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3. Effective, Practical PON Monitoring Beyond the Splitter

Author

Parkin, Neil, Minoughan, Sophie, and Iqbal, Md Asif

Subjects
Electrical Engineering and Systems Science - Signal Processing
Abstract

Monitoring beyond the splitter in a PON is costly due to the need for additional hardware. A non-standard monitoring wavelength can reduce cost and increase the visibility of customers to 97% on a C+ GPON more...

Published
2022

4. An investigation into the influence of trust on the sharing of practical knowledge in technology producing small to medium enterprises (SMEs)

Author

Parkin, Neil, Penlington, Roge, and Connor, Chris

Subjects
658.02, H900 Others in Engineering, N100 Business studies
Abstract

This study that uses ethnographic research methods explores how trust influences the sharing of practical knowledge in technology producing SMEs. More specifically, this project investigates how trust behaviours influence the sharing of various types of tacit and explicit practical knowledge. Currently, practice theory research recommends how practical knowledge can be shared however, efforts to share practical knowledge generally fail due to trust not been developed adequately in the collaborative relationships formed by companies. This research aims to inform practice theory of how SMEs can develop collaborative relationships more effectively. To succeed, these companies are particularly dependent on collaborative working as a source for growth and competitive advantage. This investigation uses a qualitative research methodology, which employs a multiple case study approach where semi-structured interviews have been conducted with six engineers, three of whom work in large companies and three in SMEs. Observations were also conducted for one case study. These participants work at various levels and the companies themselves are based in a variety of geographic locations across the UK. Based on the use of a thematic analysis on the interview data it was possible to characterise a practical knowledge sharing culture. In addition, the research outlines the specific perceptions and experiences of participants who adopted trust based strategies for sharing practical knowledge over the life of a project. By applying a method devised in this research called narrative mapping, it was possible to identify patterns between trust behaviours and types of practical knowledge shared from participants' anecdotes. As the interviewees' anecdotes relate to specific relationship phases over a project life cycle, the research was able to build up a picture of how trust develops over the life stages of a project. The findings provide a novel way of helping SMEs to develop effective collaborative relationships and associated working practices and inform future trust and practice theory research. more...

Published
2020

6. Performance comparison of the Maxim and Sedia Limiting Antigen Avidity assays for HIV incidence surveillance

Author

Sempa, Joseph B, Welte, Alex, Busch, Michael P, Hall, Jake, Hampton, Dylan, Facente, Shelley N, Keating, Sheila M, Marson, Kara, Parkin, Neil, Pilcher, Christopher D, Murphy, Gary, Grebe, Eduard, and Assays, on behalf of the Consortium for the Evaluation and Performance of HIV Incidence more...

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Clinical Sciences, Infectious Diseases, HIV/AIDS, Sexually Transmitted Infections, Infection, Good Health and Well Being, Algorithms, Cross-Sectional Studies, Epidemics, Female, HIV Antigens, HIV Infections, HIV-1, Humans, Incidence, Kenya, Population Surveillance, Viral Load, Consortium for the Evaluation and Performance of HIV Incidence Assays, General Science & Technology
Abstract

BackgroundTwo manufacturers, Maxim Biomedical and Sedia Biosciences Corporation, supply CDC-approved versions of the HIV-1 Limiting Antigen Avidity EIA (LAg) for detecting 'recent' HIV infection in cross-sectional incidence estimation. This study assesses and compares the performance of the two assays for incidence surveillance.MethodsWe ran both assays on a panel of 2,500 well-characterized HIV-1-infected specimens. We analysed concordance of assay results, assessed reproducibility using repeat testing and estimated mean durations of recent infection (MDRIs) and false-recent rates (FRRs) for a range of normalized optical density (ODn) thresholds, alone and in combination with viral load thresholds. We defined three hypothetical surveillance scenarios, similar to the Kenyan and South African epidemics, and a concentrated epidemic. These scenarios allowed us to evaluate the precision of incidence estimates obtained by means of various recent infection testing algorithms (RITAs) based on each of the two assays.ResultsThe Maxim assay produced lower ODn values than the Sedia assay on average, largely as a result of higher calibrator readings (mean OD of 0.749 vs. 0.643), with correlation of normalized readings lower (R2 = 0.908 vs. R2 = 0.938). Reproducibility on blinded control specimens was slightly better for Maxim. The MDRI of a Maxim-based algorithm at the 'standard' threshold (ODn ≤1.5 & VL >1,000) was 201 days (95% CI: 180,223) and for Sedia 171 (152,191). The difference Differences in MDRI were estimated at 32.7 (22.9,42.8) and 30.9 days (21.7,40.7) for the two algorithms, respectively. Commensurately, the Maxim algorithm had a higher FRR in treatment-naive subjects (1.7% vs. 1.1%). The two assays produced similar precision of incidence estimates in the three surveillance scenarios.ConclusionsDifferences between the assays can be primarily attributed to the calibrators supplied by the manufacturers. Performance for surveillance was extremely similar, although different thresholds were optimal (i.e. produced the lowest variance of incidence estimates) and at any given ODn threshold, different estimates of MDRI and FRR were obtained. The two assays cannot be treated as interchangeable: assay and algorithm-specific performance characteristic estimates must be used for survey planning and incidence estimation. more...

Published
2019

7. Computational analysis of antibody dynamics identifies recent HIV-1 infection

Author

Seaton, Kelly E, Vandergrift, Nathan A, Deal, Aaron W, Rountree, Wes, Bainbridge, John, Grebe, Eduard, Anderson, David A, Sawant, Sheetal, Shen, Xiaoying, Yates, Nicole L, Denny, Thomas N, Liao, Hua-Xin, Haynes, Barton F, Robb, Merlin L, Parkin, Neil, Santos, Breno R, Garrett, Nigel, Price, Matthew A, Naniche, Denise, Duerr, Ann C, Keating, Sheila, Hampton, Dylan, Facente, Shelley, Marson, Kara, Welte, Alex, Pilcher, Christopher D, Cohen, Myron S, and Tomaras, Georgia D more...

