locked Bag 815, Carlton South, Vic. 3053, Australia
| | - Elaine Lee
- Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute, Locked Bag 815, Carlton South, Vic. 3053, Australia
| | - Doris Chibo
- Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute, Locked Bag 815, Carlton South, Vic. 3053, Australia
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16
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Gibson KM, Steiner MC, Kassaye S, Maldarelli F, Grossman Z, Pérez-Losada M, Crandall KA. A 28-Year History of HIV-1 Drug Resistance and Transmission in Washington, DC. Front Microbiol 2019; 10:369. [PMID: 30906285 PMCID: PMC6418020 DOI: 10.3389/fmicb.2019.00369] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 02/12/2019] [Indexed: 01/06/2023] Open
Abstract
Washington, DC consistently has one of the highest annual rates of new HIV-1 diagnoses in the United States over the last 10 years. To guide intervention and prevention strategies to combat DC HIV infection, it is helpful to understand HIV transmission dynamics in a historical context. Toward this aim, we conducted a retrospective study (years 1987-2015) of 3,349 HIV pol sequences (1,026 bp) from 1,996 individuals living in the DC area belonging to three different cohorts. We coupled HIV sequence data with clinical information (sex, risk factor, race/ethnicity, viral load, subtype, anti-retroviral regimen) to identify circulating drug resistant mutations (DRM) and transmission clusters and assess their persistence over time. Of the transmission clusters identified in the DC area, 78.0 and 31.7% involved MSM and heterosexuals, respectively. The longest spread of time for a single cluster was 5 years (2007-2012) using a distance-based network inference approach and 27 years (1987-2014) using a maximum likelihood phylogenetic approach. We found eight subtypes and nine recombinants. Genetic diversity increased steadily over time with a slight peak in 2009 and remained constant thereafter until 2015. Nucleotide diversity also increased over time while relative genetic diversity (BEAST) remained relatively steady over the last 28 years with slight increases since 2000 in subtypes B and C. Sequences from individuals on drug therapy contained the highest total number of DRMs (1,104-1,600) and unique DRMs (63-97) and the highest proportion (>20%) of resistant individuals. Heterosexuals (43.94%), MSM (40.13%), and unknown (44.26%) risk factors showed similar prevalence of DRMs, while injection drug users had a lower prevalence (33.33%). Finally, there was a 60% spike in the number of codons with DRMs between 2007 and 2010. Past patterns of HIV transmission and DRM accumulation over time described here will help to predict future efficacy of ART drugs based on DRMs persisting over time and identify risk groups of interest for prevention and intervention efforts within the DC population. Our results show how longitudinal data can help to understand the temporal dynamics of HIV-1 at the local level.
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Affiliation(s)
- Keylie M. Gibson
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, United States
| | - Margaret C. Steiner
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, United States
| | - Seble Kassaye
- Department of Medicine, Georgetown University, Washington, DC, United States
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, Host-Virus Interaction Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Zehava Grossman
- HIV Dynamics and Replication Program, Host-Virus Interaction Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
- Sackler Faculty of Medicine, School of Public Health, Tel Aviv University, Tel Aviv, Israel
| | - Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, United States
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
- Department of Epidemiology and Biostatistics, Milken Institute School of Public Health, George Washington University, Washington, DC, United States
| | - Keith A. Crandall
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, United States
- Department of Epidemiology and Biostatistics, Milken Institute School of Public Health, George Washington University, Washington, DC, United States
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17
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Capetti A, Rizzardini G. Choosing appropriate pharmacotherapy for drug-resistant HIV. Expert Opin Pharmacother 2019; 20:667-678. [DOI: 10.1080/14656566.2019.1570131] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Amedeo Capetti
- Divisione Malattie Infettive, Aziende Socio Sanitarie Territoriale Fatebenefratelli Sacco, Milano, Italy
| | - Giuliano Rizzardini
- Divisione Malattie Infettive, Aziende Socio Sanitarie Territoriale Fatebenefratelli Sacco, Milano, Italy
- Faculty of Health Sciences, School of Clinical Medicine, Whitwaterstrand University, Johannesburg, South Africa
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18
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Petersen A, Cowan SA, Nielsen J, Fischer TK, Fonager J. Characterisation of HIV-1 transmission clusters and drug-resistant mutations in Denmark, 2004 to 2016. Euro Surveill 2018; 23:1700633. [PMID: 30401010 PMCID: PMC6337072 DOI: 10.2807/1560-7917.es.2018.23.44.1700633] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
This study describes the prevalence of human immunodeficiency virus (HIV) drug resistance mutations among 1,815 patients in Denmark from 2004 to 2016 and characterises transmission clusters. POL sequences were analysed for subtype, drug resistance mutations and phylogenetic relationship. The prevalence of surveillance drug resistance mutations (SDRM) was 6.7%, while the prevalence of drug resistance mutations (DRM) with a clinical impact was 12.3%. We identified 197 transmission clusters with 706 patients. Patients 40 years or older were less likely to be members of a transmission cluster and patients in transmission clusters were less likely to be infected abroad. The proportion of late presenters (LP) was lower in active compared with inactive clusters. Large active clusters consisted of more men who have sex with men (MSM), had members more frequently infected in Denmark and contained a significantly lower proportion of LP and significantly fewer patients with DRM than small active clusters. Subtyping demonstrated that the Danish HIV epidemic is gradually becoming more composed of non-B subtypes/circulating recombinant forms. This study shows that active HIV-1 transmission has become increasingly MSM-dominated and that the recent increase in SDRM and DRM prevalence is not associated with more sustained transmission within identified transmission networks or clusters.
