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Dennis AM, Volz E, Frost AMSD, Hossain M, Poon AF, Rebeiro PF, Vermund SH, Sterling TR, Kalish ML. HIV-1 Transmission Clustering and Phylodynamics Highlight the Important Role of Young Men Who Have Sex with Men. AIDS Res Hum Retroviruses 2018; 34:879-888. [PMID: 30027754 PMCID: PMC6204570 DOI: 10.1089/aid.2018.0039] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
More persons living with HIV reside in the Southern United States than in any other region, yet little is known about HIV molecular epidemiology in the South. We used cluster and phylodynamic analyses to evaluate HIV transmission patterns in middle Tennessee. We performed cross-sectional analyses of HIV-1 pol sequences and clinical data collected from 2001 to 2015 among persons attending the Vanderbilt Comprehensive Care Clinic. Transmission clusters were identified using maximum likelihood phylogenetics and patristic distance differences. Demographic, risk behavior, and clinical factors were assessed evaluating “active” clusters (clusters including sequences sampled 2011–2015) and associations estimated with logistic regression. Transmission risk ratios for men who have sex with men (MSM) were estimated with phylodynamic models. Among 2915 persons (96% subtype-B sequences), 963 (33%) were members of 292 clusters (distance ≤1.5%, size range 2–39). Most clusters (62%, n = 690 persons) were active, either being newly identified (n = 80) or showing expansion on existing clusters (n = 101). Correlates of active clustering among persons with sequences collected during 2011–2015 included MSM risk and ≤30 years of age. Active clusters were significantly more concentrated in MSM and younger persons than historical clusters. Young MSM (YMSM) (≤26.4 years) had high estimated transmission risk [risk ratio = 4.04 (2.85–5.65) relative to older MSM] and were much more likely to transmit to YMSM. In this Tennessee cohort, transmission clusters over time were more concentrated by MSM and younger age, with high transmission risk among and between YMSM, highlighting the importance of interventions among this group. Detecting active clusters could help direct interventions to disrupt ongoing transmission chains.
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Affiliation(s)
- Ann M. Dennis
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina
| | - Erik Volz
- Department of Infectious Disease Epidemiology and Centre for Outbreak Analysis and Modeling, Imperial College, London, United Kingdom
| | | | - Mukarram Hossain
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Art F.Y. Poon
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | - Peter F. Rebeiro
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Sten H. Vermund
- Department of Epidemiology of Microbial Diseases, Yale University School of Public Health, New Haven, Connecticut
| | - Timothy R. Sterling
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Marcia L. Kalish
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
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Ndashimye E, Avino M, Kyeyune F, Nankya I, Gibson RM, Nabulime E, Poon AF, Kityo C, Mugyenyi P, Quiñones-Mateu ME, Arts EJ. Absence of HIV-1 Drug Resistance Mutations Supports the Use of Dolutegravir in Uganda. AIDS Res Hum Retroviruses 2018; 34:404-414. [PMID: 29353487 DOI: 10.1089/aid.2017.0205] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To screen for drug resistance and possible treatment with Dolutegravir (DTG) in treatment-naive patients and those experiencing virologic failure during first-, second-, and third-line combined antiretroviral therapy (cART) in Uganda. Samples from 417 patients in Uganda were analyzed for predicted drug resistance upon failing a first- (N = 158), second- (N = 121), or third-line [all 51 involving Raltegravir (RAL)] treatment regimen. HIV-1 pol gene was amplified and sequenced from plasma samples. Drug susceptibility was interpreted using the Stanford HIV database algorithm and SCUEAL was used for HIV-1 subtyping. Frequency of resistance to nucleoside reverse transcriptase inhibitors (NRTIs) (95%) and non-NRTI (NNRTI, 96%) was high in first-line treatment failures. Despite lack of NNRTI-based treatment for years, NNRTI resistance remained stable in 55% of patients failing second-line or third-line treatment, and was also at 10% in treatment-naive Ugandans. DTG resistance (n = 366) was not observed in treatment-naive individuals or individuals failing first- and second-line cART, and only found in two patients failing third-line cART, while 47% of the latter had RAL- and Elvitegravir-resistant HIV-1. Secondary mutations associated with DTG resistance were found in 2%-10% of patients failing third-line cART. Of 14 drugs currently available for cART in Uganda, resistance was readily observed to all antiretroviral drugs (except for DTG) in Ugandan patients failing first-, second-, or even third-line treatment regimens. The high NNRTI resistance in first-line treatment in Uganda even among treatment-naive patients calls for the use of DTG to reach the UNAIDS 90:90:90 goals.
