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Ng TTL, Su J, Lao HY, Lui WW, Chan CTM, Leung AWS, Jim SHC, Lee LK, Shehzad S, Tam KKG, Leung KSS, Tang F, Yam WC, Luo R, Siu GKH. Long-Read Sequencing with Hierarchical Clustering for Antiretroviral Resistance Profiling of Mixed Human Immunodeficiency Virus Quasispecies. Clin Chem 2023; 69:1174-1185. [PMID: 37537871 DOI: 10.1093/clinchem/hvad108] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/28/2023] [Indexed: 08/05/2023]
Abstract
BACKGROUND HIV infections often develop drug resistance mutations (DRMs), which can increase the risk of virological failure. However, it has been difficult to determine if minor mutations occur in the same genome or in different virions using Sanger sequencing and short-read sequencing methods. Oxford Nanopore Technologies (ONT) sequencing may improve antiretroviral resistance profiling by allowing for long-read clustering. METHODS A new ONT sequencing-based method for profiling DRMs in HIV quasispecies was developed and validated. The method used hierarchical clustering of long amplicons that cover regions associated with different types of antiretroviral drugs. A gradient series of an HIV plasmid and 2 plasma samples was prepared to validate the clustering performance. The ONT results were compared to those obtained with Sanger sequencing and Illumina sequencing in 77 HIV-positive plasma samples to evaluate the diagnostic performance. RESULTS In the validation study, the abundance of detected quasispecies was concordant with the predicted result with the R2 of > 0.99. During the diagnostic evaluation, 59/77 samples were successfully sequenced for DRMs. Among 18 failed samples, 17 were below the limit of detection of 303.9 copies/μL. Based on the receiver operating characteristic analysis, the ONT workflow achieved an F1 score of 0.96 with a cutoff of 0.4 variant allele frequency. Four cases were found to have quasispecies with DRMs, in which 2 harbored quasispecies with more than one class of DRMs. Treatment modifications were recommended for these cases. CONCLUSIONS Long-read sequencing coupled with hierarchical clustering could differentiate the quasispecies resistance profiles in HIV-infected samples, providing a clearer picture for medical care.
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Affiliation(s)
- Timothy Ting-Leung Ng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Junhao Su
- Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Hiu-Yin Lao
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Wui-Wang Lui
- Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Chloe Toi-Mei Chan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Amy Wing-Sze Leung
- Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Stephanie Hoi-Ching Jim
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Lam-Kwong Lee
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Sheeba Shehzad
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Kingsley King-Gee Tam
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Kenneth Siu-Sing Leung
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Forrest Tang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Wing-Cheong Yam
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Ruibang Luo
- Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
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Kemp SA, Charles OJ, Derache A, Smidt W, Martin DP, Iwuji C, Adamson J, Govender K, de Oliveira T, Dabis F, Pillay D, Goldstein RA, Gupta RK. HIV-1 Evolutionary Dynamics under Nonsuppressive Antiretroviral Therapy. mBio 2022; 13:e0026922. [PMID: 35446121 PMCID: PMC9239331 DOI: 10.1128/mbio.00269-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/28/2022] [Indexed: 12/19/2022] Open
Abstract
Prolonged virologic failure on 2nd-line protease inhibitor (PI)-based antiretroviral therapy (ART) without emergence of major protease mutations is well recognized and provides an opportunity to study within-host evolution in long-term viremic individuals. Using next-generation sequencing and in silico haplotype reconstruction, we analyzed whole-genome sequences from longitudinal plasma samples of eight chronically infected HIV-1-positive individuals failing 2nd-line regimens from the French National Agency for AIDS and Viral Hepatitis Research (ANRS) 12249 Treatment as Prevention (TasP) trial. On nonsuppressive ART, there were large fluctuations in synonymous and nonsynonymous variant frequencies despite stable viremia. Reconstructed haplotypes provided evidence for selective sweeps during periods of partial adherence, and viral haplotype competition, during periods of low drug exposure. Drug resistance mutations in reverse transcriptase (RT) were used as markers of viral haplotypes in the reservoir, and their distribution over time indicated recombination. We independently observed linkage disequilibrium decay, indicative of recombination. These data highlight dramatic changes in virus population structure that occur during stable viremia under nonsuppressive ART. IMPORTANCE HIV-1 infections are most commonly initiated with a single founder virus and are characterized by extensive inter- and intraparticipant genetic diversity. However, existing literature on HIV-1 intrahost population dynamics is largely limited to untreated infections, predominantly in subtype B-infected individuals. The manuscript characterizes viral population dynamics in long-term viremic treatment-experienced individuals, which has not been previously characterized. These data are particularly relevant for understanding HIV dynamics but can also be applied to other RNA viruses. With this unique data set we propose that the virus is highly unstable, and we have found compelling evidence of HIV-1 within-host viral diversification, recombination, and haplotype competition during nonsuppressive ART.
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Affiliation(s)
- Steven A. Kemp
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, United Kingdom
| | - Oscar J. Charles
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Anne Derache
- Africa Health Research Institute, Durban, South Africa
| | - Werner Smidt
- Africa Health Research Institute, Durban, South Africa
| | - Darren P. Martin
- Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Collins Iwuji
- Africa Health Research Institute, Durban, South Africa
- Research Department of Infection and Population Health, University College London, United Kingdom
| | - John Adamson
- Africa Health Research Institute, Durban, South Africa
| | | | - Tulio de Oliveira
- Africa Health Research Institute, Durban, South Africa
- KRISP - KwaZulu-Natal Research and Innovation Sequencing Platform, UKZN, Durban, South Africa
| | - Francois Dabis
- INSERM U1219-Centre Inserm Bordeaux Population Health, Université de Bordeaux, France
- Université de Bordeaux, ISPED, Centre INSERM U1219-Bordeaux Population Health, France
| | - Deenan Pillay
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Richard A. Goldstein
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Ravindra K. Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, United Kingdom
- Africa Health Research Institute, Durban, South Africa
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Nduva GM, Otieno F, Kimani J, McKinnon LR, Cholette F, Sandstrom P, Graham SM, Price MA, Smith AD, Bailey RC, Hassan AS, Esbjörnsson J, Sanders EJ. Phylogeographic Assessment Reveals Geographic Sources of HIV-1 Dissemination Among Men Who Have Sex With Men in Kenya. Front Microbiol 2022; 13:843330. [PMID: 35356525 PMCID: PMC8959701 DOI: 10.3389/fmicb.2022.843330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 01/19/2022] [Indexed: 12/14/2022] Open
Abstract
HIV-1 transmission dynamics involving men who have sex with men (MSM) in Africa are not well understood. We investigated the rates of HIV-1 transmission between MSM across three regions in Kenya: Coast, Nairobi, and Nyanza. We analyzed 372 HIV-1 partial pol sequences sampled during 2006-2019 from MSM in Coast (N = 178, 47.9%), Nairobi (N = 137, 36.8%), and Nyanza (N = 57, 15.3%) provinces in Kenya. Maximum-likelihood (ML) phylogenetics and Bayesian inference were used to determine HIV-1 clusters, evolutionary dynamics, and virus migration rates between geographic regions. HIV-1 sub-subtype A1 (72.0%) was most common followed by subtype D (11.0%), unique recombinant forms (8.9%), subtype C (5.9%), CRF 21A2D (0.8%), subtype G (0.8%), CRF 16A2D (0.3%), and subtype B (0.3%). Forty-six clusters (size range 2-20 sequences) were found-half (50.0%) of which had evidence of extensive HIV-1 mixing among different provinces. Data revealed an exponential increase in infections among MSM during the early-to-mid 2000s and stable or decreasing transmission dynamics in recent years (2017-2019). Phylogeographic inference showed significant (Bayes factor, BF > 3) HIV-1 dissemination from Coast to Nairobi and Nyanza provinces, and from Nairobi to Nyanza province. Strengthening HIV-1 prevention programs to MSM in geographic locations with higher HIV-1 prevalence among MSM (such as Coast and Nairobi) may reduce HIV-1 incidence among MSM in Kenya.
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Affiliation(s)
- George M. Nduva
- Department of Translational Medicine, Lund University, Lund, Sweden
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Joshua Kimani
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Lyle R. McKinnon
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Francois Cholette
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- National Microbiology Laboratory at the JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Paul Sandstrom
- National Microbiology Laboratory at the JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Susan M. Graham
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Epidemiology, University of Washington, Seattle, WA, United States
| | - Matt A. Price
- IAVI, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
| | - Adrian D. Smith
- Nuffield Department of Medicine, The University of Oxford, Oxford, United Kingdom
| | - Robert C. Bailey
- Nyanza Reproductive Health Society, Kisumu, Kenya
- Division of Epidemiology and Biostatistics, University of Illinois Chicago, Chicago, IL, United States
| | - Amin S. Hassan
- Department of Translational Medicine, Lund University, Lund, Sweden
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, Lund, Sweden
- Nuffield Department of Medicine, The University of Oxford, Oxford, United Kingdom
| | - Eduard J. Sanders
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, The University of Oxford, Oxford, United Kingdom
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4
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Nduva GM, Otieno F, Kimani J, Wahome E, McKinnon LR, Cholette F, Majiwa M, Masika M, Mutua G, Anzala O, Graham SM, Gelmon L, Price MA, Smith AD, Bailey RC, Baele G, Lemey P, Hassan AS, Sanders EJ, Esbjörnsson J. Quantifying rates of HIV-1 flow between risk groups and geographic locations in Kenya: A country-wide phylogenetic study. Virus Evol 2022; 8:veac016. [PMID: 35356640 PMCID: PMC8962731 DOI: 10.1093/ve/veac016] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/23/2022] [Accepted: 03/01/2022] [Indexed: 12/14/2022] Open
Abstract
In Kenya, HIV-1 key populations including men having sex with men (MSM), people who inject drugs (PWID) and female sex workers (FSW) are thought to significantly contribute to HIV-1 transmission in the wider, mostly heterosexual (HET) HIV-1 transmission network. However, clear data on HIV-1 transmission dynamics within and between these groups are limited. We aimed to empirically quantify rates of HIV-1 flow between key populations and the HET population, as well as between different geographic regions to determine HIV-1 'hotspots' and their contribution to HIV-1 transmission in Kenya. We used maximum-likelihood phylogenetic and Bayesian inference to analyse 4058 HIV-1 pol sequences (representing 0.3 per cent of the epidemic in Kenya) sampled 1986-2019 from individuals of different risk groups and regions in Kenya. We found 89 per cent within-risk group transmission and 11 per cent mixing between risk groups, cyclic HIV-1 exchange between adjoining geographic provinces and strong evidence of HIV-1 dissemination from (i) West-to-East (i.e. higher-to-lower HIV-1 prevalence regions), and (ii) heterosexual-to-key populations. Low HIV-1 prevalence regions and key populations are sinks rather than major sources of HIV-1 transmission in Kenya. Targeting key populations in Kenya needs to occur concurrently with strengthening interventions in the general epidemic.