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Affiliation(s)
- Andreas Petersen
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark,European Public Health Microbiology (EUPHEM) training programme, European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Susan A Cowan
- Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Jens Nielsen
- Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Thea K Fischer
- Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
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19
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Prevalence of Transmitted HIV drug resistance in antiretroviral treatment naïve newly diagnosed individuals in China. Sci Rep 2018; 8:12273. [PMID: 30115986 PMCID: PMC6095875 DOI: 10.1038/s41598-018-29202-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 05/24/2018] [Indexed: 12/17/2022] Open
Abstract
To investigate the prevalence and temporal trend of transmitted drug resistance (TDR), a nationwide cross-sectional survey was conducted among 5627 ART naïve newly diagnosed HIV-infected individuals in 2015 in China. Totally 4704 partial pol sequences were obtained. Among them, the most common HIV-1 circulating recombinant form (CRF) or subtype was CRF01_AE (39.0%), followed by CRF07_BC (35.6%), CRF08_BC (8.9%), and subtype B (5.5%). TDR mutations were found in 3.6% of the cases, with 1.1% harboring TDR to protease inhibitors (PIs), 1.3% having TDR to nucleoside reverse transcriptase inhibitors (NRTIs), and 1.6% to non-nucleoside reverse transcriptase inhibitors (NNRTIs). No significant difference was found in the prevalence of TDR, as compared with the results of another nationwide survey performed among ART naïve HIV-infected people in between 2004 and 2005, except in the 16-25 year-old group. In addition, four drug-resistant transmission clusters were identified in phylogenetic trees, accounting for 6.2% (9/145) of the individuals with TDR. Although the rate of TDR remained relatively low in the past 10 years in China, surveillance is still needed to monitor the trend of TDR and to optimize the first-line regimens.
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20
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Ross LL, Shortino D, Shaefer MS. Changes from 2000 to 2009 in the Prevalence of HIV-1 Containing Drug Resistance-Associated Mutations from Antiretroviral Therapy-Naive, HIV-1-Infected Patients in the United States. AIDS Res Hum Retroviruses 2018; 34:672-679. [PMID: 29732898 PMCID: PMC6080107 DOI: 10.1089/aid.2017.0295] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Pre-existing HIV drug resistance can jeopardize first-line antiretroviral therapy (ART) success. Changes in the prevalence of drug resistance-associated mutations (DRMs) were analyzed from HIV-infected, ART-naive, U.S. individuals seeking ART treatment from 2000 to 2009. HIV DRM data from 3,829 ART-naive subjects were analyzed by year of sample collection using International Antiviral Society-United States (IAS-USA) and World Health Organization (WHO) “surveillance” DRM definitions; minor IAS-USA-defined DRMs were excluded. IAS-USA DRM prevalence between 2000 and 2009 was 14%, beginning with 8% in 2000 and 13% in 2009. The greatest incidence was observed in 2007 (17%). Overall, IAS-USA-defined non-nucleoside reverse transcriptase inhibitor (NNRTI) DRMs were 9.5%; nucleoside reverse transcriptase inhibitor (NRTI): 4%, and major protease inhibitor (PI): 3%. The most frequently detected IAS-USA-defined DRMs by class were NNRTI: K103N/S (4%), NRTI: M41L (1.5%), and PI: L90M (1%). Overall, WHO-defined DRM prevalence was 13% (5% in 2000; 13% in 2009). By class, NNRTI prevalence was 6%, NRTI: 6%, and PI: 3.2%. The most frequent WHO-defined DRMs were NRTI: codon T215 (3.0%), NNRTI: K103N/S (4%), and PI: L90 (1%). WHO-defined NNRTI DRMs declined significantly (p = .0412) from 2007 to 2009. The overall prevalence of HIV-1 containing major IAS-USA or WHO-defined DRMs to ≥2 or ≥3 classes was 2% and <1%, respectively. The prevalence of HIV-1 with WHO-defined dual- or triple-class resistance significantly declined (p = .0461) from 2008 (4%) to 2009 (<1%). In this U.S. cohort, the prevalence of HIV-1 DRMs increased from 2000 onward, peaked between 2005 and 2007, and then declined between 2008 and 2009; the detection of WHO-defined dual- or triple-class DRM similarly decreased from 2008 to 2009.
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Affiliation(s)
- Lisa L. Ross
- ViiV Healthcare, Research Triangle Park, North Carolina
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21
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Pinto AN, Hawke K, Castley A, Chibo D, Giallonardo FD, Cooper C, Sawleshwarkar S, Kelleher A, Dwyer DE. HIV-1 subtype diversity, transmitted drug resistance and phylogenetics in Australia. Future Virol 2018. [DOI: 10.2217/fvl-2018-0031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Australia has maintained a low prevalence of HIV, with a mainly concentrated epidemic and successful public health response. With the widespread availability of HIV genotyping for resistance testing, and development of phylogenetic methodologies, the field of molecular epidemiology has evolved a deeper understanding of diversity and transmission dynamics of HIV. Studies combining HIV genotype with epidemiological data have allowed insights to be gained into the changing subtype diversity, rates of transmitted drug resistance and transmission networks of HIV in Australia. This review provides an overview of HIV molecular epidemiology studies in Australia.