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Immunology, HIV/AIDS, Sexually Transmitted Infections, Vaccine Related, Biotechnology, Infectious Diseases, Vaccine Related (AIDS), Prevention, Immunization, Infection, Good Health and Well Being, Antibody Affinity, Antigen-Antibody Reactions, Biomarkers, Computational Biology, HIV Antibodies, HIV Antigens, HIV Infections, HIV-1, Humans, Immunoglobulin G, Incidence, Retrospective Studies, Time Factors, CEPHIA group, AIDS/HIV, Antigen, Immunoglobulins, Biomedical and clinical sciences, Health sciences
Abstract

Accurate HIV-1 incidence estimation is critical to the success of HIV-1 prevention strategies. Current assays are limited by high false recent rates (FRRs) in certain populations and a short mean duration of recent infection (MDRI). Dynamic early HIV-1 antibody response kinetics were harnessed to identify biomarkers for improved incidence assays. We conducted retrospective analyses on circulating antibodies from known recent and longstanding infections and evaluated binding and avidity measurements of Env and non-Env antigens and multiple antibody forms (i.e., IgG, IgA, IgG3, IgG4, dIgA, and IgM) in a diverse panel of 164 HIV-1-infected participants (clades A, B, C). Discriminant function analysis identified an optimal set of measurements that were subsequently evaluated in a 324-specimen blinded biomarker validation panel. These biomarkers included clade C gp140 IgG3, transmitted/founder clade C gp140 IgG4 avidity, clade B gp140 IgG4 avidity, and gp41 immunodominant region IgG avidity. MDRI was estimated at 215 day or alternatively, 267 days. FRRs in untreated and treated subjects were 5.0% and 3.6%, respectively. Thus, computational analysis of dynamic HIV-1 antibody isotype and antigen interactions during infection enabled design of a promising HIV-1 recency assay for improved cross-sectional incidence estimation. more...

Published
2017

8. HIV-1 Drug Resistance Mutations: Potential Applications for Point-of-Care Genotypic Resistance Testing.

Author

Rhee, Soo-Yon, Jordan, Michael R, Raizes, Elliot, Chua, Arlene, Parkin, Neil, Kantor, Rami, Van Zyl, Gert U, Mukui, Irene, Hosseinipour, Mina C, Frenkel, Lisa M, Ndembi, Nicaise, Hamers, Raph L, Rinke de Wit, Tobias F, Wallis, Carole L, Gupta, Ravindra K, Fokam, Joseph, Zeh, Clement, Schapiro, Jonathan M, Carmona, Sergio, Katzenstein, David, Tang, Michele, Aghokeng, Avelin F, De Oliveira, Tulio, Wensing, Annemarie MJ, Gallant, Joel E, Wainberg, Mark A, Richman, Douglas D, Fitzgibbon, Joseph E, Schito, Marco, Bertagnolio, Silvia, Yang, Chunfu, and Shafer, Robert W more...

Subjects
Humans, HIV-1, HIV Infections, Ritonavir, Reverse Transcriptase Inhibitors, Protease Inhibitors, Treatment Failure, Drug Therapy, Combination, Drug Resistance, Viral, Mutation, Point-of-Care Systems, Lopinavir, Genotyping Techniques, Darunavir, Atazanavir Sulfate, Drug Therapy, Combination, Drug Resistance, Viral, General Science & Technology, MD Multidisciplinary
Abstract

The increasing prevalence of acquired and transmitted HIV-1 drug resistance is an obstacle to successful antiretroviral therapy (ART) in the low- and middle-income countries (LMICs) hardest hit by the HIV-1 pandemic. Genotypic drug resistance testing could facilitate the choice of initial ART in areas with rising transmitted drug resistance (TDR) and enable care-providers to determine which individuals with virological failure (VF) on a first- or second-line ART regimen require a change in treatment. An inexpensive near point-of-care (POC) genotypic resistance test would be useful in settings where the resources, capacity, and infrastructure to perform standard genotypic drug resistance testing are limited. Such a test would be particularly useful in conjunction with the POC HIV-1 viral load tests that are currently being introduced in LMICs. A POC genotypic resistance test is likely to involve the use of allele-specific point mutation assays for detecting drug-resistance mutations (DRMs). This study proposes that two major nucleoside reverse transcriptase inhibitor (NRTI)-associated DRMs (M184V and K65R) and four major NNRTI-associated DRMs (K103N, Y181C, G190A, and V106M) would be the most useful for POC genotypic resistance testing in LMIC settings. One or more of these six DRMs was present in 61.2% of analyzed virus sequences from ART-naïve individuals with intermediate or high-level TDR and 98.8% of analyzed virus sequences from individuals on a first-line NRTI/NNRTI-containing regimen with intermediate or high-level acquired drug resistance. The detection of one or more of these DRMs in an ART-naïve individual or in a individual with VF on a first-line NRTI/NNRTI-containing regimen may be considered an indication for a protease inhibitor (PI)-containing regimen or closer virological monitoring based on cost-effectiveness or country policy. more...

Published
2015

13. High levels of HIV drug resistance among adults failing second-line antiretroviral therapy in Namibia

Author

Jordan, Michael R., Hamunime, Ndapewa, Bikinesi, Leonard, Sawadogo, Souleymane, Agolory, Simon, Shiningavamwe, Andreas N., Negussie, Taffa, Fisher-Walker, Christa L., Raizes, Elliot G., Mutenda, Nicholus, Hunter, Christian J., Dean, Natalie, Steegen, Kim, Kana, Vibha, Carmona, Sergio, Yang, Chunfu, Tang, Alice M., Parkin, Neil, and Hong, Steven Y. more...

Published
2020
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14. Bioinformatic data processing pipelines in support of next-generation sequencing-based HIV drug resistance testing: the Winnipeg Consensus

Author

Ji, Hezhao, Enns, Eric, Brumme, Chanson J., Parkin, Neil, Howison, Mark, Lee, Emma R., Capina, Rupert, Marinier, Eric, Avila-Rios, Santiago, Sandstrom, Paul, Domselaar, Gary Van, Harrigan, Richard, Paredes, Roger, Kantor, Rami, and Noguera-Julian, Marc more...