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Affiliation(s)
- George M Nduva
- Department of Translational Medicine, Lund University, Faculty of Medicine, Lund University, Box 117 SE-221 00 Lund, Sweden
- Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya
| | - Frederick Otieno
- Nyanza Reproductive Health Society, United Mall, P.O. Box 1764, Kisumu, Kenya
| | - Joshua Kimani
- Department of Medical Microbiology, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, University of Manitoba (Bannatyne campus), Winnipeg MB R3E 0J9, Canada
| | - Elizabeth Wahome
- Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya
| | - Lyle R McKinnon
- Department of Medical Microbiology, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, University of Manitoba (Bannatyne campus), Winnipeg MB R3E 0J9, Canada
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Private Bag X7, Congella 4013, South Africa
| | - Francois Cholette
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, University of Manitoba (Bannatyne campus), Winnipeg MB R3E 0J9, Canada
- National Microbiology Laboratory at the JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, 745 Logan Avenue, Winnipeg, Canada
| | - Maxwell Majiwa
- Kenya Medical Research Institute/Center for Global Health Research, KEMRI-CGHR, P.O. Box 20778-00202, Kisumu, Kenya
| | - Moses Masika
- Faculty of Health Sciences 3RD Floor Wing B, KAVI Institute of Clinical Research, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
| | - Gaudensia Mutua
- Faculty of Health Sciences 3RD Floor Wing B, KAVI Institute of Clinical Research, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
| | - Omu Anzala
- Faculty of Health Sciences 3RD Floor Wing B, KAVI Institute of Clinical Research, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
| | - Susan M Graham
- Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya
- Department of Epidemiology, University of Washington, Office of the Chair, UW Box # 351619, Seattle, DC, USA
| | - Larry Gelmon
- Department of Medical Microbiology, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, University of Manitoba (Bannatyne campus), Winnipeg MB R3E 0J9, Canada
| | - Matt A Price
- IAVI Global Headquarters, 125 Broad Street, 9th Floor, New York, NY 10004, USA
- Department of Epidemiology and Biostatistics, University of California, Mission Hall: Global Health & Clinical Sciences Building, 550 16th Street, 2nd Floor, San Francisco, CA 94158-2549, USA
| | - Adrian D Smith
- Nuffield Department of Medicine, The University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK
| | - Robert C Bailey
- Nyanza Reproductive Health Society, United Mall, P.O. Box 1764, Kisumu, Kenya
- Division of Epidemiology and Biostatistics, University of Illinois at Chicago, 1603 W Taylor St, Chicago, IL 60612, USA
| | - Guy Baele
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Evolutionary and Computational Virology, Rega-Herestraat 49-box 1040, Leuven 3000, Belgium
| | - Philippe Lemey
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Evolutionary and Computational Virology, Rega-Herestraat 49-box 1040, Leuven 3000, Belgium
| | - Amin S Hassan
- Department of Translational Medicine, Lund University, Faculty of Medicine, Lund University, Box 117 SE-221 00 Lund, Sweden
- Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya
| | - Eduard J Sanders
- Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya
- Nuffield Department of Medicine, The University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, Faculty of Medicine, Lund University, Box 117 SE-221 00 Lund, Sweden
- Nuffield Department of Medicine, The University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK
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Global Variability of V3 Loop Tetrapeptide Motif: a Concern for HIV-1 Neutralizing Antibodies-based Vaccine Design and Antiretroviral Therapy. JOURNAL OF MEDICAL MICROBIOLOGY AND INFECTIOUS DISEASES 2021. [DOI: 10.52547/jommid.9.3.108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Takayanagi T. Presence of long-term stable quasispecies of human immunodeficiency virus type 1 inferred using a quasi-steady-state multiscale model. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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7
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The Evolution of Dendritic Cell Immunotherapy against HIV-1 Infection: Improvements and Outlook. J Immunol Res 2020; 2020:9470102. [PMID: 32537473 PMCID: PMC7267878 DOI: 10.1155/2020/9470102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 04/28/2020] [Indexed: 12/18/2022] Open
Abstract
Dendritic cells (DC) are key phagocytic cells that play crucial roles in both the innate and adaptive immune responses against the human immunodeficiency virus type 1 (HIV-1). By processing and presenting pathogen-derived antigens, dendritic cells initiate a directed response against infected cells. They activate the adaptive immune system upon recognition of pathogen-associated molecular patterns (PAMPs) on infected cells. During the course of HIV-1 infection, a successful adaptive (cytotoxic CD8+ T-cell) response is necessary for preventing the progression and spread of infection in a variety of cells. Dendritic cells have thus been recognized as a valuable tool in the development of immunotherapeutic approaches and vaccines effective against HIV-1. The advancements in dendritic cell vaccines in cancers have paved the way for applications of this form of immunotherapy to HIV-1 infection. Clinical trials with patients infected with HIV-1 who are well-suppressed by antiretroviral therapy (ART) were recently performed to assess the efficacy of DC vaccines, with the goal of mounting an HIV-1 antigen-specific T-cell response, ideally to clear infection and eliminate the need for long-term ART. This review summarizes and compares methods and efficacies of a number of DC vaccine trials utilizing autologous dendritic cells loaded with HIV-1 antigens. The potential for advancement and novel strategies of improving efficacy of this type of immunotherapy is also discussed.
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8
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Nduva GM, Hassan AS, Nazziwa J, Graham SM, Esbjörnsson J, Sanders EJ. HIV-1 Transmission Patterns Within and Between Risk Groups in Coastal Kenya. Sci Rep 2020; 10:6775. [PMID: 32317722 PMCID: PMC7174422 DOI: 10.1038/s41598-020-63731-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/30/2020] [Indexed: 11/09/2022] Open
Abstract
HIV-1 transmission patterns within and between populations at different risk of HIV-1 acquisition in Kenya are not well understood. We investigated HIV-1 transmission networks in men who have sex with men (MSM), injecting drug users (IDU), female sex workers (FSW) and heterosexuals (HET) in coastal Kenya. We used maximum-likelihood and Bayesian phylogenetics to analyse new (N = 163) and previously published (N = 495) HIV-1 polymerase sequences collected during 2005-2019. Of the 658 sequences, 131 (20%) were from MSM, 58 (9%) IDU, 109 (17%) FSW, and 360 (55%) HET. Overall, 206 (31%) sequences formed 61 clusters. Most clusters (85%) consisted of sequences from the same risk group, suggesting frequent within-group transmission. The remaining clusters were mixed between HET/MSM (7%), HET/FSW (5%), and MSM/FSW (3%) sequences. One large IDU-exclusive cluster was found, indicating an independent sub-epidemic among this group. Phylodynamic analysis of this cluster revealed a steady increase in HIV-1 infections among IDU since the estimated origin of the cluster in 1987. Our results suggest mixing between high-risk groups and heterosexual populations and could be relevant for the development of targeted HIV-1 prevention programmes in coastal Kenya.
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Affiliation(s)
- George M Nduva
- Lund University, Lund, Sweden
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
| | - Amin S Hassan
- Lund University, Lund, Sweden
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Susan M Graham
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- University of Washington, Seattle, WA, USA
| | - Joakim Esbjörnsson
- Lund University, Lund, Sweden.
- The University of Oxford, Oxford, United Kingdom.
| | - Eduard J Sanders
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- The University of Oxford, Oxford, United Kingdom
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9
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The Determination of HIV-1 RT Mutation Rate, Its Possible Allosteric Effects, and Its Implications on Drug Resistance. Viruses 2020; 12:v12030297. [PMID: 32182845 PMCID: PMC7150816 DOI: 10.3390/v12030297] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/02/2020] [Accepted: 03/06/2020] [Indexed: 12/31/2022] Open
Abstract
The high mutation rate of the human immunodeficiency virus type 1 (HIV-1) plays a major role in treatment resistance, from the development of vaccines to therapeutic drugs. In addressing the crux of the issue, various attempts to estimate the mutation rate of HIV-1 resulted in a large range of 10−5–10−3 errors/bp/cycle due to the use of different types of investigation methods. In this review, we discuss the different assay methods, their findings on the mutation rates of HIV-1 and how the locations of mutations can be further analyzed for their allosteric effects to allow for new inhibitor designs. Given that HIV is one of the fastest mutating viruses, it serves as a good model for the comprehensive study of viral mutations that can give rise to a more horizontal understanding towards overall viral drug resistance as well as emerging viral diseases.
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Ghorbani A, Ngunjiri JM, Lee CW. Influenza A Virus Subpopulations and Their Implication in Pathogenesis and Vaccine Development. Annu Rev Anim Biosci 2019; 8:247-267. [PMID: 31479617 DOI: 10.1146/annurev-animal-021419-083756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The concept of influenza A virus (IAV) subpopulations emerged approximately 75 years ago, when Preben von Magnus described "incomplete" virus particles that interfere with the replication of infectious virus. It is now widely accepted that infectious particles constitute only a minor portion of biologically active IAV subpopulations. The IAV quasispecies is an extremely diverse swarm of biologically and genetically heterogeneous particle subpopulations that collectively influence the evolutionary fitness of the virus. This review summarizes the current knowledge of IAV subpopulations, focusing on their biologic and genomic diversity. It also discusses the potential roles IAV subpopulations play in virus pathogenesis and live attenuated influenza vaccine development.
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Affiliation(s)
- Amir Ghorbani
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio 44691, USA; , , .,Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio 43210, USA
| | - John M Ngunjiri
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio 44691, USA; , ,
| | - Chang-Won Lee
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio 44691, USA; , , .,Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio 43210, USA
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11
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Hassan AS, Esbjörnsson J, Wahome E, Thiong’o A, Makau GN, Price MA, Sanders EJ. HIV-1 subtype diversity, transmission networks and transmitted drug resistance amongst acute and early infected MSM populations from Coastal Kenya. PLoS One 2018; 13:e0206177. [PMID: 30562356 PMCID: PMC6298690 DOI: 10.1371/journal.pone.0206177] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/08/2018] [Indexed: 11/21/2022] Open
Abstract
Background HIV-1 molecular epidemiology amongst men who have sex with men (MSM) in sub-Saharan Africa remains not well characterized. We aimed to determine HIV-1 subtype distribution, transmission clusters and transmitted drug resistance (TDR) in acute and early infected MSM from Coastal Kenya. Methods Analysis of HIV-1 partial pol sequences from MSM recruited 2005–2017 and sampled within six months of the estimated date of infection. Volunteers were classified as men who have sex with men exclusively (MSME) or with both men and women (MSMW). HIV-1 subtype and transmission clusters were determined by maximum-likelihood phylogenetics. TDR mutations were determined using the Stanford HIV drug resistance database. Results Of the 97 volunteers, majority (69%) were MSMW; 74%, 16%, 9% and 1% had HIV-1 subtypes A1, D, C or G, respectively. Overall, 65% formed transmission clusters, with substantial mixing between MSME and MSMW. Majority of volunteer sequences were either not linked to any reference sequence (56%) or clustered exclusively with sequences of Kenyan origin (19%). Eight (8% [95% CI: 4–16]) had at least one TDR mutation against nucleoside (n = 2 [2%]) and/or non-nucleoside (n = 7 [7%]) reverse transcriptase inhibitors. The most prevalent TDR mutation was K103N (n = 5), with sequences forming transmission clusters of two and three taxa each. There were no significant differences in HIV-1 subtype distribution and TDR between MSME and MSMW. Conclusions This HIV-1 MSM epidemic was predominantly sub-subtype A1, of Kenyan origin, with many transmission clusters and having intermediate level of TDR. Targeted HIV-1 prevention, early identification and care interventions are warranted to break the transmission cycle amongst MSM from Coastal Kenya.