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Affiliation(s)
- Angie N Pinto
- The Kirby Institute, The University of New South Wales, UNSW Sydney, Australia
| | - Karen Hawke
- South Australian Health & Medical Research Institute, Adelaide, South Australia
| | - Allison Castley
- PathWest, Clinical Immunology, Department of Health, Murdoch, Western Australia, Australia
| | - Doris Chibo
- HIV Characterization Laboratory, Victorian Infectious Diseases Reference Laboratory, Doherty Institute, Melbourne, Victoria, Australia
| | | | - Craig Cooper
- Positive Life NSW, Sydney, New South Wales, Australia
| | - Shailendra Sawleshwarkar
- The University of Sydney, Faculty of Medicine & Health, Westmead Clinical School, Western Sydney Sexual Health Centre, Parramatta, New South Wales, Australia
| | - Anthony Kelleher
- The Kirby Institute, The University of New South Wales, UNSW Sydney, Australia
| | - Dominic E Dwyer
- NSWHP-ICPMR, Westmead Hospital, Westmead, NSW, Australia
- Westmead Clinical School, University of Sydney, Westmead, Australia
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22
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Levintow SN, Okeke NL, Hué S, Mkumba L, Virkud A, Napravnik S, Sebastian J, Miller WC, Eron JJ, Dennis AM. Prevalence and Transmission Dynamics of HIV-1 Transmitted Drug Resistance in a Southeastern Cohort. Open Forum Infect Dis 2018; 5:ofy178. [PMID: 30151407 PMCID: PMC6101542 DOI: 10.1093/ofid/ofy178] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/18/2018] [Indexed: 12/26/2022] Open
Abstract
Background Transmitted drug resistance (TDR) compromises clinical management and outcomes. Transmitted drug resistance surveillance and identification of growing transmission clusters are needed in the Southeast, the epicenter of the US HIV epidemic. Our study investigated prevalence and transmission dynamics in North Carolina. Methods We analyzed surveillance drug resistance mutations (SDRMs) using partial pol sequences from patients presenting to 2 large HIV outpatient clinics from 1997 to 2014. Transmitted drug resistance prevalence was defined as ≥1 SDRMs among antiretroviral therapy (ART)–naïve patients. Binomial regression was used to characterize prevalence by calendar year, drug class, and demographic and clinical factors. We assessed the transmission networks of patients with TDR with maximum likelihood trees and Bayesian methods including background pol sequences (n = 15 246). Results Among 1658 patients with pretherapy resistance testing, ≥1 SDRMs was identified in 199 patients, with an aggregate TDR prevalence of 12% (95% confidence interval, 10% to 14%) increasing over time (P = .02). Resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs; 8%) was common, followed by nucleoside reverse transcriptase inhibitors (4%) and protease inhibitors (2%). Factors associated with TDR were being a man reporting sex with men, white race, young age, higher CD4 cell count, and being a member of a transmission cluster. Transmitted drug resistance was identified in 106 clusters ranging from 2 to 26 members. Cluster resistance was primarily NNRTI and dominated by ART-naïve patients or those with unknown ART initiation. Conclusions Moderate TDR prevalence persists in North Carolina, predominantly driven by NNRTI resistance. Most TDR cases were identified in transmission clusters, signifying multiple local transmission networks and TDR circulation among ART-naïve persons. Transmitted drug resistance surveillance can detect transmission networks and identify patients for enhanced services to promote early treatment.
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Affiliation(s)
- Sara N Levintow
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
| | - Nwora Lance Okeke
- Division of Infectious Diseases, Duke University, Durham, North Carolina
| | - Stephane Hué
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Laura Mkumba
- Division of Infectious Diseases, Duke University, Durham, North Carolina
| | - Arti Virkud
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
| | - Sonia Napravnik
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina.,Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina
| | - Joseph Sebastian
- Campbell University School of Osteopathic Medicine, South Lillington, North Carolina
| | - William C Miller
- Division of Epidemiology, College of Public Health, The Ohio State University, Columbus, Ohio
| | - Joseph J Eron
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina.,Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina
| | - Ann M Dennis
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina
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23
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Fabeni L, Alteri C, Di Carlo D, Orchi N, Carioti L, Bertoli A, Gori C, Forbici F, Continenza F, Maffongelli G, Pinnetti C, Vergori A, Mondi A, Ammassari A, Borghi V, Giuliani M, De Carli G, Pittalis S, Grisetti S, Pennica A, Mastroianni CM, Montella F, Cristaudo A, Mussini C, Girardi E, Andreoni M, Antinori A, Ceccherini-Silberstein F, Perno CF, Santoro MM. Dynamics and phylogenetic relationships of HIV-1 transmitted drug resistance according to subtype in Italy over the years 2000-14. J Antimicrob Chemother 2018; 72:2837-2845. [PMID: 29091206 DOI: 10.1093/jac/dkx231] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 06/09/2017] [Indexed: 11/14/2022] Open
Abstract
Background Transmitted drug-resistance (TDR) remains a critical aspect for the management of HIV-1-infected individuals. Thus, studying the dynamics of TDR is crucial to optimize HIV care. Methods In total, 4323 HIV-1 protease/reverse-transcriptase sequences from drug-naive individuals diagnosed in north and central Italy between 2000 and 2014 were analysed. TDR was evaluated over time. Maximum-likelihood and Bayesian phylogenetic trees with bootstrap and Bayesian-probability supports defined transmission clusters. Results Most individuals were males (80.2%) and Italian (72.1%), with a median (IQR) age of 37 (30-45) years. MSM accounted for 42.2% of cases, followed by heterosexuals (36.4%). Non-B subtype infections accounted for 30.8% of the overall population and increased over time (<2005-14: 19.5%-38.5%, P < 0.0001), particularly among Italians (<2005-14: 6.5%-28.8%, P < 0.0001). TDR prevalence was 8.8% and increased over time in non-B subtypes (<2005-14: 2%-7.1%, P = 0.018). Overall, 467 transmission clusters (involving 1207 individuals; 27.9%) were identified. The prevalence of individuals grouping in transmission clusters increased over time in both B (<2005-14: 12.9%-33.5%, P = 0.001) and non-B subtypes (<2005-14: 18.4%-41.9%, P = 0.006). TDR transmission clusters were 13.3% within the overall cluster observed and dramatically increased in recent years (<2005-14: 14.3%-35.5%, P = 0.005). This recent increase was mainly due to non-B subtype-infected individuals, who were also more frequently involved in large transmission clusters than those infected with a B subtype [median number of individuals in transmission clusters: 7 (IQR 6-19) versus 4 (3-4), P = 0.047]. Conclusions The epidemiology of HIV transmission changed greatly over time; the increasing number of transmission clusters (sometimes with drug resistance) shows that detection and proper treatment of the multi-transmitters is a major target for controlling HIV spread.