Subjects
Drug therapy, Standards, Genetic aspects, Research, HIV infections -- Drug therapy, DNA sequencing -- Research, Drug resistance -- Genetic aspects -- Research, Medical research, Medical informatics -- Standards
Abstract

1 | INTRODUCTION Successful antiretroviral therapy (ART) suppresses HIV viral load, reduces the incidence of new infections and increases the life expectancy of infected individuals [1-5]. However, HIV drug resistance [...], Introduction: Next-generation sequencing (NGS) has several advantages over conventional Sanger sequencing for HIV drug resistance (HIVDR) genotyping, including detection and quantitation of low-abundance variants bearing drug resistance mutations (DRMs). However, the high HIV genomic diversity, unprecedented large volume of data, complexity of analysis and potential for error pose significant challenges for data processing. Several NGS analysis pipelines have been developed and used in HIVDR research; however, the absence of uniformity in data processing strategies results in lack of consistency and comparability of outputs from different pipelines. To fill this gap, an international symposium on bioinformatic strategies for NGS-based HIVDR testing was held in February 2018 in Winnipeg, Canada, convening laboratory scientists, bioinformaticians and clinicians involved in four recently developed, publicly available NGS HIVDR pipelines. The goal of this symposium was to establish a consensus on effective bioinformatic strategies for NGS data management and its use for HIVDR reporting. Discussion: Essential functionalities of an NGS HIVDR pipeline were divided into five analytic blocks: (1) NGS read quality control (QC)/quality assurance (QA); (2) NGS read alignment and reference mapping; (3) HIV variant calling and variant QC; (4) NGS HIVDR reporting; and (5) extended data applications and additional considerations for data management. The consensuses reached among the participants on all major aspects of these blocks are summarized here. They encompass not only recommended data management and analysis strategies, but also detailed bioinformatic approaches that help ensure accuracy of the derived HIVDR analysis outputs for both research and potential clinical use. Conclusions: While NGS is being adopted more broadly in HIVDR testing laboratories, data processing is often a bottleneck hindering its generalized application. The proposed standardization of NGS read QC/QA, read alignment and reference mapping, variant calling and QC, HIVDR reporting and relevant data management strategies in this "Winnipeg Consensus" may serve as a starting guideline for NGS HIVDR data processing that informs the refinement of existing pipelines and those yet to be developed. Moreover, the bioinformatic strategies presented here may apply more broadly to NGS data analysis of microbes harbouring significant genomic diversity. Keywords: next-generation sequencing; HIV drug resistance test; bioinformatics; pipeline; Winnipeg Consensus; guideline more...

Published
2018
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15. Performance comparison of next generation sequencing analysis pipelines for HIV-1 drug resistance testing

Author

Lee, Emma R., Parkin, Neil, Jennings, Cheryl, Brumme, Chanson J., Enns, Eric, Casadellà, Maria, Howison, Mark, Coetzer, Mia, Avila-Rios, Santiago, Capina, Rupert, Marinier, Eric, Van Domselaar, Gary, Noguera-Julian, Marc, Kirkby, Don, Knaggs, Jeff, Harrigan, Richard, Quiñones-Mateu, Miguel, Paredes, Roger, Kantor, Rami, Sandstrom, Paul, and Ji, Hezhao more...

Published
2020
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19. Sequence and Phenotypic Analysis for Resistance Monitoring in Hepatitis C Virus Drug Development: Recommendations From the HCV DRAG

Author

Kwong, Ann D., Najera, Isabel, Bechtel, Jill, Bowden, Scott, Fitzgibbon, Joseph, Harrington, Patrick, Kempf, Dale, Kieffer, Tara L., Koletzki, Diana, Kukolj, George, Lim, Sharlene, Pilot–Matias, Tami, Lin, Kai, Mani, Nina, Mo, Hongmei, O'Rear, Jules, Otto, Michael, Parkin, Neil, Pawlotsky, Jean–Michel, Petropoulos, Chris, Picchio, Gaston, Ralston, Robert, Reeves, Jacqueline D., Schooley, Robert T., Seiwert, Scott, Standring, David, Stuyver, Lieven, Sullivan, James, and Miller, Veronica more...

Published
2011
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26. Integrase strand transfer inhibitor (INSTI)-resistance mutations for the surveillance of transmitted HIV-1 drug resistance

Author

Tzou, Philip L, Rhee, Soo-Yon, Descamps, Diane, Clutter, Dana S, Hare, Bradley, Mor, Orna, Grude, Maxime, Parkin, Neil, Jordan, Michael R, Bertagnolio, Silvia, Schapiro, Jonathan M, Harrigan, P Richard, Geretti, Anna Maria, Marcelin, Anne-Genevieve, Shafer, Robert W, and Grp, WHO HIVResNet Working more...

Subjects
0301 basic medicine, Microbiology (medical), Genotype, Pyridones, 030106 microbiology, Human immunodeficiency virus (HIV), Integrase inhibitor, HIV Infections, HIV Integrase, Drug resistance, medicine.disease_cause, Piperazines, 03 medical and health sciences, chemistry.chemical_compound, Drug Resistance, Viral, Oxazines, Prevalence, medicine, Humans, Gene Regulatory Networks, Pharmacology (medical), HIV Integrase Inhibitors, Original Research, Pharmacology, Mutation, biology, Transmission (medicine), Virology, Integrase, Integrase strand transfer inhibitor, Phenotype, 030104 developmental biology, Infectious Diseases, chemistry, Epidemiological Monitoring, Dolutegravir, HIV-1, biology.protein, Heterocyclic Compounds, 3-Ring
Abstract

Background Integrase strand transfer inhibitors (INSTIs) are expected to be widely adopted globally, requiring surveillance of resistance emergence and transmission. Objectives We therefore sought to develop a standardized list of INSTI-resistance mutations suitable for the surveillance of transmitted INSTI resistance. Methods To characterize the suitability of the INSTI-resistance mutations for transmitted HIV-1 drug resistance (TDR) surveillance, we classified them according to their presence on published expert lists, conservation in INSTI-naive persons, frequency in INSTI-treated persons and contribution to reduced in vitro susceptibility. Mutation prevalences were determined using integrase sequences from 17302 INSTI-naive and 2450 INSTI-treated persons; 53.3% of the INSTI-naive sequences and 20.0% of INSTI-treated sequences were from non-B subtypes. Approximately 10% of sequences were from persons who received dolutegravir alone or a first-generation INSTI followed by dolutegravir. Results Fifty-nine previously recognized (or established) INSTI-resistance mutations were present on one or more of four published expert lists. They were classified into three main non-overlapping groups: 29 relatively common non-polymorphic mutations, occurring in five or more individuals and significantly selected by INSTI treatment; 8 polymorphic mutations; and 22 rare mutations. Among the 29 relatively common INSTI-selected mutations, 24 emerged as candidates for inclusion on a list of INSTI surveillance drug-resistance mutations: T66A/I/K, E92G/Q, G118R, F121Y, E138A/K/T, G140A/C/S, Y143C/H/R/S, S147G, Q148H/R/K, N155H, S230R and R263K. Conclusions A set of 24 non-polymorphic INSTI-selected mutations is likely to be useful for quantifying INSTI-associated TDR. This list may require updating as more sequences become available from INSTI-experienced persons infected with HIV-1 non-subtype B viruses and/or receiving dolutegravir. more...