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Affiliation(s)
- Amin S. Hassan
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Lund University, Lund, Sweden
- * E-mail:
| | | | | | | | - George N. Makau
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Lund University, Lund, Sweden
| | - Mathew A. Price
- International AIDS Vaccine Initiative, New York, New York, United States of America
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, California, United States of America
| | - Eduard J. Sanders
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Oxford University, Oxford, United Kingdom
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12
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Wertheim JO, Oster AM, Murrell B, Saduvala N, Heneine W, Switzer WM, Johnson JA. Maintenance and reappearance of extremely divergent intra-host HIV-1 variants. Virus Evol 2018; 4:vey030. [PMID: 30538823 PMCID: PMC6279948 DOI: 10.1093/ve/vey030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Understanding genetic variation in human immunodeficiency virus (HIV) is clinically and immunologically important for patient treatment and vaccine development. We investigated the longitudinal intra-host genetic variation of HIV in over 3,000 individuals in the US National HIV Surveillance System with at least four reported HIV-1 polymerase (pol) sequences. In this population, we identified 149 putative instances of superinfection (i.e. an individual sequentially infected with genetically divergent, polyphyletic viruses). Unexpectedly, we discovered a group of 240 individuals with consecutively sampled viral strains that were >0.015 substitutions/site divergent, despite remaining monophyletic in the phylogeny. Viruses in some of these individuals had a maximum genetic divergence approaching that found between two random, unrelated HIV-1 subtype-B pol sequences within the US population. Individuals with these highly divergent viruses tended to be diagnosed nearly a decade earlier in the epidemic than people with superinfection or virus with less intra-host genetic variation, and they had distinct transmission risk factor profiles. To better understand this genetic variation in cases with extremely divergent, monophyletic viruses, we performed molecular clock phylogenetic analysis. Our findings suggest that, like Hepatitis C virus, extremely divergent HIV lineages can be maintained within an individual and reemerge over a period of years.
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Affiliation(s)
- Joel O Wertheim
- Department of Medicine, University of California, San Diego, USA
| | - Alexandra M Oster
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, USA
| | - Ben Murrell
- Department of Medicine, University of California, San Diego, USA
| | | | - Walid Heneine
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, USA
| | - William M Switzer
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, USA
| | - Jeffrey A Johnson
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, USA
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13
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Perrier M, Désiré N, Storto A, Todesco E, Rodriguez C, Bertine M, Le Hingrat Q, Visseaux B, Calvez V, Descamps D, Marcelin AG, Charpentier C. Evaluation of different analysis pipelines for the detection of HIV-1 minority resistant variants. PLoS One 2018; 13:e0198334. [PMID: 29856864 PMCID: PMC5983569 DOI: 10.1371/journal.pone.0198334] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/17/2018] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE Reliable detection of HIV minority resistant variants (MRVs) requires bioinformatics analysis with specific algorithms to obtain good quality alignments. The aim of this study was to analyze ultra-deep sequencing (UDS) data using different analysis pipelines. METHODS HIV-1 protease, reverse transcriptase (RT) and integrase sequences from antiretroviral-naïve patients were obtained using GS-Junior® (Roche) and MiSeq® (Illumina) platforms. MRVs were defined as variants harbouring resistance-mutation present at a frequency of 1%-20%. Reads were analyzed using different alignment algorithms: Amplicon Variant Analyzer®, Geneious® compared to SmartGene® NGS HIV-1 module. RESULTS 101 protease and 51 RT MRVs identified in 139 protease and 124 RT sequences generated with a GS-Junior® platform were analyzed using AVA® and SmartGene® software. The correlation coefficients for the MRVs were R2 = 0.974 for protease and R2 = 0.972 for RT. Discordances (n = 13 in protease and n = 15 in RT) mainly concerned low-level MRVs (i.e., with frequencies of 1%-2%, n = 18/28) and they were located in homopolymeric regions (n = 10/15). Geneious® and SmartGene® software were used to analyze 143 protease, 45 RT and 26 integrase MRVs identified in 172 protease, 69 RT, and 72 integrase sequences generated with a MiSeq® platform. The correlation coefficients for the MRVs were R2 = 0.987 for protease, R2 = 0.995 for RT and R2 = 0.993 for integrase. Discordances (n = 9 in protease, n = 3 in RT, and n = 3 in integrase) mainly concerned low-level MRVs (n = 13/15). CONCLUSION We found an excellent correlation between the various UDS analysis pipelines that we tested. However, our results indicate that specific attention should be paid to low-level MRVs, for which the use of two different analysis pipelines and visual inspection of sequences alignments might be beneficial. Thus, our results argue for use of a 2% threshold for MRV detection, rather than the 1% threshold, to minimize misalignments and time-consuming sight reading steps essential to ensure accurate results for MRV frequencies below 2%.
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Affiliation(s)
- Marine Perrier
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France
| | - Nathalie Désiré
- Sorbonne University, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France
- Hôpital Pitié Salpêtrière, Laboratoire de Virologie, Paris, France
| | - Alexandre Storto
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France
| | - Eve Todesco
- Sorbonne University, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France
- Hôpital Pitié Salpêtrière, Laboratoire de Virologie, Paris, France
| | - Christophe Rodriguez
- Département de Microbiologie, Next-Generation Sequencing Platform pACT, IMRB Créteil, Créteil, France
- Institut Mondor de Recherche Biomédicale U955, Créteil, France
| | - Mélanie Bertine
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France
| | - Quentin Le Hingrat
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France
| | - Benoit Visseaux
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France
| | - Vincent Calvez
- Sorbonne University, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France
- Hôpital Pitié Salpêtrière, Laboratoire de Virologie, Paris, France
| | - Diane Descamps
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne University, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France
- Hôpital Pitié Salpêtrière, Laboratoire de Virologie, Paris, France
| | - Charlotte Charpentier
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France
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14
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Zhou Z, Tang K, Zhang G, Wadonda-Kabondo N, Moyo K, Rowe LA, DeVos JR, Wagar N, Zheng DP, Guo H, Nkengasong J, Frace M, Sammons S, Yang C. Detection of minority drug resistant mutations in Malawian HIV-1 subtype C-positive patients initiating and on first-line antiretroviral therapy. Afr J Lab Med 2018; 7:708. [PMID: 29977795 PMCID: PMC6018132 DOI: 10.4102/ajlm.v7i1.708] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 02/01/2018] [Indexed: 11/21/2022] Open
Abstract
Background Minority drug resistance mutations (DRMs) that are often missed by Sanger sequencing are clinically significant, as they can cause virologic failure in individuals treated with antiretroviral therapy (ART) drugs. Objective This study aimed to estimate the prevalence of minor DRMs among patients enrolled in a Malawi HIV drug resistance monitoring survey at baseline and at one year after initiation of ART. Methods Forty-one plasma specimens collected from HIV-1 subtype C-positive patients and seven clonal control samples were analysed using ultra-deep sequencing technology. Results Deep sequencing identified all 72 DRMs detected by Sanger sequencing at the level of ≥20% and 79 additional minority DRMs at the level of < 20% from the 41 Malawian clinical specimens. Overall, DRMs were detected in 85% of pre-ART and 90.5% of virologic failure patients by deep sequencing. Among pre-ART patients, deep sequencing identified a statistically significant higher prevalence of DRMs to nucleoside reverse transcriptase inhibitors (NRTIs) compared with Sanger sequencing. The difference was mainly due to the high prevalence of minority K65R and M184I mutations. Most virologic failure patients harboured DRMs against both NRTIs and non-nucleoside reverse transcriptase inhibitors (NNRTIs). These minority DRMs contributed to the increased or enhanced virologic failures in these patients. Conclusion The results revealed the presence of minority DRMs to NRTIs and NNRTIs in specimens collected at baseline and virologic failure time points. These minority DRMs not only increased resistance levels to NRTIs and NNRTIs for the prescribed ART, but also expanded resistance to additional major first-line ART drugs. This study suggested that drug resistance testing that uses more sensitive technologies, is needed in this setting.
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Affiliation(s)
- Zhiyong Zhou
- International Laboratory Branch, Division of Global HIV & TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Kevin Tang
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Guoqing Zhang
- International Laboratory Branch, Division of Global HIV & TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | | | - Kundai Moyo
- Department of Preventive Health, Ministry of Health, Lilongwe, Malawi
| | - Lori A Rowe
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Joshua R DeVos
- International Laboratory Branch, Division of Global HIV & TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Nick Wagar
- International Laboratory Branch, Division of Global HIV & TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Du-Ping Zheng
- International Laboratory Branch, Division of Global HIV & TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Hongxiong Guo
- International Laboratory Branch, Division of Global HIV & TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - John Nkengasong
- International Laboratory Branch, Division of Global HIV & TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Mike Frace
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Scott Sammons
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Chunfu Yang
- International Laboratory Branch, Division of Global HIV & TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
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15
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The Transmission and Evolution of HIV-1 Quasispecies within One Couple: a Follow-up Study based on Next-Generation Sequencing. Sci Rep 2018; 8:1404. [PMID: 29362487 PMCID: PMC5780463 DOI: 10.1038/s41598-018-19783-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 01/04/2018] [Indexed: 11/09/2022] Open
Abstract
Next-generation sequencing (NGS) has been successfully used to trace HIV-1 infection. In this study, we investigated the transmission and evolution of HIV-1 quasispecies in a couple infected through heterosexual behavior. A heterosexual couple in which both partners were infected with HIV-1 was followed up for 54 months. Blood samples including whole-blood and plasma samples, were collected at various time points. After HIV-1 subtyping, NGS (Miseq platform) was used to sequence the env region of the HIV-1 quasispecies. Genetic distances were calculated, and phylogenetic trees were generated. We found both partners were infected with HIV-1 subtype circulating recombinant form (CRF), CRF65_cpx. The quasispecies distribution was relatively tightly clustered in the phylogenetic tree during early infection. Over time, the distribution of HIV-1 quasispecies gradually became more dispersed at 12th months, with a progressive increase in gene diversity. By 37th months, the sequences obtained for both partners formed different clusters in the phylogenetic tree. These results suggest that the HIV-1 contact tracing results generated by the Miseq platform may be more reliable than other conventional sequencing methods, which can provide important information about the transmission and evolution of HIV-1. Our findings may help to better target preventative interventions for promoting public health.
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16
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Fun A, Leitner T, Vandekerckhove L, Däumer M, Thielen A, Buchholz B, Hoepelman AIM, Gisolf EH, Schipper PJ, Wensing AMJ, Nijhuis M. Impact of the HIV-1 genetic background and HIV-1 population size on the evolution of raltegravir resistance. Retrovirology 2018; 15:1. [PMID: 29304821 PMCID: PMC5755036 DOI: 10.1186/s12977-017-0384-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/23/2017] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Emergence of resistance against integrase inhibitor raltegravir in human immunodeficiency virus type 1 (HIV-1) patients is generally associated with selection of one of three signature mutations: Y143C/R, Q148K/H/R or N155H, representing three distinct resistance pathways. The mechanisms that drive selection of a specific pathway are still poorly understood. We investigated the impact of the HIV-1 genetic background and population dynamics on the emergence of raltegravir resistance. Using deep sequencing we analyzed the integrase coding sequence (CDS) in longitudinal samples from five patients who initiated raltegravir plus optimized background therapy at viral loads > 5000 copies/ml. To investigate the role of the HIV-1 genetic background we created recombinant viruses containing the viral integrase coding region from pre-raltegravir samples from two patients in whom raltegravir resistance developed through different pathways. The in vitro selections performed with these recombinant viruses were designed to mimic natural population bottlenecks. RESULTS Deep sequencing analysis of the viral integrase CDS revealed that the virological response to raltegravir containing therapy inversely correlated with the relative amount of unique sequence variants that emerged suggesting diversifying selection during drug pressure. In 4/5 patients multiple signature mutations representing different resistance pathways were observed. Interestingly, the resistant population can consist of a single resistant variant that completely dominates the population but also of multiple variants from different resistance pathways that coexist in the viral population. We also found evidence for increased diversification after stronger bottlenecks. In vitro selections with low viral titers, mimicking population bottlenecks, revealed that both recombinant viruses and HXB2 reference virus were able to select mutations from different resistance pathways, although typically only one resistance pathway emerged in each individual culture. CONCLUSIONS The generation of a specific raltegravir resistant variant is not predisposed in the genetic background of the viral integrase CDS. Typically, in the early phases of therapy failure the sequence space is explored and multiple resistance pathways emerge and then compete for dominance which frequently results in a switch of the dominant population over time towards the fittest variant or even multiple variants of similar fitness that can coexist in the viral population.