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Affiliation(s)
- L Fabeni
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - C Alteri
- University of Rome Tor Vergata, Rome, Italy
| | - D Di Carlo
- University of Rome Tor Vergata, Rome, Italy
| | - N Orchi
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - L Carioti
- University of Rome Tor Vergata, Rome, Italy
| | - A Bertoli
- University of Rome Tor Vergata, Rome, Italy
| | - C Gori
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - F Forbici
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - F Continenza
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | | | - C Pinnetti
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - A Vergori
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - A Mondi
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - A Ammassari
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - V Borghi
- Modena University Hospital, Modena, Italy
| | - M Giuliani
- San Gallicano Dermatological Institute, IRCCS, Rome, Italy
| | - G De Carli
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - S Pittalis
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - S Grisetti
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | | | | | - F Montella
- S. Giovanni Addolorata Hospital, Rome, Italy
| | - A Cristaudo
- San Gallicano Dermatological Institute, IRCCS, Rome, Italy
| | - C Mussini
- Modena University Hospital, Modena, Italy
| | - E Girardi
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - M Andreoni
- University Hospital Tor Vergata, Rome, Italy
| | - A Antinori
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | | | - C F Perno
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
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24
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Socías ME, Nosova E, Kerr T, Hayashi K, Harrigan PR, Shoveller J, Montaner J, Milloy MJ. Patterns of Transmitted Drug Resistance and Virological Response to First-line Antiretroviral Treatment Among Human Immunodeficiency Virus-Infected People Who Use Illicit Drugs in a Canadian Setting. Clin Infect Dis 2018; 65:796-802. [PMID: 28482025 DOI: 10.1093/cid/cix428] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 05/03/2017] [Indexed: 11/14/2022] Open
Abstract
Background Transmitted drug resistance (TDR) may compromise response to antiretroviral therapy (ART). However, there are limited data on TDR patterns and impacts among people who use illicit drugs (PWUD). Methods Data were drawn from 2 prospective cohorts of PWUD in Vancouver, Canada. We characterized patterns of TDR among human immunodeficiency virus (HIV)-infected PWUD, and assessed its impacts on first-line ART virological outcomes. Results Between 1996 and 2015, among 573 ART-naive PWUD (18% with recent HIV infection), the overall TDR prevalence was 9.8% (95% confidence interval [CI], 7.3%-12.2%), with an increasing trend over time, from 8.5% in 1996-1999 to 21.1% in 2010-2015 (P = .003), mainly driven by resistance to nonnucleoside reverse transcriptase inhibitors (NNRTIs). TDR-associated mutations were more common for NNRTIs (5.4%), followed by nucleoside reverse transcriptase inhibitors (3.0%) and protease inhibitors (1.9%). TDR prevalence was lower among recently infected PWUD (adjusted odds ratio, 0.39 [95% CI, .15-.87]). Participants with TDR had higher risk of virological failure than those without TDR (log-rank P = .037) in the first year of ART. Conclusions Between 1996 and 2015, TDR prevalence increased significantly among PWUD in Vancouver. Higher risk of virological failure among PWUD with TDR may be explained by some inappropriate ART prescribing, as well as undetected minority resistant variants in participants with chronic HIV infection. Our findings support baseline resistance testing early in the course of HIV infection to guide ART selection among PWUD in our setting.