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Affiliation(s)
- Emmanuel Ndashimye
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Mariano Avino
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | - Fred Kyeyune
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Immaculate Nankya
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Richard M. Gibson
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Eva Nabulime
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Art F.Y. Poon
- Department of Microbiology and Immunology, Western University, London, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | - Cissy Kityo
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Peter Mugyenyi
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Miguel E. Quiñones-Mateu
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Eric J. Arts
- Department of Microbiology and Immunology, Western University, London, Canada
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Lapp H, Bala S, Balhoff JP, Bouck A, Goto N, Holder M, Holland R, Holloway A, Katayama T, Lewis PO, Mackey AJ, Osborne BI, Piel WH, Pond SLK, Poon AF, Qiu WG, Stajich JE, Stoltzfus A, Thierer T, Vilella AJ, Vos RA, Zmasek CM, Zwickl DJ, Vision TJ. The 2006 NESCent Phyloinformatics Hackathon: A Field Report. Evol Bioinform Online 2017. [DOI: 10.1177/117693430700300016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In December, 2006, a group of 26 software developers from some of the most widely used life science programming toolkits and phylogenetic software projects converged on Durham, North Carolina, for a Phyloinformatics Hackathon, an intense five-day collaborative software coding event sponsored by the National Evolutionary Synthesis Center (NESCent). The goal was to help researchers to integrate multiple phylogenetic software tools into automated workflows. Participants addressed deficiencies in interoperability between programs by implementing “glue code” and improving support for phylogenetic data exchange standards (particularly NEXUS) across the toolkits. The work was guided by use-cases compiled in advance by both developers and users, and the code was documented as it was developed. The resulting software is freely available for both users and developers through incorporation into the distributions of several widely-used open-source toolkits. We explain the motivation for the hackathon, how it was organized, and discuss some of the outcomes and lessons learned. We conclude that hackathons are an effective mode of solving problems in software interoperability and usability, and are underutilized in scientific software development.
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Affiliation(s)
- Hilmar Lapp
- National Evolutionary Synthesis Center, 2024 W. Main St., Suite A200, Durham NC 27705, U.S.A
| | - Sendu Bala
- Dunn Human Nutrition Unit, Medical Research Council, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - James P. Balhoff
- National Evolutionary Synthesis Center, 2024 W. Main St., Suite A200, Durham NC 27705, U.S.A
| | - Amy Bouck
- Department of Biology, CB 3280, University of North Carolina, Chapel Hill, NC 27599
- Department of Biology, Duke University, P.O. Box 90338, Durham, NC 27708, U.S.A
| | - Naohisa Goto
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565–0871, Japan
| | - Mark Holder
- School of Computational Science, 150-F Dirac Science Library, Florida State University, Tallahassee, Florida 32306–4120, U.S.A
| | - Richard Holland
- EMBL—European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Alisha Holloway
- Section of Evolution and Ecology, Center for Population Biology, 3347 Storer Hall, University of California, Davis, CA 95616, U.S.A
| | - Toshiaki Katayama
- Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108–0071, Japan
| | - Paul O. Lewis
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Unit 3043, Storrs, CT 06269-3043, U.S.A
| | - Aaron J. Mackey
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA 19426, U.S.A
| | | | - William H. Piel
- Peabody Museum of Natural History, Yale University, 170 Whitney Ave., New Haven CT 06511, U.S.A
| | - Sergei L. Kosakovsky Pond
- University of California, San Diego, Division of Comparative Pathology and Antiviral Research Center, 150 West Washington Street, San Diego, CA 92103
| | - Art F.Y. Poon
- University of California, San Diego, Division of Comparative Pathology and Antiviral Research Center, 150 West Washington Street, San Diego, CA 92103
| | - Wei-Gang Qiu
- Department of Biological Sciences, Hunter College, City University of New York, 695 Park Ave, New York, NY 10021, U.S.A
| | - Jason E. Stajich
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, U.S.A
| | - Arlin Stoltzfus
- Biochemical Science Division, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 8310, Gaithersburg, MD, 20899-8310
| | - Tobias Thierer
- Biomatters Ltd, Level 6, 220 Queen St, Auckland, New Zealand
| | - Albert J. Vilella
- EMBL—European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Rutger A. Vos