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Affiliation(s)
- Axel Fun
- Department of Medical Microbiology, Virology, University Medical Center Utrecht, Heidelberglaan 100, HP G04.614, 3584 CX, Utrecht, The Netherlands
| | - Thomas Leitner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Linos Vandekerckhove
- Department of General Internal Medicine and Infectious Diseases, Ghent University Hospital, Ghent, Belgium
| | - Martin Däumer
- Institute of Immunology and Genetics, Kaiserslautern, Germany
| | | | - Bernd Buchholz
- Pediatric Clinic, University Medical Center Mannheim, Mannheim, Germany
| | - Andy I M Hoepelman
- Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Elizabeth H Gisolf
- Department of Internal Medicine, Rijnstate Hospital, Arnhem, The Netherlands
| | - Pauline J Schipper
- Department of Medical Microbiology, Virology, University Medical Center Utrecht, Heidelberglaan 100, HP G04.614, 3584 CX, Utrecht, The Netherlands
| | - Annemarie M J Wensing
- Department of Medical Microbiology, Virology, University Medical Center Utrecht, Heidelberglaan 100, HP G04.614, 3584 CX, Utrecht, The Netherlands.,Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Monique Nijhuis
- Department of Medical Microbiology, Virology, University Medical Center Utrecht, Heidelberglaan 100, HP G04.614, 3584 CX, Utrecht, The Netherlands.
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Ratmann O, Wymant C, Colijn C, Danaviah S, Essex M, Frost S, Gall A, Gaseitsiwe S, Grabowski MK, Gray R, Guindon S, von Haeseler A, Kaleebu P, Kendall M, Kozlov A, Manasa J, Minh BQ, Moyo S, Novitsky V, Nsubuga R, Pillay S, Quinn TC, Serwadda D, Ssemwanga D, Stamatakis A, Trifinopoulos J, Wawer M, Brown AL, de Oliveira T, Kellam P, Pillay D, Fraser C, on behalf of the PANGEA-HIV Consort. HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences. AIDS Res Hum Retroviruses 2017; 33:1083-1098. [PMID: 28540766 PMCID: PMC5597042 DOI: 10.1089/aid.2017.0061] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
To characterize HIV-1 transmission dynamics in regions where the burden of HIV-1 is greatest, the “Phylogenetics and Networks for Generalised HIV Epidemics in Africa” consortium (PANGEA-HIV) is sequencing full-genome viral isolates from across sub-Saharan Africa. We report the first 3,985 PANGEA-HIV consensus sequences from four cohort sites (Rakai Community Cohort Study, n = 2,833; MRC/UVRI Uganda, n = 701; Mochudi Prevention Project, n = 359; Africa Health Research Institute Resistance Cohort, n = 92). Next-generation sequencing success rates varied: more than 80% of the viral genome from the gag to the nef genes could be determined for all sequences from South Africa, 75% of sequences from Mochudi, 60% of sequences from MRC/UVRI Uganda, and 22% of sequences from Rakai. Partial sequencing failure was primarily associated with low viral load, increased for amplicons closer to the 3′ end of the genome, was not associated with subtype diversity except HIV-1 subtype D, and remained significantly associated with sampling location after controlling for other factors. We assessed the impact of the missing data patterns in PANGEA-HIV sequences on phylogeny reconstruction in simulations. We found a threshold in terms of taxon sampling below which the patchy distribution of missing characters in next-generation sequences (NGS) has an excess negative impact on the accuracy of HIV-1 phylogeny reconstruction, which is attributable to tree reconstruction artifacts that accumulate when branches in viral trees are long. The large number of PANGEA-HIV sequences provides unprecedented opportunities for evaluating HIV-1 transmission dynamics across sub-Saharan Africa and identifying prevention opportunities. Molecular epidemiological analyses of these data must proceed cautiously because sequence sampling remains below the identified threshold and a considerable negative impact of missing characters on phylogeny reconstruction is expected.
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Affiliation(s)
- Oliver Ratmann
- MRC Centre for Outbreak Analyses and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Chris Wymant
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Caroline Colijn
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Siva Danaviah
- Africa Health Research Institute, KwaZulu-Natal, South Africa
| | - Max Essex
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Simon Frost
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Astrid Gall
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Mary K. Grabowski
- Department of Epidemiology Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Rakai Health Sciences Program, Entebbe, Uganda
| | - Ronald Gray
- Department of Epidemiology Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Rakai Health Sciences Program, Entebbe, Uganda
| | - Stephane Guindon
- Department of Statistics, University of Auckland, Auckland, New Zealand
- Laboratoire d'Informatique, de Robotique et de Microelectronique de Montpellier–UMR 5506, CNRS & UM, Montpellier, France
| | - Arndt von Haeseler
- Centre for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria
- Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | | | - Michelle Kendall
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Alexey Kozlov
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Justen Manasa
- Africa Health Research Institute, KwaZulu-Natal, South Africa
| | - Bui Quang Minh
- Centre for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Vlad Novitsky
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | | | | | - Thomas C. Quinn
- Rakai Health Sciences Program, Entebbe, Uganda
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland
- Department of Medicine Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - David Serwadda
- Rakai Health Sciences Program, Entebbe, Uganda
- Makerere University School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
| | | | - Alexandros Stamatakis
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Jana Trifinopoulos
- Centre for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria
| | - Maria Wawer
- Department of Epidemiology Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Rakai Health Sciences Program, Entebbe, Uganda
| | - Andy Leigh Brown
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Tulio de Oliveira
- Nelson R. Mandela School of Medicine, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Paul Kellam
- Department of Infectious Diseases and Immunity, Imperial College London, United Kingdom
| | - Deenan Pillay
- Africa Health Research Institute, KwaZulu-Natal, South Africa
- Division of Infection & Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Christophe Fraser
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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Epaulard O, Signori-Schmuck A, Larrat S, Kulkarni O, Blum MG, Fusillier K, Blanc M, Leclercq P, François O, Morand P. Ultradeep sequencing of B and non-B HIV-1 subtypes: Viral diversity and drug resistance mutations before and after one month of antiretroviral therapy in naive patients. J Clin Virol 2017; 95:13-19. [PMID: 28830014 DOI: 10.1016/j.jcv.2017.07.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 04/06/2017] [Accepted: 07/21/2017] [Indexed: 11/16/2022]
Abstract
BACKGROUND Ultradeep pyrosequencing technologies permit an assessment of the genetic diversity and the presence and frequency of minority variants in a viral population. The effect of these parameters on the outcome of highly active antiretroviral therapy (HAART) in HIV-infected patients is poorly understood. OBJECTIVES The present study used the pyrosequencing Roche 454 prototype assay to determine whether antiretroviral efficacy is correlated with viral diversity and minority drug resistance mutations in HIV-infected treatment-naive patients and to compare assay performance in B and non-B subtypes. STUDY DESIGN The study included 30 HIV-1 infected naive patients (20 with subtype non-B and 10 with subtype B). Ultradeep pyrosequencing of protease and reverse transcriptase genes was performed at baseline and 1 month after HAART initiation. Plasma HIV VL was measured at 0 and after 1, 3, and 6 months of HAART. RESULTS Pre-HAART minority drug resistance mutations were observed to NRTI in 4 patients, to NNRTI in 6 patients, and to PI in 1 patient; there was no difference in HAART-induced VL decay between patients. Pre-HAART diversity was significantly correlated with the time elapsed since HIV-1 infection diagnosis, but not with the subtype, VL, or CD4 count. Patients with an undetectable VL after 3 months of HAART had a higher pre-HAART diversity. Pre- and post-HAART diversities were not statistically different. There was no difference in assay performance between subtype B and non-B. CONCLUSIONS A high pre-HAART viral diversity might have a positive effect on the outcome of HAART. Pre-therapeutic minority drug resistance mutations are uncommon in naive patients.
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Affiliation(s)
- Olivier Epaulard
- Infectious Disease Unit, Centre Hospitalier Universitaire Grenoble Alpes, CS10217, 38043 Grenoble Cedex 9, France; Team "HIV and human persistent viruses", Institut de Biologie Structurale, UMR5075 CNRS-CEA-UGA, Grenoble, France; Fédération d'Infectiologie Multidisciplinaire de l'Arc Alpin, Université Grenoble Alpes, France.
| | - Anne Signori-Schmuck
- Team "HIV and human persistent viruses", Institut de Biologie Structurale, UMR5075 CNRS-CEA-UGA, Grenoble, France; Fédération d'Infectiologie Multidisciplinaire de l'Arc Alpin, Université Grenoble Alpes, France; Virology Laboratory, Infectious Agents Department, Centre Hospitalier Universitaire Grenoble Alpes, CS10217, 38043 Grenoble Cedex 9, France
| | - Sylvie Larrat
- Team "HIV and human persistent viruses", Institut de Biologie Structurale, UMR5075 CNRS-CEA-UGA, Grenoble, France; Fédération d'Infectiologie Multidisciplinaire de l'Arc Alpin, Université Grenoble Alpes, France; Virology Laboratory, Infectious Agents Department, Centre Hospitalier Universitaire Grenoble Alpes, CS10217, 38043 Grenoble Cedex 9, France
| | - Om Kulkarni
- Computational and Mathematical Biology, TIMC-IMAG UMR 5525 UJF-INPG-CNRS, Domaine de la Merci, 38706 La Tronche Cedex, France
| | - Michael G Blum
- Computational and Mathematical Biology, TIMC-IMAG UMR 5525 UJF-INPG-CNRS, Domaine de la Merci, 38706 La Tronche Cedex, France
| | - Katia Fusillier
- Virology Laboratory, Infectious Agents Department, Centre Hospitalier Universitaire Grenoble Alpes, CS10217, 38043 Grenoble Cedex 9, France
| | - Myriam Blanc
- Infectious Disease Unit, Centre Hospitalier Universitaire Grenoble Alpes, CS10217, 38043 Grenoble Cedex 9, France; Fédération d'Infectiologie Multidisciplinaire de l'Arc Alpin, Université Grenoble Alpes, France
| | - Pascale Leclercq
- Infectious Disease Unit, Centre Hospitalier Universitaire Grenoble Alpes, CS10217, 38043 Grenoble Cedex 9, France; Fédération d'Infectiologie Multidisciplinaire de l'Arc Alpin, Université Grenoble Alpes, France
| | - Olivier François
- Computational and Mathematical Biology, TIMC-IMAG UMR 5525 UJF-INPG-CNRS, Domaine de la Merci, 38706 La Tronche Cedex, France
| | - Patrice Morand
- Team "HIV and human persistent viruses", Institut de Biologie Structurale, UMR5075 CNRS-CEA-UGA, Grenoble, France; Fédération d'Infectiologie Multidisciplinaire de l'Arc Alpin, Université Grenoble Alpes, France; Virology Laboratory, Infectious Agents Department, Centre Hospitalier Universitaire Grenoble Alpes, CS10217, 38043 Grenoble Cedex 9, France
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19
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Quer J, Rodríguez-Frias F, Gregori J, Tabernero D, Soria ME, García-Cehic D, Homs M, Bosch A, Pintó RM, Esteban JI, Domingo E, Perales C. Deep sequencing in the management of hepatitis virus infections. Virus Res 2017; 239:115-125. [PMID: 28040474 DOI: 10.1016/j.virusres.2016.12.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 11/10/2016] [Accepted: 12/22/2016] [Indexed: 02/07/2023]
Abstract
The hepatitis viruses represent a major public health problem worldwide. Procedures for characterization of the genomic composition of their populations, accurate diagnosis, identification of multiple infections, and information on inhibitor-escape mutants for treatment decisions are needed. Deep sequencing methodologies are extremely useful for these viruses since they replicate as complex and dynamic quasispecies swarms whose complexity and mutant composition are biologically relevant traits. Population complexity is a major challenge for disease prevention and control, but also an opportunity to distinguish among related but phenotypically distinct variants that might anticipate disease progression and treatment outcome. Detailed characterization of mutant spectra should permit choosing better treatment options, given the increasing number of new antiviral inhibitors available. In the present review we briefly summarize our experience on the use of deep sequencing for the management of hepatitis virus infections, particularly for hepatitis B and C viruses, and outline some possible new applications of deep sequencing for these important human pathogens.