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Affiliation(s)
- M Eugenia Socías
- British Columbia Centre for Excellence in HIV/AIDS.,Department of Medicine, University of British Columbia, St Paul's Hospital, Vancouver
| | | | - Thomas Kerr
- British Columbia Centre for Excellence in HIV/AIDS.,Department of Medicine, University of British Columbia, St Paul's Hospital, Vancouver
| | - Kanna Hayashi
- British Columbia Centre for Excellence in HIV/AIDS.,Faculty of Health Sciences, Simon Fraser University, Burnaby
| | - P Richard Harrigan
- British Columbia Centre for Excellence in HIV/AIDS.,Department of Medicine, University of British Columbia, St Paul's Hospital, Vancouver
| | - Jeannie Shoveller
- British Columbia Centre for Excellence in HIV/AIDS.,School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Julio Montaner
- British Columbia Centre for Excellence in HIV/AIDS.,Department of Medicine, University of British Columbia, St Paul's Hospital, Vancouver
| | - M-J Milloy
- British Columbia Centre for Excellence in HIV/AIDS.,Department of Medicine, University of British Columbia, St Paul's Hospital, Vancouver
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25
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Smith SJ, Zhao XZ, Burke TR, Hughes SH. Efficacies of Cabotegravir and Bictegravir against drug-resistant HIV-1 integrase mutants. Retrovirology 2018; 15:37. [PMID: 29769116 PMCID: PMC5956922 DOI: 10.1186/s12977-018-0420-7] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/04/2018] [Indexed: 12/17/2022] Open
Abstract
Background Integrase strand transfer inhibitors (INSTIs) are the class of antiretroviral (ARV) drugs most recently approved by the FDA for the treatment of HIV-1 infections. INSTIs block the strand transfer reaction catalyzed by HIV-1 integrase (IN) and have been shown to potently inhibit infection by wild-type HIV-1. Of the three current FDA-approved INSTIs, Dolutegravir (DTG), has been the most effective, in part because treatment does not readily select for resistant mutants. However, recent studies showed that when INSTI-experienced patients are put on a DTG-salvage therapy, they have reduced response rates. Two new INSTIs, Cabotegravir (CAB) and Bictegravir (BIC), are currently in late-stage clinical trials. Results Both CAB and BIC had much broader antiviral profiles than RAL and EVG against the INSTI-resistant single, double, and triple HIV-1 mutants used in this study. BIC was more effective than DTG against several INSTI-resistant mutants. Overall, in terms of their ability to inhibit a broad range of INSTI-resistant IN mutants, BIC was superior to DTG, and DTG was superior to CAB. Modeling the binding of CAB, BIC, and DTG within the active site of IN suggested that the “left side” of the INSTI pharmacophore (the side away from the viral DNA) was important in determining the ability of the compound to inhibit the IN mutants we tested. Conclusions Of the two INSTIs in late stage clinical trials, BIC appears to be better able to inhibit the replication of a broad range of IN mutants. BIC retained potency against several of the INSTI-resistant mutants that caused a decrease in susceptibility to DTG. Electronic supplementary material The online version of this article (10.1186/s12977-018-0420-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Steven J Smith
- HIV Dynamics and Replication Program, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD, USA
| | - Xue Zhi Zhao
- Chemical Biology Laboratory, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD, USA
| | - Terrence R Burke
- Chemical Biology Laboratory, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD, USA
| | - Stephen H Hughes
- HIV Dynamics and Replication Program, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD, USA.
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26
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De Clercq E. Role of tenofovir alafenamide (TAF) in the treatment and prophylaxis of HIV and HBV infections. Biochem Pharmacol 2017; 153:2-11. [PMID: 29225131 DOI: 10.1016/j.bcp.2017.11.023] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 11/28/2017] [Indexed: 02/07/2023]
Abstract
Tenofovir (TFV) is the cornerstone of the treatment and prophylaxis of HIV infections. It has been routinely used in its prodrug form TDF (tenofovir disoproxil fumarate) combined with emtricitabine ((-)FTC) and other antiretroviral agents. TDF has now been replaced by TAF (tenofovir alafenamide) which allows better uptake by the lymphoid tissue. In combination with elvitegravir (E), cobicistat (C), emtricitabine (F), TAF can be advocated as an STR (single tablet regimen, Genvoya®) for the treatment of HIV infections. In this combination, E and C may in the future be replaced by bictegravir. The prophylaxis of HIV infection is momentarily based upon Truvada®, the combination of F with TDF, which in the future may also be replaced by TAF. TAF (Vemlidy®) has also replaced TDF (Viread®) for the treatment of hepatitis B virus (HBV) infections. Both TDF and TAF offer little or no risk for virus-drug resistance. As compared to TDF, TAF limits the risk for nephrotoxicity and loss of bone mineral density. What remains to be settled, however, before the universal use of TAF could be recommended, is its safety during pregnancy and its applicability in the treatment of tuberculosis, in combination with rifampicin.
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Affiliation(s)
- Erik De Clercq
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Herestraat 49, B-3000 Leuven, Belgium.
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27
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Lipson SM, Karalis G, Karthikeyan L, Ozen FS, Gordon RE, Ponnala S, Bao J, Samarrai W, Wolfe E. Mechanism of Anti-rotavirus Synergistic Activity by Epigallocatechin Gallate and a Proanthocyanidin-Containing Nutraceutical. FOOD AND ENVIRONMENTAL VIROLOGY 2017; 9:434-443. [PMID: 28466464 DOI: 10.1007/s12560-017-9299-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 04/19/2017] [Indexed: 06/07/2023]
Abstract
Epigallocatechin gallate (EGCG) of green tea and the nutraceutical CystiCran®-40 (containing 40% proanthocyanidins) of the cranberry plant have been associated with antiviral activity. The purpose of this work was to determine the mechanism of antiviral synergy between each compound. Coliphage T4II (phage T4) and the rotavirus strain SA-11(RTV) were used as model virus systems. Individual and combined flavonoids structural and molecular weight analyses were performed by NMR and HPCL/MS, respectively. A suboptimal concentration of EGCG or C-40 alone or in combination reduced phage infectivity by ≤10%. Similarly, EGCG (30 µg/ml) and C-40 (25 µg/ml), respectively, reduced RTV titers by 3 and 13%. However, RTV titers were reduced by 32% (p < .05) with both flavonoids used in combination. RTV was not recognized in host cells by electron microscopy 24-h post-inoculation. NMR and HPLC/MS findings revealed significant structural and potential changes in molecular weight of the flavonoids in complex.