- Department of Zoology, University of British Columbia, #2370-6270 University Blvd., Vancouver, B.C. V6T 1Z4, Canada
| | | | - Derrick J. Zwickl
- National Evolutionary Synthesis Center, 2024 W. Main St., Suite A200, Durham NC 27705, U.S.A
| | - Todd J. Vision
- National Evolutionary Synthesis Center, 2024 W. Main St., Suite A200, Durham NC 27705, U.S.A
- Department of Biology, CB 3280, University of North Carolina, Chapel Hill, NC 27599
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Jacka B, Applegate T, Krajden M, Olmstead A, Harrigan PR, Marshall BDL, DeBeck K, Milloy MJ, Lamoury F, Pybus OG, Lima VD, Magiorkinis G, Montoya V, Montaner J, Joy J, Woods C, Dobrer S, Dore GJ, Poon AF, Grebely J. Phylogenetic clustering of hepatitis C virus among people who inject drugs in Vancouver, Canada. Hepatology 2014; 60:1571-1580. [PMID: 25042607 PMCID: PMC4211947 DOI: 10.1002/hep.27310] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 07/08/2014] [Indexed: 12/20/2022]
Abstract
UNLABELLED Little is known about factors associated with hepatitis C virus (HCV) transmission among people who inject drugs (PWID). Phylogenetic clustering and associated factors were evaluated among PWID in Vancouver, Canada. Data were derived from the Vancouver Injection Drug Users Study. Participants who were HCV antibody-positive at enrolment and those with HCV antibody seroconversion during follow-up (1996 to 2012) were tested for HCV RNA and sequenced (Core-E2 region). Phylogenetic trees were inferred using maximum likelihood analysis and clusters were identified using ClusterPicker (90% bootstrap threshold, 0.05 genetic distance threshold). Factors associated with clustering were assessed using logistic regression. Among 655 eligible participants, HCV genotype prevalence was: G1a: 48% (n=313), G1b: 6% (n=41), G2a: 3% (n=20), G2b: 7% (n=46), G3a: 33% (n=213), G4a: <1% (n=4), G6a: 1% (n=8), G6e: <1% (n=1), and unclassifiable: 1% (n=9). The mean age was 36 years, 162 (25%) were female, and 164 (25%) were HIV+. Among 501 participants with HCV G1a and G3a, 31% (n=156) were in a pair/cluster. Factors independently associated with phylogenetic clustering included: age <40 (versus age≥40, adjusted odds ratio [AOR]=1.64; 95% confidence interval [CI] 1.03, 2.63), human immunodeficiency virus (HIV) infection (AOR=1.82; 95% CI 1.18, 2.81), HCV seroconversion (AOR=3.05; 95% CI 1.40, 6.66), and recent syringe borrowing (AOR 1.59; 95% CI 1.07, 2.36). CONCLUSION In this sample of PWID, one-third demonstrated phylogenetic clustering. Factors independently associated with phylogenetic clustering included younger age, recent HCV seroconversion, prevalent HIV infection, and recent syringe borrowing. Strategies to enhance the delivery of prevention and/or treatment strategies to those with HIV and recent HCV seroconversion should be explored, given an increased likelihood of HCV transmission in these subpopulations.
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Affiliation(s)
- B Jacka
- Viral Hepatitis Clinical Research Program, The Kirby Institute,
UNSW Australia, Sydney NSW, Australia
| | - T Applegate
- Viral Hepatitis Clinical Research Program, The Kirby Institute,
UNSW Australia, Sydney NSW, Australia
| | - M Krajden
- BC Centre for Disease Control, Vancouver BC
| | - A Olmstead
- BC Centre for Disease Control, Vancouver BC
| | - PR Harrigan
- BC Centre for Excellence in HIV/AIDS, St Paul's Hospital,
Vancouver BC
| | - BDL Marshall
- Department of Epidemiology, Brown University, Providence, RI,
USA
| | - K DeBeck
- BC Centre for Excellence in HIV/AIDS, St Paul's Hospital,
Vancouver BC,School of Public Policy, Simon Fraser University, Vancouver, BC,
Canada
| | - M-J Milloy
- BC Centre for Excellence in HIV/AIDS, St Paul's Hospital,
Vancouver BC,Department of Family Practice, Faculty of Medicine, University of
British Columbia, Vancouver, BC
| | - F Lamoury
- Viral Hepatitis Clinical Research Program, The Kirby Institute,
UNSW Australia, Sydney NSW, Australia
| | - OG Pybus
- Department of Zoology, University of Oxford
| | - VD Lima
- BC Centre for Excellence in HIV/AIDS, St Paul's Hospital,
Vancouver BC,Division of AIDS, Department of Medicine, Faculty of Medicine,
University of British Columbia, Vancouver, BC, Canada
| | - G Magiorkinis
- Department of Zoology, University of Oxford,Virus Reference Department, Public Health England, London,
UK
| | - V Montoya
- BC Centre for Disease Control, Vancouver BC
| | - J Montaner
- BC Centre for Excellence in HIV/AIDS, St Paul's Hospital,
Vancouver BC,Division of AIDS, Department of Medicine, Faculty of Medicine,
University of British Columbia, Vancouver, BC, Canada
| | - J Joy
- BC Centre for Excellence in HIV/AIDS, St Paul's Hospital,
Vancouver BC
| | - C Woods
- BC Centre for Excellence in HIV/AIDS, St Paul's Hospital,
Vancouver BC
| | - S Dobrer
- BC Centre for Excellence in HIV/AIDS, St Paul's Hospital,
Vancouver BC
| | - GJ Dore
- Viral Hepatitis Clinical Research Program, The Kirby Institute,
UNSW Australia, Sydney NSW, Australia
| | - AF Poon