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Affiliation(s)
- Josep Quer
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Research-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autonoma de Barcelona, 08035, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Francisco Rodríguez-Frias
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Josep Gregori
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Research-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autonoma de Barcelona, 08035, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Roche Diagnostics, S.L., Sant Cugat del Vallés, Spain
| | - David Tabernero
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Maria Eugenia Soria
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Research-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autonoma de Barcelona, 08035, Barcelona, Spain
| | - Damir García-Cehic
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Research-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autonoma de Barcelona, 08035, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Maria Homs
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Albert Bosch
- Department of Microbiology, Enteric Virus Laboratory, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Rosa María Pintó
- Department of Microbiology, Enteric Virus Laboratory, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Juan Ignacio Esteban
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Research-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autonoma de Barcelona, 08035, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Esteban Domingo
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Celia Perales
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Research-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autonoma de Barcelona, 08035, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
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20
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Raj VS, Hundie GB, Schürch AC, Smits SL, Pas SD, Le Pogam S, Janssen HLA, de Knegt RJ, Osterhaus ADME, Najera I, Boucher CA, Haagmans BL. Identification of HCV Resistant Variants against Direct Acting Antivirals in Plasma and Liver of Treatment Naïve Patients. Sci Rep 2017; 7:4688. [PMID: 28680115 PMCID: PMC5498547 DOI: 10.1038/s41598-017-04931-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/22/2017] [Indexed: 02/06/2023] Open
Abstract
Current standard-of-care treatment of chronically infected hepatitis C virus (HCV) patients involves direct-acting antivirals (DAA). However, concerns exist regarding the emergence of drug -resistant variants and subsequent treatment failure. In this study, we investigate potential natural drug-resistance mutations in the NS5B gene of HCV genotype 1b from treatment-naïve patients. Population-based sequencing and 454 deep sequencing of NS5B gene were performed on plasma and liver samples obtained from 18 treatment- naïve patients. The quasispecies distribution in plasma and liver samples showed a remarkable overlap in each patient. Although unique sequences in plasma or liver were observed, in the majority of cases the most dominant sequences were shown to be identical in both compartments. Neither in plasma nor in the liver codon changes were detected at position 282 that cause resistance to nucleos(t)ide analogues. However, in 10 patients the V321I change conferring resistance to nucleos(t)ide NS5B polymerase inhibitors and in 16 patients the C316N/Y/H non-nucleoside inhibitors were found mainly in liver samples. In conclusion, 454-deep sequencing of liver and plasma compartments in treatment naïve patients provides insight into viral quasispecies and the pre-existence of some drug-resistant variants in the liver, which are not necessarily present in plasma.
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Affiliation(s)
- V Stalin Raj
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Anita C Schürch
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Saskia L Smits
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.,Viroclinics Biosciences BV, Rotterdam, The Netherlands
| | - Suzan D Pas
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Sophie Le Pogam
- Virology Discovery, Pharma Research Early Development Hoffmann La Roche, Nutley, NJ, USA
| | - Harry L A Janssen
- Department of Gastroenterology and Hepatology, Erasmus Medical Center, Rotterdam, The Netherlands.,Division of Gastroenterology, University Health Network, Toronto, Canada
| | - Rob J de Knegt
- Department of Gastroenterology and Hepatology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Albert D M E Osterhaus
- Artemis One health, Utrecht, The Netherlands.,Center for Infection Medicine and Zoonoses Research, University of Veterinary Medicine, Hannover, Germany
| | - Isabel Najera
- Virology Discovery, Pharma Research Early Development Hoffmann La Roche, Nutley, NJ, USA
| | - Charles A Boucher
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
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21
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Zanini F, Puller V, Brodin J, Albert J, Neher RA. In vivo mutation rates and the landscape of fitness costs of HIV-1. Virus Evol 2017; 3:vex003. [PMID: 28458914 PMCID: PMC5399928 DOI: 10.1093/ve/vex003] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Mutation rates and fitness costs of deleterious mutations are difficult to measure in vivo but essential for a quantitative understanding of evolution. Using whole genome deep sequencing data from longitudinal samples during untreated HIV-1 infection, we estimated mutation rates and fitness costs in HIV-1 from the dynamics of genetic variation. At approximately neutral sites, mutations accumulate with a rate of 1.2 × 10-5 per site per day, in agreement with the rate measured in cell cultures. We estimated the rate from G to A to be the largest, followed by the other transitions C to T, T to C, and A to G, while transversions are less frequent. At other sites, mutations tend to reduce virus replication. We estimated the fitness cost of mutations at every site in the HIV-1 genome using a model of mutation selection balance. About half of all non-synonymous mutations have large fitness costs (>10 percent), while most synonymous mutations have costs <1 percent. The cost of synonymous mutations is especially low in most of pol where we could not detect measurable costs for the majority of synonymous mutations. In contrast, we find high costs for synonymous mutations in important RNA structures and regulatory regions. The intra-patient fitness cost estimates are consistent across multiple patients, indicating that the deleterious part of the fitness landscape is universal and explains a large fraction of global HIV-1 group M diversity.
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Affiliation(s)
- Fabio Zanini
- Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Vadim Puller
- Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Johanna Brodin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, SE-171 76 Stockholm, Sweden
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, SE-171 76 Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska Institute, SE-171 76, Stockholm, Sweden
| | - Richard A. Neher
- Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
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22
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Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing. Virus Res 2016; 239:106-114. [PMID: 28039047 DOI: 10.1016/j.virusres.2016.12.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 11/25/2016] [Accepted: 12/16/2016] [Indexed: 11/20/2022]
Abstract
Deep sequencing is a powerful and cost-effective tool to characterize the genetic diversity and evolution of virus populations. While modern sequencing instruments readily cover viral genomes many thousand fold and very rare variants can in principle be detected, sequencing errors, amplification biases, and other artifacts can limit sensitivity and complicate data interpretation. For this reason, the number of studies using whole genome deep sequencing to characterize viral quasi-species in clinical samples is still limited. We have previously undertaken a large scale whole genome deep sequencing study of HIV-1 populations. Here we discuss the challenges, error profiles, control experiments, and computational test we developed to quantify the accuracy of variant frequency estimation.
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23
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HIV Drug Resistance Mutations (DRMs) Detected by Deep Sequencing in Virologic Failure Subjects on Therapy from Hunan Province, China. PLoS One 2016; 11:e0149215. [PMID: 26895182 PMCID: PMC4760947 DOI: 10.1371/journal.pone.0149215] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/28/2016] [Indexed: 11/19/2022] Open
Abstract
Objective Determine HIV drug resistance mutations (DRMs) prevalence at low and high levels in ART-experienced patients experiencing virologic failure (VF). Methods 29 subjects from 18 counties in Hunan Province that experienced VF were evaluated for the prevalence of DRMs (Stanford DRMs with an algorithm value ≥15, include low-, intermediate and high-level resistance) by both Sanger sequencing (SS) and deep sequencing (DS) to 1% frequency levels. Results DS was performed on samples from 29 ART-experienced subjects; the median viral load 4.95×104 c/ml; 82.76% subtype CRF01_AE. 58 DRMs were detected by DS. 18 DRMs were detected by SS. Of the 58 mutations detected by DS, 40 were at levels <20% frequency (26 NNRTI, 12 NRTI and 2 PI) and the majority of these 95.00% (38/40) were not detected by standard genotyping. Of these 40 low-level DRMs, 16 (40%) were detected at frequency levels of 1–4% and 24 (60%) at levels of 5–19%. SS detected 15 of 17 (88.24%) DRMs at levels ≥ 20% that were detected by DS. The only variable associated with the detection of DRMs by DS was ART adherence (missed doses in the prior 7 days); all patients that reported missing a dose in the last 7 days had DRMs detected by DS. Conclusions DS of VF samples from treatment experienced subjects infected with primarily AE subtype frequently identified Stanford HIVdb NRTI and NNRTI resistance mutations with an algorithm value 15. Low frequency level resistant variants detected by DS were frequently missed by standard genotyping in VF specimens from antiretroviral-experienced subjects.
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24
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Vazquez-Guillen JM, Palacios-Saucedo GC, Rivera-Morales LG, Garcia-Campos J, Ortiz-Lopez R, Noguera-Julian M, Paredes R, Vielma-Ramirez HJ, Ramirez TJ, Chavez-Garcia M, Lopez-Guillen P, Briones-Lara E, Sanchez-Sanchez LM, Vazquez-Martinez CA, Rodriguez-Padilla C. Mutations Related to Antiretroviral Resistance Identified by Ultra-Deep Sequencing in HIV-1 Infected Children under Structured Interruptions of HAART. PLoS One 2016; 11:e0147591. [PMID: 26807922 PMCID: PMC4725846 DOI: 10.1371/journal.pone.0147591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 01/06/2016] [Indexed: 02/05/2023] Open
Abstract
Although Structured Treatment Interruptions (STI) are currently not considered an alternative strategy for antiretroviral treatment, their true benefits and limitations have not been fully established. Some studies suggest the possibility of improving the quality of life of patients with this strategy; however, the information that has been obtained corresponds mostly to studies conducted in adults, with a lack of knowledge about its impact on children. Furthermore, mutations associated with antiretroviral resistance could be selected due to sub-therapeutic levels of HAART at each interruption period. Genotyping methods to determine the resistance profiles of the infecting viruses have become increasingly important for the management of patients under STI, thus low-abundance antiretroviral drug-resistant mutations (DRM’s) at levels under limit of detection of conventional genotyping (<20% of quasispecies) could increase the risk of virologic failure. In this work, we analyzed the protease and reverse transcriptase regions of the pol gene by ultra-deep sequencing in pediatric patients under STI with the aim of determining the presence of high- and low-abundance DRM’s in the viral rebounds generated by the STI. High-abundance mutations in protease and high- and low-abundance mutations in reverse transcriptase were detected but no one of these are directly associated with resistance to antiretroviral drugs. The results could suggest that the evaluated STI program is virologically safe, but strict and carefully planned studies, with greater numbers of patients and interruption/restart cycles, are still needed to evaluate the selection of DRM’s during STI.