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Affiliation(s)
- S M Lipson
- Department of Biology, Health Promotions, and Health Care Management, St. Francis Colllege, 180 Remsen Street, Brooklyn Heights, NY, 11201, USA.
| | - G Karalis
- Department of Biology, Health Promotions, and Health Care Management, St. Francis Colllege, 180 Remsen Street, Brooklyn Heights, NY, 11201, USA
| | | | - F S Ozen
- Department of Biology, Health Promotions, and Health Care Management, St. Francis Colllege, 180 Remsen Street, Brooklyn Heights, NY, 11201, USA
| | - R E Gordon
- Mount Sinai Medical Center, New York, NY, USA
| | - S Ponnala
- Department of Biology, Health Promotions, and Health Care Management, St. Francis Colllege, 180 Remsen Street, Brooklyn Heights, NY, 11201, USA
| | - J Bao
- Avomeen Analytical Services, Ann Arbor, MI, USA
| | - W Samarrai
- NYC Collleg Technology, CUNY, Brooklyn, NY, USA
| | - E Wolfe
- Department of Biology, Health Promotions, and Health Care Management, St. Francis Colllege, 180 Remsen Street, Brooklyn Heights, NY, 11201, USA
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Pérez-Losada M, Castel AD, Lewis B, Kharfen M, Cartwright CP, Huang B, Maxwell T, Greenberg AE, Crandall KA. Characterization of HIV diversity, phylodynamics and drug resistance in Washington, DC. PLoS One 2017; 12:e0185644. [PMID: 28961263 PMCID: PMC5621693 DOI: 10.1371/journal.pone.0185644] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 09/16/2017] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Washington DC has a high burden of HIV with a 2.0% HIV prevalence. The city is a national and international hub potentially containing a broad diversity of HIV variants; yet few sequences from DC are available on GenBank to assess the evolutionary history of HIV in the US capital. Towards this general goal, here we analyze extensive sequence data and investigate HIV diversity, phylodynamics, and drug resistant mutations (DRM) in DC. METHODS Molecular HIV-1 sequences were collected from participants infected through 2015 as part of the DC Cohort, a longitudinal observational study of HIV+ patients receiving care at 13 DC clinics. Sequences were paired with Cohort demographic, risk, and clinical data and analyzed using maximum likelihood, Bayesian and coalescent approaches of phylogenetic, network and population genetic inference. We analyzed 601 sequences from 223 participants for int (~864 bp) and 2,810 sequences from 1,659 participants for PR/RT (~1497 bp). RESULTS Ninety-nine and 94% of the int and PR/RT sequences, respectively, were identified as subtype B, with 14 non-B subtypes also detected. Phylodynamic analyses of US born infected individuals showed that HIV population size varied little over time with no significant decline in diversity. Phylogenetic analyses grouped 13.5% of the int sequences into 14 clusters of 2 or 3 sequences, and 39.0% of the PR/RT sequences into 203 clusters of 2-32 sequences. Network analyses grouped 3.6% of the int sequences into 4 clusters of 2 sequences, and 10.6% of the PR/RT sequences into 76 clusters of 2-7 sequences. All network clusters were detected in our phylogenetic analyses. Higher proportions of clustered sequences were found in zip codes where HIV prevalence is highest (r = 0.607; P<0.00001). We detected a high prevalence of DRM for both int (17.1%) and PR/RT (39.1%), but only 8 int and 12 PR/RT amino acids were identified as under adaptive selection. We observed a significant (P<0.0001) association between main risk factors (men who have sex with men and heterosexuals) and genotypes in the five well-supported clusters with sufficient sample size for testing. DISCUSSION Pairing molecular data with clinical and demographic data provided novel insights into HIV population dynamics in Washington, DC. Identification of populations and geographic locations where clustering occurs can inform and complement active surveillance efforts to interrupt HIV transmission.
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Affiliation(s)
- Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Ashburn, VA, United States of America
- CIBIO-InBIO, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Milken Institute School of Public Health, Department of Epidemiology and Biostatistics, The George Washington University, Washington, DC, United States of America
| | - Amanda D. Castel
- Milken Institute School of Public Health, Department of Epidemiology and Biostatistics, The George Washington University, Washington, DC, United States of America
| | - Brittany Lewis
- Milken Institute School of Public Health, Department of Epidemiology and Biostatistics, The George Washington University, Washington, DC, United States of America
| | - Michael Kharfen
- District of Columbia Department of Health, Washington, DC, United States of America
| | | | - Bruce Huang
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Ashburn, VA, United States of America
| | - Taylor Maxwell
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Ashburn, VA, United States of America
| | - Alan E. Greenberg
- Milken Institute School of Public Health, Department of Epidemiology and Biostatistics, The George Washington University, Washington, DC, United States of America
| | - Keith A. Crandall
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Ashburn, VA, United States of America
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Aldous AM, Castel AD, Parenti DM. Prevalence and trends in transmitted and acquired antiretroviral drug resistance, Washington, DC, 1999-2014. BMC Res Notes 2017; 10:474. [PMID: 28893321 PMCID: PMC5594524 DOI: 10.1186/s13104-017-2764-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 08/31/2017] [Indexed: 11/29/2022] Open
Abstract
Background Drug resistance limits options for antiretroviral therapy (ART) and results in poorer health outcomes among HIV-infected persons. We sought to characterize resistance patterns and to identify predictors of resistance in Washington, DC. Methods We analyzed resistance in the DC Cohort, a longitudinal study of HIV-infected persons in care in Washington, DC. We measured cumulative drug resistance (CDR) among participants with any genotype between 1999 and 2014 (n = 3411), transmitted drug resistance (TDR) in ART-naïve persons (n = 1503), and acquired drug resistance (ADR) in persons with genotypes before and after ART initiation (n = 309). Using logistic regression, we assessed associations between patient characteristics and transmitted resistance to any antiretroviral. Results Prevalence of TDR was 20.5%, of ADR 40.5%, and of CDR 45.1% in the respective analysis groups. From 2004 to 2013, TDR prevalence decreased for nucleoside and nucleotide analogue reverse transcriptase inhibitors (15.0 to 5.5%; p = 0.0003) and increased for integrase strand transfer inhibitors (INSTIs) (0.0–1.4%; p = 0.04). In multivariable analysis, TDR was not associated with age, race/ethnicity, HIV risk group, or years from HIV diagnosis. Conclusions In this urban cohort of HIV-infected persons, almost half of participants tested had evidence of CDR; and resistance to INSTIs was increasing. If this trend continues, inclusion of the integrase-encoding region in baseline genotype testing should be strongly considered.