Published
2019
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31. Clinical impact of pretreatment human immunodeficiency virus drug resistance in people initiating nonnucleoside reverse transcriptase inhibitor-containing antiretroviral therapy: A systematic review and meta-analysis

Author

Clinical Virology, Medische Microbiologie, MMB, Infection & Immunity, MMB opleiding Arts microbioloog, Bertagnolio, Silvia, Hermans, Lucas, Jordan, Michael R., Avila-Rios, Santiago, Iwuji, Collins, Derache, Anne, Delaporte, Eric, Wensing, Annemarie, Aves, Theresa, Borhan, A. S.M., Leenus, Alvin, Parkin, Neil, Doherty, Meg, Inzaule, Seth, Mbuagbaw, Lawrence, Clinical Virology, Medische Microbiologie, MMB, Infection & Immunity, MMB opleiding Arts microbioloog, Bertagnolio, Silvia, Hermans, Lucas, Jordan, Michael R., Avila-Rios, Santiago, Iwuji, Collins, Derache, Anne, Delaporte, Eric, Wensing, Annemarie, Aves, Theresa, Borhan, A. S.M., Leenus, Alvin, Parkin, Neil, Doherty, Meg, Inzaule, Seth, and Mbuagbaw, Lawrence more...

Published
2021

32. Assays for estimating HIV incidence: updated global market assessment and estimated economic value

Author

Morrison, Charles S., Homan, Rick, Mack, Natasha, Seepolmuang, Pairin, Averill, Megan, Taylor, Jamilah, Osborn, Jennifer, Dailey, Peter, Parkin, Neil, Ongarello, Stefano, and Mastro, Timothy D.

Subjects
Prevention, Economic aspects, Models, Cost benefit analysis, HIV infections -- Prevention, Sentinel surveillance -- Economic aspects, Public health administration -- Models, Sentinel health events -- Economic aspects, HIV infection -- Prevention
Abstract

Introduction Measures of HIV incidence are important public health indicators that describe the intensity of the HIV epidemic, are used to evaluate the impact of prevention interventions, help policymakers better [...], : Introduction: Accurate incidence estimates are needed to characterize the HIV epidemic and guide prevention efforts. HIV Incidence assays are cost?effective laboratory assays that provide incidence estimates from cross?sectional surveys. We conducted a global market assessment of HIV incidence assays under three market scenarios and estimated the economic value of improved incidence assays. Methods: We interviewed 27 stakeholders, and reviewed journal articles, working group proceedings, and manufacturers? sales figures. We determined HIV incidence assay use in 2014, and estimated use in 2015 to 2017 and in 5 to 10?years under three market scenarios, as well as the cost of conducting national and key population surveys using an HIV incidence assay with improved performance. Results: Global 2014 HIV incidence assay use was 308,900 tests, highest in Asia and mostly for case? and population?based surveillance. Estimated 2015 to 2017 use was 94,475 annually, with declines due to China and the United States discontinuing incidence assay use for domestic surveillance. Annual projected 5 to 10 year use under scenario 1 ? no change in technology ? was 94,475. For scenario 2 ? a moderately improved incidence assay ? projected annual use was 286,031. Projected annual use for scenario 3 ? game?changing technologies with an HIV incidence assay part of (a) standard confirmatory testing, and (b) standard rapid testing, were 500,000 and 180 million, respectively. As HIV incidence assay precision increases, decreased sample sizes required for incidence estimation resulted in $5 to 23 million annual reductions in survey costs and easily offset the approximately $3 million required to develop a new assay. Conclusions: Improved HIV incidence assays could substantially reduce HIV incidence estimation costs. Continued development of HIV incidence assays with improved performance is required to realize these cost benefits. more...

Published
2017
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34. A novel substrate-based HIV-1 protease inhibitor drug resistance mechanism

Author

Nijhuis, Monique, Van Maarseveen, Noortje M., Lastere, Stephane, Schipper, Pauline, Coakley, Eoin, Glass, Barbel, Rovenska, Mirka, De Jong, Dorien, Chappey, Colombe, Goedegebuure, Irma W., Heilek-Snyder, Gabrielle, Dulude, Dominic, Cammack, Nick, Brakier-Gingras, Lea, Konvalinka, Jan, Parkin, Neil, Krausslich, Hans-Georg, Brun-Vezinet, Francoise, and Boucher, Charles A.B. more...

Subjects
Care and treatment, Usage, HIV infections -- Care and treatment, Protease inhibitors -- Usage, HIV infection -- Care and treatment
Abstract

Background HIV protease inhibitor (PI) therapy results in the rapid selection of drug resistant viral variants harbouring one or two substitutions in the viral protease. To combat PI resistance development, [...] more...

Published
2007

35. Differential impact on thymidine analogue mutations of emtricitabine and lamivudine susceptibility

Author

Gerondelis, Peter, Parkin, Neil, and Ross, Lisa L.

Subjects
Thymidine -- Health aspects, Lamivudine -- Health aspects, Health
Abstract

The phenotypic impact of commonly observed nucleoside reverse transcriptase inhibitors (NRTIs) resistance-associated mutations in the absence of M1841 or V was examined using patient samples with paired susceptibility results of lamivudine (3TC) and emtricitabine (FTC) to determine if difference exists. Results reveal that 3TC and FTC might provide differential efficacy in some patient with prior NRT1 experience or in patients infected with virus harboring thymidine analogue mutations (TAMs) in the absence of M184V or I. more...

Published
2006

37. Phenotypic and genotypic HIV-1 drug resistance assays provide complementary information

Author

Parkin, Neil, Chappey, Colombe, Maroldo, Laura, Bates, Michael, Hellmann, Nicholas S., and Petropoulos, Christos J.

Subjects
Immunological research -- Analysis, Phenotype -- Physiological aspects, Genotype -- Physiological aspects, Drug resistance -- Physiological aspects, Drug resistance -- Research, HIV infection -- Prevention, HIV infection -- Care and treatment, HIV infection -- Health aspects, Health
Abstract

Research has been conducted on the HIV-1 drug resistance. The accuracy of the genotype and phenotype tests in providing HIV-1 grug resistance information has been tested and the results demonstrate that the combined use of the tests can provide additional information which is clinically-relevant. more...