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Affiliation(s)
- Jose Manuel Vazquez-Guillen
- Laboratorio de Inmunología y Virología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
| | - Gerardo C. Palacios-Saucedo
- División de Investigación, Departamento de Pediatría e Infectología Pediátrica, Unidad Médica de Alta Especialidad, Hospital de Especialidades No. 25, Instituto Mexicano del Seguro Social, Monterrey, Nuevo León, México
- * E-mail:
| | - Lydia G. Rivera-Morales
- Laboratorio de Inmunología y Virología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
| | - Jorge Garcia-Campos
- División de Investigación, Departamento de Pediatría e Infectología Pediátrica, Unidad Médica de Alta Especialidad, Hospital de Especialidades No. 25, Instituto Mexicano del Seguro Social, Monterrey, Nuevo León, México
| | - Rocio Ortiz-Lopez
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina and Centro de Investigación y Desarrollo en Ciencias de la Salud, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
| | - Marc Noguera-Julian
- Institut de Recerca de la SIDA, IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, España and Cátedra de la SIDA, Universitat de Vic, Vic, España
| | - Roger Paredes
- Institut de Recerca de la SIDA, IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, España and Cátedra de la SIDA, Universitat de Vic, Vic, España
| | - Herlinda J. Vielma-Ramirez
- Laboratorio de Inmunología y Virología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
| | - Teresa J. Ramirez
- Laboratorio Estatal de Salud Pública del Estado de Nuevo León, Secretaría de Salud, Nuevo León, México
| | - Marcelino Chavez-Garcia
- División de Investigación, Departamento de Pediatría e Infectología Pediátrica, Unidad Médica de Alta Especialidad, Hospital de Especialidades No. 25, Instituto Mexicano del Seguro Social, Monterrey, Nuevo León, México
| | - Paulo Lopez-Guillen
- Unidad de Infectología “Dr. Juan I. Menchaca”, Hospital General Regional No. 45, Instituto Mexicano del Seguro Social, Jalisco, México
| | - Evangelina Briones-Lara
- División de Investigación, Departamento de Pediatría e Infectología Pediátrica, Unidad Médica de Alta Especialidad, Hospital de Especialidades No. 25, Instituto Mexicano del Seguro Social, Monterrey, Nuevo León, México
| | - Luz M. Sanchez-Sanchez
- División de Investigación, Departamento de Pediatría e Infectología Pediátrica, Unidad Médica de Alta Especialidad, Hospital de Especialidades No. 25, Instituto Mexicano del Seguro Social, Monterrey, Nuevo León, México
| | - Carlos A. Vazquez-Martinez
- División de Investigación, Departamento de Pediatría e Infectología Pediátrica, Unidad Médica de Alta Especialidad, Hospital de Especialidades No. 25, Instituto Mexicano del Seguro Social, Monterrey, Nuevo León, México
| | - Cristina Rodriguez-Padilla
- Laboratorio de Inmunología y Virología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
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25
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Huang DW, Raley C, Jiang MK, Zheng X, Liang D, Rehman MT, Highbarger HC, Jiao X, Sherman B, Ma L, Chen X, Skelly T, Troyer J, Stephens R, Imamichi T, Pau A, Lempicki RA, Tran B, Nissley D, Lane HC, Dewar RL. Towards Better Precision Medicine: PacBio Single-Molecule Long Reads Resolve the Interpretation of HIV Drug Resistant Mutation Profiles at Explicit Quasispecies (Haplotype) Level. JOURNAL OF DATA MINING IN GENOMICS & PROTEOMICS 2016; 7:182. [PMID: 26949565 PMCID: PMC4775093 DOI: 10.4172/2153-0602.1000182] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Development of HIV-1 drug resistance mutations (HDRMs) is one of the major reasons for the clinical failure of antiretroviral therapy. Treatment success rates can be improved by applying personalized anti-HIV regimens based on a patient's HDRM profile. However, the sensitivity and specificity of the HDRM profile is limited by the methods used for detection. Sanger-based sequencing technology has traditionally been used for determining HDRM profiles at the single nucleotide variant (SNV) level, but with a sensitivity of only ≥ 20% in the HIV population of a patient. Next Generation Sequencing (NGS) technologies offer greater detection sensitivity (~ 1%) and larger scope (hundreds of samples per run). However, NGS technologies produce reads that are too short to enable the detection of the physical linkages of individual SNVs across the haplotype of each HIV strain present. In this article, we demonstrate that the single-molecule long reads generated using the Third Generation Sequencer (TGS), PacBio RS II, along with the appropriate bioinformatics analysis method, can resolve the HDRM profile at a more advanced quasispecies level. The case studies on patients' HIV samples showed that the quasispecies view produced using the PacBio method offered greater detection sensitivity and was more comprehensive for understanding HDRM situations, which is complement to both Sanger and NGS technologies. In conclusion, the PacBio method, providing a promising new quasispecies level of HDRM profiling, may effect an important change in the field of HIV drug resistance research.
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Affiliation(s)
- Da Wei Huang
- Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
- National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Castle Raley
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - Min Kang Jiang
- Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - Xin Zheng
- Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - Dun Liang
- Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - M Tauseef Rehman
- Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - Helene C. Highbarger
- Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - Xiaoli Jiao
- Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - Brad Sherman
- Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - Liang Ma
- Critical Care Medicine Department, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Xiaofeng Chen
- Advanced Biomedical Computing Center, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - Thomas Skelly
- Advanced Biomedical Computing Center, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - Jennifer Troyer
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
- National Human Genome Research Institute, National Institutes of Health, Rockville, MD, 20852, USA
| | - Robert Stephens
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - Tomozumi Imamichi
- Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - Alice Pau
- Division of Clinical Research, National Institute of Allergy & Infectious Diseases, USA
| | - Richard A Lempicki
- Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - Bao Tran
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - Dwight Nissley
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
| | - H Clifford Lane
- Division of Clinical Research, National Institute of Allergy & Infectious Diseases, USA
| | - Robin L. Dewar
- Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA
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26
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Bellecave P, Recordon-Pinson P, Fleury H. Evaluation of Automatic Analysis of Ultradeep Pyrosequencing Raw Data to Determine Percentages of HIV Resistance Mutations in Patients Followed-Up in Hospital. AIDS Res Hum Retroviruses 2016; 32:85-92. [PMID: 26529549 DOI: 10.1089/aid.2015.0201] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
A major obstacle to using next generation sequencing (NGS) technology in clinical routine practice is reliable data analysis. Thousands of sequences need to be aligned and validated, to exclude sequencing artifacts and generate accurate results. We compared two analysis pipelines for Roche 454 ultradeep pyrosequencing (UDPS) raw data generated from HIV-1 clinical samples: a commercial and fully automated Web-based software NGS HIV-1 Module (SmartGene, Zug, Switzerland) vs. the Amplicon Variant Analyzer software (AVA, 454 Life Sciences; Roche). Results were also compared to those obtained with Sanger sequencing. HIV-1 reverse transcriptase and protease genes from 34 plasma samples were submitted to Sanger sequencing and GS Junior UDPS. Raw UDPS data (sff files) from all samples were analyzed with AVA 2.7 software plus manual review of the alignments and the fully automated SmartGene NGS HIV-1 Module prototype (SMG). Results obtained with both analysis pipelines showed good correlation (85.0%). Divergent results were mainly observed at homopolymer positions, such as K101, where the frame-aware alignment and error corrections of the automated approach were more efficient and more accurate, both in terms of detecting and quantifying drug resistance mutations. Our study shows that NGS data can easily be analyzed via a fully automated analysis pipeline, here the SmartGene NGS HIV-1 Module, thus minimizing the need for manual review of alignments by the user, otherwise essential to ensure accurate results. Such automated analysis pipelines may facilitate the adoption of NGS platforms in the routine clinical laboratory.
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Affiliation(s)
- Pantxika Bellecave
- CNRS-UMR 5234, Microbiologie Fondamentale et Pathogénicité, Université Bordeaux Segalen, Bordeaux, France
- Centre Hospitalier Universitaire de Bordeaux (CHU), Laboratoire de Virologie, Bordeaux, France
| | - Patricia Recordon-Pinson
- CNRS-UMR 5234, Microbiologie Fondamentale et Pathogénicité, Université Bordeaux Segalen, Bordeaux, France
- Centre Hospitalier Universitaire de Bordeaux (CHU), Laboratoire de Virologie, Bordeaux, France
| | - Hervé Fleury
- CNRS-UMR 5234, Microbiologie Fondamentale et Pathogénicité, Université Bordeaux Segalen, Bordeaux, France
- Centre Hospitalier Universitaire de Bordeaux (CHU), Laboratoire de Virologie, Bordeaux, France
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Zanini F, Brodin J, Thebo L, Lanz C, Bratt G, Albert J, Neher RA. Population genomics of intrapatient HIV-1 evolution. eLife 2015; 4:e11282. [PMID: 26652000 PMCID: PMC4718817 DOI: 10.7554/elife.11282] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/08/2015] [Indexed: 12/18/2022] Open
Abstract
Many microbial populations rapidly adapt to changing environments with multiple variants competing for survival. To quantify such complex evolutionary dynamics in vivo, time resolved and genome wide data including rare variants are essential. We performed whole-genome deep sequencing of HIV-1 populations in 9 untreated patients, with 6-12 longitudinal samples per patient spanning 5-8 years of infection. The data can be accessed and explored via an interactive web application. We show that patterns of minor diversity are reproducible between patients and mirror global HIV-1 diversity, suggesting a universal landscape of fitness costs that control diversity. Reversions towards the ancestral HIV-1 sequence are observed throughout infection and account for almost one third of all sequence changes. Reversion rates depend strongly on conservation. Frequent recombination limits linkage disequilibrium to about 100 bp in most of the genome, but strong hitch-hiking due to short range linkage limits diversity.
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Affiliation(s)
- Fabio Zanini
- Evolutionary Dynamics and Biophysics, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Johanna Brodin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Lina Thebo
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Christa Lanz
- Evolutionary Dynamics and Biophysics, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Göran Bratt
- Department of Clinical Science and Education, Stockholm South General Hospital, Stockholm, Sweden
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Richard A Neher
- Evolutionary Dynamics and Biophysics, Max Planck Institute for Developmental Biology, Tübingen, Germany
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28
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Evolution of Newcastle Disease Virus Quasispecies Diversity and Enhanced Virulence after Passage through Chicken Air Sacs. J Virol 2015; 90:2052-63. [PMID: 26656697 DOI: 10.1128/jvi.01801-15] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 12/01/2015] [Indexed: 01/01/2023] Open
Abstract
UNLABELLED It has been reported that lentogenic Newcastle disease virus (NDV) isolates have the potential to become velogenic after their transmission and circulation in chickens, but the underlying mechanism is unclear. In this study, a highly velogenic NDV variant, JS10-A10, was generated from the duck-origin lentogenic isolate JS10 through 10 consecutive passages in chicken air sacs. The velogenic properties of this selected variant were determined using mean death time (MDT) assays, intracerebral pathogenicity index (ICPI), the intravenous pathogenicity index (IVPI), histopathology, and the analysis of host tissue tropism. In contrast, JS10 remained lentogenic after 20 serial passages in chicken eggs (JS10-E20). The JS10, JS10-A10, and JS10-E20 genomes were sequenced and found to be nearly identical, suggesting that both JS10-A10 and JS10-E20 were directly generated from JS10. To investigate the mechanism for virulence enhancement, the partial genome covering the F0 cleavage site of JS10 and its variants were analyzed using ultradeep pyrosequencing (UDPS) and the proportions of virulence-related genomes in the quasispecies were calculated. Velogenic NDV genomes accumulated as a function of JS10 passaging through chicken air sacs. Our data suggest that lentogenic NDV strains circulating among poultry might be a risk factor to future potential velogenic NDV outbreaks in chickens. IMPORTANCE An avirulent isolate, JS10, was passaged through chicken air sacs and embryos, and the pathogenicity of the variants was assessed. A virulent variant, JS10-A10, was generated from consecutive passage in air sacs. We developed a deep-sequencing approach to detect low-frequency viral variants across the NDV genome. We observed that virulence enhancement of JS10 was due to the selective accumulation of velogenic quasispecies and the concomitant disappearance of lentogenic quasispecies. Our results suggest that because it is difficult to avoid contact between natural waterfowl reservoirs and sensitive poultry operations, circulating lentogenic NDV strains may represent a potential reservoir for emergent velogenic NDV strains that could cause outbreaks in chickens.