- BC Centre for Excellence in HIV/AIDS, St Paul's Hospital,
Vancouver BC
| | - J Grebely
- Viral Hepatitis Clinical Research Program, The Kirby Institute,
UNSW Australia, Sydney NSW, Australia
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5
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Lee GQ, Harrigan PR, Dong W, Poon AF, Heera J, Demarest J, Rinehart A, Chapman D, Valdez H, Portsmouth S. Comparison of population and 454 "deep" sequence analysis for HIV type 1 tropism versus the original trofile assay in non-B subtypes. AIDS Res Hum Retroviruses 2013; 29:979-84. [PMID: 23350534 DOI: 10.1089/aid.2012.0338] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
HIV-1 tropism can be predicted using V3 genotypic algorithms. The performance of these prediction algorithms for non-B subtypes is poorly characterized. Here, we use these genotypic algorithms to predict viral tropism of HIV-1 subtype A, B, C, and D to find apparent sensitivity, specificity, and concordance against a recombinant phenotypic assay, the original Trofile assay. This is a substudy of an epidemiological study (Pfizer A4001064). Plasma samples were selected to represent a large number of DM/X4 and R5 viruses. The HIV-1 env gene V3 loop was genotyped by Sanger sequencing (N=260) or 454 "deep" sequencing (N=280). Sequences were scored with g2p[coreceptor], PSSM X4/R5, PSSM SI/NSI, and PSSM subtype C matrices. Overall, non-B subtypes tropism prediction had similar concordance and apparent sensitivity and specificity as subtype B in predicting Trofile's results in both population sequencing (81.3%, 65.6%, and 90.5% versus 84.2%, 78.5%, and 88.2%) and 454 "deep" sequencing (82.3%, 80.0%, and 83.6% versus 86.8%, 92.0%, and 82.6%) using g2p[coreceptor]. By population sequencing, subtype A had lower sensitivity, whereas subtype D had lower specificity for non-R5 predictions, both in comparison to subtype B. 454 "deep" sequencing improved subtype A sensitivity but not subtype D. Subtype C had greater concordance than subtype B regardless of sequencing methods. In conclusion, genotypic tropism prediction algorithms may be applied to non-B HIV-1 subtypes with caution. Collective analysis of non-B subtypes revealed a performance similar to subtype B, whereas a subtype-specific analysis revealed overestimation (subtype D) or underestimation (subtype A).
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Affiliation(s)
- Guinevere Q. Lee
- BC Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Experimental Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - P. Richard Harrigan
- BC Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Division of AIDS, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Winnie Dong
- BC Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Art F.Y. Poon
- BC Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | | | | | - Alex Rinehart
- ViiV Healthcare, Research Triangle Park, North Carolina
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Poon AF, McGovern RA, Mo T, Knapp DJ, Brenner B, Routy JP, Wainberg MA, Harrigan PR. Dates of HIV infection can be estimated for seroprevalent patients by coalescent analysis of serial next-generation sequencing data. AIDS 2011; 25:2019-26. [PMID: 21832936 DOI: 10.1097/qad.0b013e32834b643c] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECTIVE To reconstruct dates of HIV infection by the coalescent analysis of longitudinal next-generation sequencing (NGS) data. DESIGN The coalescent predicts the time that has elapsed since the most recent common ancestor (MRCA) of a population. Because HIV tends to undergo severe bottlenecks upon transmission, the MRCA may be a good predictor of the time of infection. NGS provides an efficient means for performing large-scale clonal sequencing of HIV populations within patients, and the ideal raw material for coalescent analysis. METHODS Baseline and follow-up plasma samples were obtained from 19 individuals enrolled into the Montréal Primary HIV Infection cohort. Dates of infection were initially estimated at baseline from nongenetic data (clinical and serological markers and patient questionnaires). HIV RNA was extracted and seven regions of the genome were amplified, subjected to parallel-tagged 454 pyrosequencing, and analyzed using the software package BEAST. RESULTS Mean estimates of the time to the MRCA per patient were significantly correlated with nongenetic estimates (Spearman's ρ = 0.65, P = 4.4 × 10(-3)). The median absolute difference between coalescent and nongenetic date estimates was smallest (median 29.4 days) for highly variable regions of the HIV genome such as env V3, and greater (median 114.9 days) for more conserved regions such as pol. CONCLUSION This application of NGS represents an important advancement, not only because accurate estimates of dates of infection can be derived retrospectively from archived specimens, but also because each analysis is patient-specific and, therefore, robust to variation in rates of HIV evolution.
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