Published
2002

40. Multi-Laboratory Comparison of Next-Generation to Sanger-Based Sequencing for HIV-1 Drug Resistance Genotyping

Author

Parkin, Neil T., primary, Avila-Rios, Santiago, additional, Bibby, David F., additional, Brumme, Chanson J., additional, Eshleman, Susan H., additional, Harrigan, P. Richard, additional, Howison, Mark, additional, Hunt, Gillian, additional, Ji, Hezhao, additional, Kantor, Rami, additional, Ledwaba, Johanna, additional, Lee, Emma R., additional, Matías-Florentino, Margarita, additional, Mbisa, Jean L., additional, Noguera-Julian, Marc, additional, Paredes, Roger, additional, Rivera-Amill, Vanessa, additional, Swanstrom, Ronald, additional, Zaccaro, Daniel J., additional, Zhang, Yinfeng, additional, Zhou, Shuntai, additional, and Jennings, Cheryl, additional more...

Published
2020
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45. Performance comparison of the Maxim and Sedia Limiting Antigen Avidity assays for HIV incidence surveillance

Author

Sempa, Joseph B., Welte, Alex, Busch, Michael P., Hall, Jake, Hampton, Dylan, Facente, Shelley N., Keating, Sheila M., Marson, Kara, Parkin, Neil, Pilcher, Christopher D., Murphy, Gary, Grebe, Eduard, Naniche, Denise, CEPHIA (Consortium for the Evaluation and Performance of HIV Incidence Assays), and Peters, Remco PH more...

Subjects
0301 basic medicine, RNA viruses, Epidemiology, HIV Antigens, Systems Engineering, HIV Infections, Pathology and Laboratory Medicine, Biochemistry, 0302 clinical medicine, Immunodeficiency Viruses, Medicine, Public and Occupational Health, 030212 general & internal medicine, Multidisciplinary, Incidence (epidemiology), Incidence, Biochemical markers, Hiv incidence, Limiting, Viral Load, Research Assessment, Vaccination and Immunization, humanities, Reproducibility, Infectious Diseases, HIV epidemiology, Medical Microbiology, Performance comparison, Viral Pathogens, Population Surveillance, Viruses, Marcadors bioquímics, Engineering and Technology, Female, Pathogens, Infection, Viral load, Algorithms, Research Article, General Science & Technology, Science, Immunology, Antiretroviral Therapy, Research and Analysis Methods, Microbiology, 03 medical and health sciences, Antigen, Antiviral Therapy, Virology, Retroviruses, Maxim, VIH (Virus), Humans, Avidity, Epidemics, Microbial Pathogens, Medicine and health sciences, business.industry, HIV (Viruses), Consortium for the Evaluation and Performance of HIV Incidence Assays, Lentivirus, Organisms, Biology and Life Sciences, HIV, 030112 virology, Kenya, Good Health and Well Being, Cross-Sectional Studies, HIV-1, Preventive Medicine, business, Quality Assurance, Viral Transmission and Infection, Biomarkers
Abstract

BackgroundTwo manufacturers, Maxim Biomedical and Sedia Biosciences Corporation, supply CDC-approved versions of the HIV-1 Limiting Antigen Avidity EIA (LAg) for detecting 'recent' HIV infection in cross-sectional incidence estimation. This study assesses and compares the performance of the two assays for incidence surveillance.MethodsWe ran both assays on a panel of 2,500 well-characterized HIV-1-infected specimens. We analysed concordance of assay results, assessed reproducibility using repeat testing and estimated mean durations of recent infection (MDRIs) and false-recent rates (FRRs) for a range of normalized optical density (ODn) thresholds, alone and in combination with viral load thresholds. We defined three hypothetical surveillance scenarios, similar to the Kenyan and South African epidemics, and a concentrated epidemic. These scenarios allowed us to evaluate the precision of incidence estimates obtained by means of various recent infection testing algorithms (RITAs) based on each of the two assays.ResultsThe Maxim assay produced lower ODn values than the Sedia assay on average, largely as a result of higher calibrator readings (mean OD of 0.749 vs. 0.643), with correlation of normalized readings lower (R2 = 0.908 vs. R2 = 0.938). Reproducibility on blinded control specimens was slightly better for Maxim. The MDRI of a Maxim-based algorithm at the 'standard' threshold (ODn ≤1.5 & VL >1,000) was 201 days (95% CI: 180,223) and for Sedia 171 (152,191). The difference Differences in MDRI were estimated at 32.7 (22.9,42.8) and 30.9 days (21.7,40.7) for the two algorithms, respectively. Commensurately, the Maxim algorithm had a higher FRR in treatment-naive subjects (1.7% vs. 1.1%). The two assays produced similar precision of incidence estimates in the three surveillance scenarios.ConclusionsDifferences between the assays can be primarily attributed to the calibrators supplied by the manufacturers. Performance for surveillance was extremely similar, although different thresholds were optimal (i.e. produced the lowest variance of incidence estimates) and at any given ODn threshold, different estimates of MDRI and FRR were obtained. The two assays cannot be treated as interchangeable: assay and algorithm-specific performance characteristic estimates must be used for survey planning and incidence estimation. more...

Published
2019

47. An RNA pseudoknot and an optimal heptameric shift site are required for highlyefficient ribosomal frameshifting on a retroviral messenger RNA

Author

Chamorro, Mario, Parkin, Neil, and Varmus, HaroldE.

Subjects
Messenger RNA -- Genetic aspects, Genetic translation -- Research, Mutation (Biology) -- Research, Science and technology
Abstract

Site-directed mutations were employed on two base-paired stems of a mouse mammary tumor virus (MMTV) RNA pseudoknot which is important for gagpro ribosomal frameshifting. The mutation products supported the predicted structure and showed the resulting impairment of frameshifting upon the loss ofeither of the two based-paired stems of MMTV. The results also indicated the critical role of the host tRNA on frameshifting efficiency. more...