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Yin F, Wu Z, Fang W, Wu C, Rayner S, Han M, Deng F, Du R, Liu J, Wang M, Wang H, Ning Q, Hu Z. Resistant mutations and quasispecies complexity of hepatitis B virus during telbivudine treatment. J Gen Virol 2015; 96:3302-3312. [DOI: 10.1099/jgv.0.000285] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Feifei Yin
- State Key Laboratory of Virology and Joint Laboratory of Invertebrate Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Zeguang Wu
- Department of Infectious Disease, Institute of Infectious Disease, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Fang
- State Key Laboratory of Virology and Joint Laboratory of Invertebrate Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Chunchen Wu
- State Key Laboratory of Virology and Joint Laboratory of Invertebrate Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Simon Rayner
- State Key Laboratory of Virology and Joint Laboratory of Invertebrate Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Meifang Han
- Department of Infectious Disease, Institute of Infectious Disease, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fei Deng
- State Key Laboratory of Virology and Joint Laboratory of Invertebrate Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Ruikun Du
- State Key Laboratory of Virology and Joint Laboratory of Invertebrate Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jinliang Liu
- State Key Laboratory of Virology and Joint Laboratory of Invertebrate Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Manli Wang
- State Key Laboratory of Virology and Joint Laboratory of Invertebrate Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Hualin Wang
- State Key Laboratory of Virology and Joint Laboratory of Invertebrate Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Qin Ning
- Department of Infectious Disease, Institute of Infectious Disease, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhihong Hu
- State Key Laboratory of Virology and Joint Laboratory of Invertebrate Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
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Iyer S, Casey E, Bouzek H, Kim M, Deng W, Larsen BB, Zhao H, Bumgarner RE, Rolland M, Mullins JI. Comparison of Major and Minor Viral SNPs Identified through Single Template Sequencing and Pyrosequencing in Acute HIV-1 Infection. PLoS One 2015; 10:e0135903. [PMID: 26317928 PMCID: PMC4552882 DOI: 10.1371/journal.pone.0135903] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 07/27/2015] [Indexed: 01/03/2023] Open
Abstract
Massively parallel sequencing (MPS) technologies, such as 454-pyrosequencing, allow for the identification of variants in sequence populations at lower levels than consensus sequencing and most single-template Sanger sequencing experiments. We sought to determine if the greater depth of population sampling attainable using MPS technology would allow detection of minor variants in HIV founder virus populations very early in infection in instances where Sanger sequencing detects only a single variant. We compared single nucleotide polymorphisms (SNPs) during acute HIV-1 infection from 32 subjects using both single template Sanger and 454-pyrosequencing. Pyrosequences from a median of 2400 viral templates per subject and encompassing 40% of the HIV-1 genome, were compared to a median of five individually amplified near full-length viral genomes sequenced using Sanger technology. There was no difference in the consensus nucleotide sequences over the 3.6kb compared in 84% of the subjects infected with single founders and 33% of subjects infected with multiple founder variants: among the subjects with disagreements, mismatches were found in less than 1% of the sites evaluated (of a total of nearly 117,000 sites across all subjects). The majority of the SNPs observed only in pyrosequences were present at less than 2% of the subject’s viral sequence population. These results demonstrate the utility of the Sanger approach for study of early HIV infection and provide guidance regarding the design, utility and limitations of population sequencing from variable template sources, and emphasize parameters for improving the interpretation of massively parallel sequencing data to address important questions regarding target sequence evolution.
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Affiliation(s)
- Shyamala Iyer
- Department of Microbiology, University of Washington, Seattle, WA, 98195, United States of America
| | - Eleanor Casey
- Department of Microbiology, University of Washington, Seattle, WA, 98195, United States of America
| | - Heather Bouzek
- Department of Microbiology, University of Washington, Seattle, WA, 98195, United States of America
| | - Moon Kim
- Department of Microbiology, University of Washington, Seattle, WA, 98195, United States of America
| | - Wenjie Deng
- Department of Microbiology, University of Washington, Seattle, WA, 98195, United States of America
| | - Brendan B. Larsen
- Department of Microbiology, University of Washington, Seattle, WA, 98195, United States of America
| | - Hong Zhao
- Department of Microbiology, University of Washington, Seattle, WA, 98195, United States of America
| | - Roger E. Bumgarner
- Department of Microbiology, University of Washington, Seattle, WA, 98195, United States of America
| | - Morgane Rolland
- US Military HIV Research Program, WRAIR, Silver Spring, MD, 20910, United States of America
- Henry Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, 20817, United States of America
| | - James I. Mullins
- Department of Microbiology, University of Washington, Seattle, WA, 98195, United States of America
- Department of Medicine, University of Washington, Seattle, WA, 98195, United States of America
- Department of Laboratory Medicine, Seattle, WA, 98195, United States of America
- * E-mail:
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Ultradeep Sequencing for Detection of Quasispecies Variants in the Major Hydrophilic Region of Hepatitis B Virus in Indonesian Patients. J Clin Microbiol 2015. [PMID: 26202119 DOI: 10.1128/jcm.00602-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Quasispecies of hepatitis B virus (HBV) with variations in the major hydrophilic region (MHR) of the HBV surface antigen (HBsAg) can evolve during infection, allowing HBV to evade neutralizing antibodies. These escape variants may contribute to chronic infections. In this study, we looked for MHR variants in HBV quasispecies using ultradeep sequencing and evaluated the relationship between these variants and clinical manifestations in infected patients. We enrolled 30 Indonesian patients with hepatitis B infection (11 with chronic hepatitis and 19 with advanced liver disease). The most common subgenotype/subtype of HBV was B3/adw (97%). The HBsAg titer was lower in patients with advanced liver disease than that in patients with chronic hepatitis. The MHR variants were grouped based on the percentage of the viral population affected: major, ≥20% of the total population; intermediate, 5% to <20%; and minor, 1% to <5%. The rates of MHR variation that were present in the major and intermediate viral population were significantly greater in patients with advanced liver disease than those in chronic patients. The most frequent MHR variants related to immune evasion in the major and intermediate populations were P120Q/T, T123A, P127T, Q129H/R, M133L/T, and G145R. The major population of MHR variants causing impaired of HBsAg secretion (e.g., G119R, Q129R, T140I, and G145R) was detected only in advanced liver disease patients. This is the first study to use ultradeep sequencing for the detection of MHR variants of HBV quasispecies in Indonesian patients. We found that a greater number of MHR variations was related to disease severity and reduced likelihood of HBsAg titer.
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32
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Emerging technologies for the clinical microbiology laboratory. Clin Microbiol Rev 2015; 27:783-822. [PMID: 25278575 DOI: 10.1128/cmr.00003-14] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In this review we examine the literature related to emerging technologies that will help to reshape the clinical microbiology laboratory. These topics include nucleic acid amplification tests such as isothermal and point-of-care molecular diagnostics, multiplexed panels for syndromic diagnosis, digital PCR, next-generation sequencing, and automation of molecular tests. We also review matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) and electrospray ionization (ESI) mass spectrometry methods and their role in identification of microorganisms. Lastly, we review the shift to liquid-based microbiology and the integration of partial and full laboratory automation that are beginning to impact the clinical microbiology laboratory.
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33
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Colman RE, Schupp JM, Hicks ND, Smith DE, Buchhagen JL, Valafar F, Crudu V, Romancenco E, Noroc E, Jackson L, Catanzaro DG, Rodwell TC, Catanzaro A, Keim P, Engelthaler DM. Detection of Low-Level Mixed-Population Drug Resistance in Mycobacterium tuberculosis Using High Fidelity Amplicon Sequencing. PLoS One 2015; 10:e0126626. [PMID: 25970423 PMCID: PMC4430321 DOI: 10.1371/journal.pone.0126626] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 04/03/2015] [Indexed: 12/20/2022] Open
Abstract
Undetected and untreated, low-levels of drug resistant (DR) subpopulations in clinical Mycobacterium tuberculosis (Mtb) infections may lead to development of DR-tuberculosis, potentially resulting in treatment failure. Current phenotypic DR susceptibility testing has a theoretical potential for 1% sensitivity, is not quantitative, and requires several weeks to complete. The use of "single molecule-overlapping reads" (SMOR) analysis with next generation DNA sequencing for determination of ultra-rare target alleles in complex mixtures provides increased sensitivity over standard DNA sequencing. Ligation free amplicon sequencing with SMOR analysis enables the detection of resistant allele subpopulations at ≥0.1% of the total Mtb population in near real-time analysis. We describe the method using standardized mixtures of DNA from resistant and susceptible Mtb isolates and the assay's performance for detecting ultra-rare DR subpopulations in DNA extracted directly from clinical sputum samples. SMOR analysis enables rapid near real-time detection and tracking of previously undetectable DR sub-populations in clinical samples allowing for the evaluation of the clinical relevance of low-level DR subpopulations. This will provide insights into interventions aimed at suppressing minor DR subpopulations before they become clinically significant.
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MESH Headings
- Antitubercular Agents/pharmacology
- Antitubercular Agents/therapeutic use
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- Drug Resistance, Multiple, Bacterial/genetics
- Gene Frequency
- Genetic Loci
- High-Throughput Nucleotide Sequencing
- Humans
- Microbial Sensitivity Tests
- Molecular Diagnostic Techniques
- Mycobacterium tuberculosis/genetics
- Polymorphism, Single Nucleotide
- Sequence Analysis, DNA
- Sputum/microbiology
- Tuberculosis, Multidrug-Resistant/diagnosis
- Tuberculosis, Multidrug-Resistant/drug therapy
- Tuberculosis, Multidrug-Resistant/microbiology
- Tuberculosis, Pulmonary/diagnosis
- Tuberculosis, Pulmonary/drug therapy
- Tuberculosis, Pulmonary/microbiology
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Affiliation(s)
- Rebecca E. Colman
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
| | - James M. Schupp
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
| | - Nathan D. Hicks
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
| | - David E. Smith
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
| | - Jordan L. Buchhagen
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
| | - Faramarz Valafar
- San Diego State University, San Diego, CA, United States of America
| | - Valeriu Crudu
- Phthisiopneumology Institute (PPI), Chisinau, Republic of Moldova
| | - Elena Romancenco
- University of California San Diego, San Diego, CA, United States of America
| | - Ecaterina Noroc
- Phthisiopneumology Institute (PPI), Chisinau, Republic of Moldova
| | - Lynn Jackson
- University of California San Diego, San Diego, CA, United States of America
| | - Donald G. Catanzaro
- University of Arkansas College of Education and Health Professions, Fayetteville, AR, United States of America
| | - Timothy C. Rodwell
- University of California San Diego, San Diego, CA, United States of America
| | - Antonino Catanzaro
- University of California San Diego, San Diego, CA, United States of America
| | - Paul Keim
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
- Center for Microbial Genetics & Genomics, Northern Arizona University, Flagstaff, AZ, United States of America
| | - David M. Engelthaler
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
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Thys K, Verhasselt P, Reumers J, Verbist BMP, Maes B, Aerssens J. Performance assessment of the Illumina massively parallel sequencing platform for deep sequencing analysis of viral minority variants. J Virol Methods 2015; 221:29-38. [PMID: 25917877 DOI: 10.1016/j.jviromet.2015.04.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 03/21/2015] [Accepted: 04/16/2015] [Indexed: 11/26/2022]
Abstract
Massively parallel sequencing (MPS) technology has opened new avenues to study viral dynamics and treatment-induced resistance mechanisms of infections such as human immunodeficiency virus (HIV) and hepatitis C virus (HCV). Whereas the Roche/454 platform has been used widely for the detection of low-frequent drug resistant variants, more recently developed short-read MPS technologies have the advantage of delivering a higher sequencing depth at a lower cost per sequenced base. This study assesses the performance characteristics of Illumina MPS technology for the characterization of genetic variability in viral populations by deep sequencing. The reported results from MPS experiments comprising HIV and HCV plasmids demonstrate that a 0.5-1% lower limit of detection can be achieved readily with Illumina MPS while retaining good accuracy also at low frequencies. Deep sequencing of a set of clinical samples (12 HIV and 9 HCV patients), designed at a similar budget for both MPS platforms, reveals a comparable lower limit of detection for Illumina and Roche/454. Finally, this study shows the possibility to apply Illumina's paired-end sequencing as a strategy to assess linkage between different mutations identified in individual viral subspecies. These results support the use of Illumina as another MPS platform of choice for deep sequencing of viral minority species.