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Affiliation(s)
- Annette M Aldous
- Department of Epidemiology and Biostatistics, The George Washington University, Milken Institute School of Public Health, Washington, DC, 20037, USA
| | - Amanda D Castel
- Department of Epidemiology and Biostatistics, The George Washington University, Milken Institute School of Public Health, Washington, DC, 20037, USA
| | - David M Parenti
- Division of Infectious Diseases, The George Washington University School of Medicine, 2150 Pennsylvania Avenue, NW, Washington, DC, USA.
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Weber IT, Harrison RW. Decoding HIV resistance: from genotype to therapy. Future Med Chem 2017; 9:1529-1538. [PMID: 28791894 PMCID: PMC5694023 DOI: 10.4155/fmc-2017-0048] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/03/2017] [Indexed: 01/14/2023] Open
Abstract
Genetic variation in HIV poses a major challenge for prevention and treatment of the AIDS pandemic. Resistance occurs by mutations in the target proteins that lower affinity for the drug or alter the protein dynamics, thereby enabling viral replication in the presence of the drug. Due to the prevalence of drug-resistant strains, monitoring the genotype of the infecting virus is recommended. Computational approaches for predicting resistance from genotype data and guiding therapy are discussed. Many prediction methods rely on rules derived from known resistance-associated mutations, however, statistical or machine learning can improve the classification accuracy and assess unknown mutations. Adding classifiers such as information on the atomic structure of the protein can further enhance the predictions.
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Affiliation(s)
- Irene T Weber
- Department of Biology, Georgia State University, PO Box 4010, Atlanta, GA 30302-4010, USA
| | - Robert W Harrison
- Department of Computer Science, Georgia State University, Atlanta, GA 30303, USA
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Margot NA, Wong P, Kulkarni R, White K, Porter D, Abram ME, Callebaut C, Miller MD. Commonly Transmitted HIV-1 Drug Resistance Mutations in Reverse-Transcriptase and Protease in Antiretroviral Treatment-Naive Patients and Response to Regimens Containing Tenofovir Disoproxil Fumarate or Tenofovir Alafenamide. J Infect Dis 2017; 215:920-927. [PMID: 28453836 DOI: 10.1093/infdis/jix015] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 01/05/2017] [Indexed: 11/12/2022] Open
Abstract
Background The presence of transmitted drug resistance mutations (TDRMs) in antiretroviral treatment (ART)-naive patients can adversely affect the outcome of ART. Methods Resistance testing was conducted in 6704 ART-naive subjects predominantly from the United States and Europe in 9 clinical studies conducted by Gilead Sciences from 2000 to 2013. Results The presence of TDRMs increased during this period (from 5.2% to 11.4%), primarily driven by an increase in nonnucleoside reverse-transcriptase (RT) inhibitor (NNRTI) resistance mutations (from 0.3% to 7.1%), particularly K103N/S (increase from 0.3% to 5.3%). Nucleoside/nucleotide RT inhibitor mutations were found in 3.1% of patients. Only 1 patient had K65R (0.01%) and 7 had M184V/I (0.1%), despite high use of tenofovir disoproxil fumarate (TDF), emtricitabine, and lamivudine and potential transmission of resistance to these drugs. At least 1 thymidine-analogue mutations was present in 2.7% of patients with 0.07% harboring T215Y/F and 2.7% harboring T215 revertant mutations (T215rev). Patients with the combination of M41L + L210W + T215rev showed full human immunodeficiency virus RNA suppression while receiving a TDF- or tenofovir alafenamide-containing regimen. Conclusions There was an overall increase of TDRMs among patients enrolling in clinical trials from 2000 through 2013, driven primarily by an increase in NNRTI resistance. However, the presence of common TDRMs, including thymidine-analogue mutations/T215rev, showed no impact on response to TDF- or tenofovir alafenamide-containing regimens.
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Affiliation(s)
| | - Pamela Wong
- Gilead Sciences, Foster City, California, USA
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Sapozhnikov J, Young JD, Patel M, Chiampas TD, Vaughn P, Badowski ME. Prevalence of HIV-1 transmitted drug resistance in the incarcerated population. HIV Med 2017; 18:756-763. [PMID: 28585361 DOI: 10.1111/hiv.12522] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2017] [Indexed: 11/28/2022]
Abstract
OBJECTIVES The aim of the study was to determine the prevalence of transmitted drug resistance (TDR)-associated mutations among treatment-naïve, incarcerated individuals with HIV-1 infection in the USA as well as the class TDR and antiretroviral (ARV) mutations present at baseline. METHODS Patients over the age of 18 years were included in the study if they had been diagnosed with HIV infection, if their HIV infection was managed through telemedicine and if they were incarcerated in the State of Illinois Department of Corrections between 10 July 2010 and 29 April 2016. Additionally, the patients were required to have a documented genotype and be ARV-naïve. A medical chart review was conducted to assess demographic information, disease burden, and risk factors for acquiring the virus. RESULTS The inclusion criteria were met for 105 patients. A total of 24 patients (23%) had a clinically significant mutation associated with resistance to any drug class. The prevalence of mutations conferring clinically significant resistance was 19% for nonnucleoside reverse transcriptase inhibitors (NNRTIs), 18% for nucleoside reverse transcriptase inhibitors (NRTIs), and 4% for protease inhibitors (PIs). Five per cent of patients had dual-class TDR to both NRTI and NNRTI drug classes and 2% of patients had mutations to both NNRTI and PI drug classes. There was no significant increase in the prevalence of clinically relevant drug resistance mutations based on demographics, burden of disease, or risk factors for acquiring the virus. CONCLUSIONS A high prevalence of TDR was identified in the ARV-naïve incarcerated population. The results of this study indicate an increased prevalence of TDR in a largely unstudied incarcerated population, demonstrating the need for increased monitoring of resistance in HIV-infected patients world-wide.