Published
1992

48. Global and regional molecular epidemiology of HIV-1, 1990–2015: a systematic review, global survey, and trend analysis

Author

Hemelaar, Joris, Elangovan, Ramyiadarsini, Yun, Jason, Dickson-Tetteh, Leslie, Fleminger, Isabella, Kirtley, Shona, Williams, Brian, Gouws-Williams, Eleanor, Ghys, Peter D, Abimiku, Alash'le G, Agwale, Simon, Archibald, Chris, Avidor, Boaz, Barbás, María Gabriela, Barre-Sinoussi, Francoise, Barugahare, Banson, Belabbes, El Hadj, Bertagnolio, Silvia, Birx, Deborah, Bobkov, Aleksei F, Brandful, James, Bredell, Helba, Brennan, Catherine A, Brooks, James, Bruckova, Marie, Buonaguro, Luigi, Buonaguro, Franco, Buttò, Stefano, Buve, Anne, Campbell, Mary, Carr, Jean, Carrera, Alex, Carrillo, Manuel Gómez, Celum, Connie, Chaplin, Beth, Charles, Macarthur, Chatzidimitriou, Dimitrios, Chen, Zhiwei, Chijiwa, Katsumi, Cooper, David, Cunningham, Philip, Dagnra, Anoumou, de Gascun, Cillian F, Del Amo, Julia, Delgado, Elena, Dietrich, Ursula, Dwyer, Dominic, Ellenberger, Dennis, Ensoli, Barbara, Essex, Max, Gao, Feng, Fleury, Herve, Fonjungo, Peter N, Foulongne, Vincent, Gadkari, Deepak A, García, Federico, Garsia, Roger, Gershy-Damet, Guy Michel, Glynn, Judith R, Goodall, Ruth, Grossman, Zehava, Lindenmeyer-Guimarães, Monick, Hahn, Beatrice, Hamers, Raph L, Hamouda, Osamah, Handema, Ray, He, Xiang, Herbeck, Joshua, Ho, David D, Holguin, Africa, Hosseinipour, Mina, Hunt, Gillian, Ito, Masahiko, Bel Hadj Kacem, Mohamed Ali, Kahle, Erin, Kaleebu, Pontiano Kaleebu, Kalish, Marcia, Kamarulzaman, Adeeba, Kang, Chun, Kanki, Phyllis, Karamov, Edward, Karasi, Jean-Claude, Kayitenkore, Kayitesi, Kelleher, Tony, Kitayaporn, Dwip, Kostrikis, Leondios G, Kucherer, Claudia, Lara, Claudia, Leitner, Thomas, Liitsola, Kirsi, Lingappa, Jai, Linka, Marek, Lorenzana de Rivera, Ivette, Lukashov, Vladimir, Maayan, Shlomo, Mayr, Luzia, McCutchan, Francine, Meda, Nicolas, Menu, Elisabeth, Mhalu, Fred, Mloka, Doreen, Mokili, John L, Montes, Brigitte, Mor, Orna, Morgado, Mariza, Mosha, Fausta, Moussi, Awatef, Mullins, James, Najera, Rafael, Nasr, Mejda, Ndembi, Nicaise, Neilson, Joel R, Nerurkar, Vivek R, Neuhann, Florian, Nolte, Claudine, Novitsky, Vlad, Nyambi, Philippe, Ofner, Marianna, Paladin, Fem J, Papa, Anna, Pape, Jean, Parkin, Neil, Parry, Chris, Peeters, Martine, Pelletier, Alexandra, Pérez-Álvarez, Lucía, Pillay, Deenan, Pinto, Angie, Quang, Trinh Duy, Rademeyer, Cecilia, Raikanikoda, Filimone, Rayfield, Mark A, Reynes, Jean-Marc, Rinke de Wit, Tobias, Robbins, Kenneth E, Rolland, Morgane, Rousseau, Christine, Salazar-Gonzales, Jesus, Salem, Hanan, Salminen, Mika, Salomon, Horacio, Sandstrom, Paul, Santiago, Mario L, Sarr, Abdoulaye D, Schroeder, Bryan, Segondy, Michel, Selhorst, Philippe, Sempala, Sylvester, Servais, Jean, Shaik, Ansari, Shao, Yiming, Slim, Amine, Soares, Marcelo A, Songok, Elijah, Stewart, Debbie, Stokes, Julie, Subbarao, Shambavi, Sutthent, Ruengpung, Takehisa, Jun, Tanuri, Amilcar, Tee, Kok Keng, Thapa, Kiran, Thomson, Michael, Tran, Tyna, Urassa, Willy, Ushijima, Hiroshi, van de Perre, Philippe, van der Groen, Guido, van Laethem, Kristel, van Oosterhout, Joep, van Sighem, Ard, van Wijngaerden, Eric, Vandamme, Anne-Mieke, Vercauteren, Jurgen, Vidal, Nicole, Wallace, Lesley, Williamson, Carolyn, Wolday, Dawit, Xu, Jianqing, Yang, Chunfu, Zhang, Linqi, Zhang, Rong, John Radcliffe Hospital [Oxford University Hospital], Centre for Statistics in Medicine, University of Oxford [Oxford], Stellenbosch University, UNAIDS [Genève, Suisse] (ONUSIDA), Institut Pasteur [Paris], Noguchi Memorial Institute for Medical Research [Accra, Ghana] (NMIMR), University of Ghana, Institute of Tropical Medicine [Antwerp] (ITM), State Key Laboratory of Silkworm Genome Biology, Southwest University, Commissariat à l'énergie atomique et aux énergies alternatives - Laboratoire d'Electronique et de Technologie de l'Information (CEA-LETI), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Georg-Speyer-Haus, The University of Sydney, National AIDS Centre, Istituto Superiore di Sanita [Rome], Harvard School of Public Health, Digital Enterprise Research Institute (DERI-NUIG), National University of Ireland [Galway] (NUI Galway), Microbiologie cellulaire et moléculaire et pathogénicité (MCMP), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Virologie, Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Pathogénèse et contrôle des infections chroniques (PCCI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre Hospitalier Universitaire de Montpellier (CHU Montpellier ), Departments of Medicine and Microbiology, University of Alabama at Birmingham [ Birmingham] (UAB), Robert Koch Institute [Berlin] (RKI), Beihang University (BUAA), Statens Serum Institut [Copenhagen], Immuno-Rhumatologie Moléculaire, Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), SANTE/SIDA [Bobo-Dioulasso, Burkina Faso], Institut de Recherche en Sciences de la Santé (IRSS) / Centre Muraz, Department of Microbiology, University of Washington School of Medicine, Department of Microbiology, Medical School, University of Thessaly [Volos] (UTH), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Africa Centre for Health and Population Studies, University of KwaZulu-Natal (UKZN)-Medical Research Council of South Africa, Lab-STICC_UBO_CID_IHSEV, Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS), State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Laboratory of Virology, CHU Rouen, Normandie Université (NU)-Normandie Université (NU), Universidade Federal do Rio de Janeiro (UFRJ), Departements of Medicine and Microbiology, University of Alabama [Tuscaloosa] (UA), Stichting HIV Monitoring [Amsterdam], Universiteit van Amsterdam (UvA), Département Génétique Internal Médecine, Hôpital Universitaire Leuven, Department of Chemical and Biomolecular Engineering [Baltimore], Johns Hopkins University (JHU), Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, China Academy of Chinese Medical Sciences, Chatzidimitriou, Dimitrios [0000-0001-9656-5898], University of Oxford, Institut Pasteur [Paris] (IP), Istituto Superiore di Sanità (ISS), Microbiologie Fondamentale et Pathogénicité (MFP), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), University of KwaZulu-Natal [Durban, Afrique du Sud] (UKZN)-Medical Research Council of South Africa, Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS), UNAIDS, Noguchi Memorial Institute for Medical Research, University of Ghana, Laboratoire d'Electronique et des Technologies de l'Information (CEA-LETI), Université Grenoble Alpes (UGA)-Direction de Recherche Technologique (CEA) (DRT (CEA)), Beihang University, Recherches Translationnelles sur le VIH et les maladies infectieuses (TransVIHMI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 1 (UM1)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Universtié Yaoundé 1 [Cameroun]-Université de Montpellier (UM), Universidade Federal do Rio de Janeiro [Rio de Janeiro] (UFRJ), Nuffield Department of Women's and Reproductive Health (NDWRH), University of Oxford- John Radcliffe Hospital [Oxford University Hospital], South African Centre for Epidemiological Modelling and Analysis, JH is supported by the Oxford University Clinical Academic Graduate School (Oxford, UK) and Linacre College, Oxford University (Oxford, UK)., WHO–UNAIDS Network for HIV Isolation Characterisation : Alash'le G Abimiku, Simon Agwale, Chris Archibald, Boaz Avidor, María Gabriela Barbás, Francoise Barre-Sinoussi, Banson Barugahare, El Hadj Belabbes, Silvia Bertagnolio, Deborah Birx, Aleksei F Bobkov, James Brandful, Helba Bredell, Catherine A Brennan, James Brooks, Marie Bruckova, Luigi Buonaguro, Franco Buonaguro, Stefano Buttò, Anne Buve, Mary Campbell, Jean Carr, Alex Carrera, Manuel Gómez Carrillo, Connie Celum, Beth Chaplin, Macarthur Charles, Dimitrios Chatzidimitriou, Zhiwei Chen, Katsumi Chijiwa, David Cooper, Philip Cunningham, Anoumou Dagnra, Cillian F de Gascun, Julia Del Amo, Elena Delgado, Ursula Dietrich, Dominic Dwyer, Dennis Ellenberger, Barbara Ensoli, Max Essex, Feng Gao, Herve Fleury, Peter N Fonjungo, Vincent Foulongne, Deepak A Gadkari, Federico García, Roger Garsia, Guy Michel Gershy-Damet, Judith R Glynn, Ruth Goodall, Zehava Grossman, Monick Lindenmeyer-Guimarães, Beatrice Hahn, Raph L Hamers, Osamah Hamouda, Ray Handema, Xiang He, Joshua Herbeck, David D Ho, Africa Holguin, Mina Hosseinipour, Gillian Hunt, Masahiko Ito, Mohamed Ali Bel Hadj Kacem, Erin Kahle, Pontiano Kaleebu Kaleebu, Marcia Kalish, Adeeba Kamarulzaman, Chun Kang, Phyllis Kanki, Edward Karamov, Jean-Claude Karasi, Kayitesi Kayitenkore, Tony Kelleher, Dwip Kitayaporn, Leondios G Kostrikis, Claudia Kucherer, Claudia Lara, Thomas Leitner, Kirsi Liitsola, Jai Lingappa, Marek Linka, Ivette Lorenzana de Rivera, Vladimir Lukashov, Shlomo Maayan, Luzia Mayr, Francine McCutchan, Nicolas Meda, Elisabeth Menu, Fred Mhalu, Doreen Mloka, John L Mokili, Brigitte Montes, Orna Mor, Mariza Morgado, Fausta Mosha, Awatef Moussi, James Mullins, Rafael Najera, Mejda Nasr, Nicaise Ndembi, Joel R Neilson, Vivek R Nerurkar, Florian Neuhann, Claudine Nolte, Vlad Novitsky, Philippe Nyambi, Marianna Ofner, Fem J Paladin, Anna Papa, Jean Pape, Neil Parkin, Chris Parry, Martine Peeters, Alexandra Pelletier, Lucía Pérez-Álvarez, Deenan Pillay, Angie Pinto, Trinh Duy Quang, Cecilia Rademeyer, Filimone Raikanikoda, Mark A Rayfield, Jean-Marc Reynes, Tobias Rinke de Wit, Kenneth E Robbins, Morgane Rolland, Christine Rousseau, Jesus Salazar-Gonzales, Hanan Salem, Mika Salminen, Horacio Salomon, Paul Sandstrom, Mario L Santiago, Abdoulaye D Sarr, Bryan Schroeder, Michel Segondy, Philippe Selhorst, Sylvester Sempala, Jean Servais, Ansari Shaik, Yiming Shao, Amine Slim, Marcelo A Soares, Elijah Songok, Debbie Stewart, Julie Stokes, Shambavi Subbarao, Ruengpung Sutthent, Jun Takehisa, Amilcar Tanuri, Kok Keng Tee, Kiran Thapa, Michael Thomson, Tyna Tran, Willy Urassa, Hiroshi Ushijima, Philippevan de Perre, Guidovan der Groen, Kristel van Laethem, Joep van Oosterhout, Ard van Sighem, Eric van Wijngaerden, Anne-Mieke Vandamme, Jurgen Vercauteren, Nicole Vidal, Lesley Wallace, Carolyn Williamson, Dawit Wolday, Jianqing Xu, Chunfu Yang, Linqi Zhang, and Rong Zhang more...