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Affiliation(s)
- J Sapozhnikov
- College of Pharmacy, Department of Pharmacy Practice, University of Illinois at Chicago, Chicago, IL, USA
| | - J D Young
- Division of Infectious Diseases, Immunology and International Medicine, Department of Medicine, University of Illinois Hospital & Health Sciences System, Chicago, IL, USA
| | - M Patel
- Division of Infectious Diseases, Immunology and International Medicine, Department of Medicine, University of Illinois Hospital & Health Sciences System, Chicago, IL, USA
| | - T D Chiampas
- College of Pharmacy, Department of Pharmacy Practice, University of Illinois at Chicago, Chicago, IL, USA
| | - P Vaughn
- College of Pharmacy, Department of Pharmacy Practice, University of Illinois at Chicago, Chicago, IL, USA
| | - M E Badowski
- College of Pharmacy, Department of Pharmacy Practice, University of Illinois at Chicago, Chicago, IL, USA
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Leung P, Eltahla AA, Lloyd AR, Bull RA, Luciani F. Understanding the complex evolution of rapidly mutating viruses with deep sequencing: Beyond the analysis of viral diversity. Virus Res 2016; 239:43-54. [PMID: 27888126 DOI: 10.1016/j.virusres.2016.10.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/24/2016] [Accepted: 10/25/2016] [Indexed: 12/24/2022]
Abstract
With the advent of affordable deep sequencing technologies, detection of low frequency variants within genetically diverse viral populations can now be achieved with unprecedented depth and efficiency. The high-resolution data provided by next generation sequencing technologies is currently recognised as the gold standard in estimation of viral diversity. In the analysis of rapidly mutating viruses, longitudinal deep sequencing datasets from viral genomes during individual infection episodes, as well as at the epidemiological level during outbreaks, now allow for more sophisticated analyses such as statistical estimates of the impact of complex mutation patterns on the evolution of the viral populations both within and between hosts. These analyses are revealing more accurate descriptions of the evolutionary dynamics that underpin the rapid adaptation of these viruses to the host response, and to drug therapies. This review assesses recent developments in methods and provide informative research examples using deep sequencing data generated from rapidly mutating viruses infecting humans, particularly hepatitis C virus (HCV), human immunodeficiency virus (HIV), Ebola virus and influenza virus, to understand the evolution of viral genomes and to explore the relationship between viral mutations and the host adaptive immune response. Finally, we discuss limitations in current technologies, and future directions that take advantage of publically available large deep sequencing datasets.
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Affiliation(s)
- Preston Leung
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia; The Kirby Institute, UNSW Australia, Sydney, NSW 2052, Australia
| | - Auda A Eltahla
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia; The Kirby Institute, UNSW Australia, Sydney, NSW 2052, Australia
| | - Andrew R Lloyd
- The Kirby Institute, UNSW Australia, Sydney, NSW 2052, Australia
| | - Rowena A Bull
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia; The Kirby Institute, UNSW Australia, Sydney, NSW 2052, Australia
| | - Fabio Luciani
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia; The Kirby Institute, UNSW Australia, Sydney, NSW 2052, Australia.
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HIV-1 drug resistance and resistance testing. INFECTION GENETICS AND EVOLUTION 2016; 46:292-307. [PMID: 27587334 DOI: 10.1016/j.meegid.2016.08.031] [Citation(s) in RCA: 200] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 08/24/2016] [Accepted: 08/27/2016] [Indexed: 12/23/2022]
Abstract
The global scale-up of antiretroviral (ARV) therapy (ART) has led to dramatic reductions in HIV-1 mortality and incidence. However, HIV drug resistance (HIVDR) poses a potential threat to the long-term success of ART and is emerging as a threat to the elimination of AIDS as a public health problem by 2030. In this review we describe the genetic mechanisms, epidemiology, and management of HIVDR at both individual and population levels across diverse economic and geographic settings. To describe the genetic mechanisms of HIVDR, we review the genetic barriers to resistance for the most commonly used ARVs and describe the extent of cross-resistance between them. To describe the epidemiology of HIVDR, we summarize the prevalence and patterns of transmitted drug resistance (TDR) and acquired drug resistance (ADR) in both high-income and low- and middle-income countries (LMICs). We also review to two categories of HIVDR with important public health relevance: (i) pre-treatment drug resistance (PDR), a World Health Organization-recommended HIVDR surveillance metric and (ii) and pre-exposure prophylaxis (PrEP)-related drug resistance, a type of ADR that can impact clinical outcomes if present at the time of treatment initiation. To summarize the implications of HIVDR for patient management, we review the role of genotypic resistance testing and treatment practices in both high-income and LMIC settings. In high-income countries where drug resistance testing is part of routine care, such an understanding can help clinicians prevent virological failure and accumulation of further HIVDR on an individual level by selecting the most efficacious regimens for their patients. Although there is reduced access to diagnostic testing and to many ARVs in LMIC, understanding the scientific basis and clinical implications of HIVDR is useful in all regions in order to shape appropriate surveillance, inform treatment algorithms, and manage difficult cases.
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