Subjects
0301 basic medicine, Serotype, Genotype, Genotyping Techniques, 030106 microbiology, DIVERSITY, MULTICENTER, VACCINE, HIV Infections, Genome, Viral, Biology, Global Health, Serogroup, SUBTYPES, 03 medical and health sciences, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Surveys and Questionnaires, INFECTION, Genetic variation, Global health, Humans, HIV vaccine, Serotyping, AIDS Vaccines, Science & Technology, Molecular epidemiology, Genetic Variation, Subtyping, 3. Good health, Trend analysis, 030104 developmental biology, Infectious Diseases, 13. Climate action, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, HIV-1, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Life Sciences & Biomedicine, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Demography
Abstract

BACKGROUND: Global genetic diversity of HIV-1 is a major challenge to the development of HIV vaccines. We aimed to estimate the regional and global distribution of HIV-1 subtypes and recombinants during 1990-2015. METHODS: We searched PubMed, EMBASE (Ovid), CINAHL (Ebscohost), and Global Health (Ovid) for HIV-1 subtyping studies published between Jan 1, 1990, and Dec 31, 2015. We collected additional unpublished HIV-1 subtyping data through a global survey. We included prevalence studies with HIV-1 subtyping data collected during 1990-2015. We grouped countries into 14 regions and analysed data for four time periods (1990-99, 2000-04, 2005-09, and 2010-15). The distribution of HIV-1 subtypes, circulating recombinant forms (CRFs), and unique recombinant forms (URFs) in individual countries was weighted according to the UNAIDS estimates of the number of people living with HIV (PLHIV) in each country to generate regional and global estimates of HIV-1 diversity in each time period. The primary outcome was the number of samples designated as HIV-1 subtypes A, B, C, D, F, G, H, J, K, CRFs, and URFs. The systematic review is registered with PROSPERO, number CRD42017067164. FINDINGS: This systematic review and global survey yielded 2203 datasets with 383 519 samples from 116 countries in 1990-2015. Globally, subtype C accounted for 46·6% (16 280 897/34 921 639 of PLHIV) of all HIV-1 infections in 2010-15. Subtype B was responsible for 12·1% (4 235 299/34 921 639) of infections, followed by subtype A (10·3%; 3 587 003/34 921 639), CRF02_AG (7·7%; 2 705 110/34 921 639), CRF01_AE (5·3%; 1 840 982/34 921 639), subtype G (4·6%; 1 591 276/34 921 639), and subtype D (2·7%; 926 255/34 921 639). Subtypes F, H, J, and K combined accounted for 0·9% (311 332/34 921 639) of infections. Other CRFs accounted for 3·7% (1 309 082/34 921 639), bringing the proportion of all CRFs to 16·7% (5 844 113/34 921 639). URFs constituted 6·1% (2 134 405/34 921 639), resulting in recombinants accounting for 22·8% (7 978 517/34 921 639) of all global HIV-1 infections. The distribution of HIV-1 subtypes and recombinants changed over time in countries, regions, and globally. At a global level during 2005-15, subtype B increased, subtypes A and D were stable, and subtypes C and G and CRF02_AG decreased. CRF01_AE, other CRFs, and URFs increased, leading to a consistent increase in the global proportion of recombinants over time. INTERPRETATION: Global and regional HIV diversity is complex and evolving, and is a major challenge to HIV vaccine development. Surveillance of the global molecular epidemiology of HIV-1 remains crucial for the design, testing, and implementation of HIV vaccines. FUNDING: None. ispartof: LANCET INFECTIOUS DISEASES vol:19 issue:2 pages:143-155 ispartof: location:United States status: published more...

Published
2018
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49. A Case of Recent Infection with a Multi-Drug-Resistant and Dual-Tropic HIV-1 in Association with Rapid Progression to AIDS (Poster#973B)

Author

Markowitz, Martin | Mohri, Hiroshi | Mehandru, Saurabh | Shet, Anita | Berry, Leslie | Kalyanaraman, Roopa | Kim, Alexandria | Chung, Chris | Jean-Pierre, Patrick | Horowitz, Amir | La Mar, Melissa | Wrin, Terri | Parkin, Neil | Poles, Michael | Petropoulos, Christos | Mullen, Michael | Boden, Daniel | Ho, David D. 1952, Markowitz, Martin | Mohri, Hiroshi | Mehandru, Saurabh | Shet, Anita | Berry, Leslie | Kalyanaraman, Roopa | Kim, Alexandria | Chung, Chris | Jean-Pierre, Patrick | Horowitz, Amir | La Mar, Melissa | Wrin, Terri | Parkin, Neil | Poles, Michael | Petropoulos, Christos | Mullen, Michael | Boden, Daniel | Ho, David D. 1952, Markowitz, Martin | Mohri, Hiroshi | Mehandru, Saurabh | Shet, Anita | Berry, Leslie | Kalyanaraman, Roopa | Kim, Alexandria | Chung, Chris | Jean-Pierre, Patrick | Horowitz, Amir | La Mar, Melissa | Wrin, Terri | Parkin, Neil | Poles, Michael | Petropoulos, Christos | Mullen, Michael | Boden, Daniel | Ho, David D. 1952, and Markowitz, Martin | Mohri, Hiroshi | Mehandru, Saurabh | Shet, Anita | Berry, Leslie | Kalyanaraman, Roopa | Kim, Alexandria | Chung, Chris | Jean-Pierre, Patrick | Horowitz, Amir | La Mar, Melissa | Wrin, Terri | Parkin, Neil | Poles, Michael | Petropoulos, Christos | Mullen, Michael | Boden, Daniel | Ho, David D. 1952 more...

Abstract

(DLPS) 5571095.0187.082, http://name.umdl.umich.edu/5571095.0187.082, http://quod.lib.umich.edu/t/text/accesspolicy.html, Where applicable, subject to copyright. Other restrictions on distribution may apply. Please go to http://www.umdl.umich.edu/ for more information. more...

Published
2005

50. Hepatitis C Genotype 4R Resistance-Associated Polymorphisms : The Achilles Heel of the Nonstructural 5A Inhibitors? Reply

Author

Miller, Veronica, Harrington, Patrick, Howe, Anita, Kieffer, Tara, Lennerstrand, Johan, Lenz, Oliver, Lontok, Erik, McPhee, Fiona, Mo, Hongmei, Parkin, Neil, Pilot-Matias, Tami, Miller, Veronica, Harrington, Patrick, Howe, Anita, Kieffer, Tara, Lennerstrand, Johan, Lenz, Oliver, Lontok, Erik, McPhee, Fiona, Mo, Hongmei, Parkin, Neil, and Pilot-Matias, Tami more...

Published
2016
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