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Affiliation(s)
- Kim Thys
- Discovery Sciences, Janssen Research & Development, Turnhoutseweg 30, B-2340 Beerse, Belgium.
| | - Peter Verhasselt
- Discovery Sciences, Janssen Research & Development, Turnhoutseweg 30, B-2340 Beerse, Belgium.
| | - Joke Reumers
- Discovery Sciences, Janssen Research & Development, Turnhoutseweg 30, B-2340 Beerse, Belgium.
| | - Bie M P Verbist
- Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, 9000 Gent, Belgium.
| | - Bart Maes
- Discovery Sciences, Janssen Research & Development, Turnhoutseweg 30, B-2340 Beerse, Belgium.
| | - Jeroen Aerssens
- Discovery Sciences, Janssen Research & Development, Turnhoutseweg 30, B-2340 Beerse, Belgium.
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Flynn WF, Chang MW, Tan Z, Oliveira G, Yuan J, Okulicz JF, Torbett BE, Levy RM. Deep sequencing of protease inhibitor resistant HIV patient isolates reveals patterns of correlated mutations in Gag and protease. PLoS Comput Biol 2015; 11:e1004249. [PMID: 25894830 PMCID: PMC4404092 DOI: 10.1371/journal.pcbi.1004249] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 03/19/2015] [Indexed: 11/18/2022] Open
Abstract
While the role of drug resistance mutations in HIV protease has been studied comprehensively, mutations in its substrate, Gag, have not been extensively cataloged. Using deep sequencing, we analyzed a unique collection of longitudinal viral samples from 93 patients who have been treated with therapies containing protease inhibitors (PIs). Due to the high sequence coverage within each sample, the frequencies of mutations at individual positions were calculated with high precision. We used this information to characterize the variability in the Gag polyprotein and its effects on PI-therapy outcomes. To examine covariation of mutations between two different sites using deep sequencing data, we developed an approach to estimate the tight bounds on the two-site bivariate probabilities in each viral sample, and the mutual information between pairs of positions based on all the bounds. Utilizing the new methodology we found that mutations in the matrix and p6 proteins contribute to continued therapy failure and have a major role in the network of strongly correlated mutations in the Gag polyprotein, as well as between Gag and protease. Although covariation is not direct evidence of structural propensities, we found the strongest correlations between residues on capsid and matrix of the same Gag protein were often due to structural proximity. This suggests that some of the strongest inter-protein Gag correlations are the result of structural proximity. Moreover, the strong covariation between residues in matrix and capsid at the N-terminus with p1 and p6 at the C-terminus is consistent with residue-residue contacts between these proteins at some point in the viral life cycle. Understanding the structure of HIV proteins and the function of drug-resistant mutations of these proteins is critical for the development of effective HIV treatments. Selected gag mutations have been shown to provide compensatory functions for protease resistance mutations and may directly contribute to the development of drug resistance. To determine associations between protease inhibitor mutations and gag, we utilized deep sequencing of HIV gag and protease from a collection of viral isolates from patients treated with highly active retroviral protease inhibitors. Deep sequencing allows for accurate measurement of mutation frequencies at each position, allowing estimation, using a novel method we developed, of the covariation between any two residues on gag. Using this information, we characterize the variation within gag and protease and identify the most strongly correlated pairs of inter- and intra-protein residues. Our results suggest that matrix and p1/p6 mutations form the core of a network of strongly correlated gag mutations and contribute to recurrent treatment failure. Extracting gag residue covariation information from the deep sequencing of patient viral samples may provide insight into structural aspects of the Gag polyprotein as well new areas for small molecule targeting to disrupt Gag function.
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Affiliation(s)
- William F. Flynn
- Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey, United States of America
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Max W. Chang
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Zhiqiang Tan
- Department of Statistics, Rutgers University, Piscataway, New Jersey, United States of America
| | - Glenn Oliveira
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jinyun Yuan
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jason F. Okulicz
- Infectious Disease Service, San Antonio Military Medical Center, San Antonio, Texas, United States of America
| | - Bruce E. Torbett
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail: (BET); (RML)
| | - Ronald M. Levy
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania, United States of America
- Department of Chemistry, and Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania, United States of America
- * E-mail: (BET); (RML)
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36
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Brodin J, Hedskog C, Heddini A, Benard E, Neher RA, Mild M, Albert J. Challenges with using primer IDs to improve accuracy of next generation sequencing. PLoS One 2015; 10:e0119123. [PMID: 25741706 PMCID: PMC4351057 DOI: 10.1371/journal.pone.0119123] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Accepted: 12/23/2014] [Indexed: 01/09/2023] Open
Abstract
Next generation sequencing technologies, like ultra-deep pyrosequencing (UDPS), allows detailed investigation of complex populations, like RNA viruses, but its utility is limited by errors introduced during sample preparation and sequencing. By tagging each individual cDNA molecule with barcodes, referred to as Primer IDs, before PCR and sequencing these errors could theoretically be removed. Here we evaluated the Primer ID methodology on 257,846 UDPS reads generated from a HIV-1 SG3Δenv plasmid clone and plasma samples from three HIV-infected patients. The Primer ID consisted of 11 randomized nucleotides, 4,194,304 combinations, in the primer for cDNA synthesis that introduced a unique sequence tag into each cDNA molecule. Consensus template sequences were constructed for reads with Primer IDs that were observed three or more times. Despite high numbers of input template molecules, the number of consensus template sequences was low. With 10,000 input molecules for the clone as few as 97 consensus template sequences were obtained due to highly skewed frequency of resampling. Furthermore, the number of sequenced templates was overestimated due to PCR errors in the Primer IDs. Finally, some consensus template sequences were erroneous due to hotspots for UDPS errors. The Primer ID methodology has the potential to provide highly accurate deep sequencing. However, it is important to be aware that there are remaining challenges with the methodology. In particular it is important to find ways to obtain a more even frequency of resampling of template molecules as well as to identify and remove artefactual consensus template sequences that have been generated by PCR errors in the Primer IDs.
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Affiliation(s)
- Johanna Brodin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
| | - Charlotte Hedskog
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alexander Heddini
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Emmanuel Benard
- Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Richard A. Neher
- Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Mattias Mild
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Unit for Support, Swedish Institute for Communicable Disease Control, Stockholm, Sweden
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
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Nelson CW, Hughes AL. Within-host nucleotide diversity of virus populations: insights from next-generation sequencing. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2015; 30:1-7. [PMID: 25481279 PMCID: PMC4316684 DOI: 10.1016/j.meegid.2014.11.026] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 11/26/2014] [Accepted: 11/27/2014] [Indexed: 01/03/2023]
Abstract
Next-generation sequencing (NGS) technology offers new opportunities for understanding the evolution and dynamics of viral populations within individual hosts over the course of infection. We review simple methods for estimating synonymous and nonsynonymous nucleotide diversity in viral genes from NGS data without the need for inferring linkage. We discuss the potential usefulness of these data for addressing questions of both practical and theoretical interest, including fundamental questions regarding the effective population sizes of within-host viral populations and the modes of natural selection acting on them.
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Affiliation(s)
- Chase W Nelson
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Austin L Hughes
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.
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Drug resistance and plasma viral RNA level after ineffective use of oral pre-exposure prophylaxis in women. AIDS 2015; 29:331-7. [PMID: 25503265 DOI: 10.1097/qad.0000000000000556] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Pre-exposure prophylaxis (PrEP) with daily oral emtricitabine (FTC)/tenofovir disoproxil fumarate may select for drug resistance if there is low adherence. METHODS Plasma viral HIV-1 RNA level, CD4+ T-cell counts, and drug resistance were evaluated among seroconverting women in the FEM-PrEP trial (clinicaltrials.gov NCT00625404) using standard clinical tests, allele-specific PCR (ASPCR), and by deep sequencing. Tenofovir, FTC, and their intracellular metabolites were measured in plasma and cells. RESULTS There was no difference in plasma HIV-1 RNA level or CD4+ cell count among seroconverters in the active arm versus those receiving placebo. Tenofovir resistance was not observed. FTC resistance was detected using clinical assays in five seroconverters (four in the active arm and one in the placebo arm); two in the active arm occurred among women having moderate concentrations of PrEP drugs in the blood. The first evidence of infection occurred at the first postenrollment visit in three of the four with FTC resistance, although none had detectable viral nucleic acids at enrollment. FTC-resistant minor variants were detected in an additional four seroconverters (one in the active arm and three in the placebo arm). CONCLUSIONS Drug resistance detected during ineffective PrEP use had characteristics suggesting transmitted infection or incubating infection prior to starting PrEP.
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Dudley DM, Bailey AL, Mehta SH, Hughes AL, Kirk GD, Westergaard RP, O'Connor DH. Cross-clade simultaneous HIV drug resistance genotyping for reverse transcriptase, protease, and integrase inhibitor mutations by Illumina MiSeq. Retrovirology 2014; 11:122. [PMID: 25533166 PMCID: PMC4302432 DOI: 10.1186/s12977-014-0122-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 12/03/2014] [Indexed: 11/30/2022] Open
Abstract
Background Viral resistance to antiretroviral therapy threatens our best methods to control and prevent HIV infection. Current drug resistance genotyping methods are costly, optimized for subtype B virus, and primarily detect resistance mutations to protease and reverse transcriptase inhibitors. With the increasing use of integrase inhibitors in first-line therapies, monitoring for integrase inhibitor drug resistance mutations is a priority. We designed a universal primer pair to PCR amplify all major group M HIV-1 viruses for genotyping using Illumina MiSeq to simultaneously detect drug resistance mutations associated with protease, nucleoside reverse transcriptase, non-nucleoside reverse transcriptase, and integrase inhibitors. Results A universal primer pair targeting the HIV pol gene was used to successfully PCR amplify HIV isolates representing subtypes A, B, C, D, CRF01_AE and CRF02_AG. The universal primers were then tested on 62 samples from a US cohort of injection drug users failing treatment after release from prison. 94% of the samples were successfully genotyped for known drug resistance mutations in the protease, reverse transcriptase and integrase gene products. Control experiments demonstrate that mutations present at ≥ 2% frequency are reliably detected and above the threshold of error for this method. New drug resistance mutations not found in the baseline sample were identified in 54% of the patient samples after treatment failure. 86% of patients with major drug resistance mutations had 1 or more mutations associated with drug resistance to the treatment regimen at the time point of treatment failure. 59% of the emerging mutations were found at frequencies between 2% and 20% of the total sequences generated, below the estimated limit of detection of current FDA-approved genotyping techniques. Primary plasma samples with viral loads as low as 799 copies/ml were successfully genotyped using this method. Conclusions Here we present an Illumina MiSeq-based HIV drug resistance genotyping assay. Our data suggests that this universal assay works across all major group M HIV-1 subtypes and identifies all drug resistance mutations in the pol gene known to confer resistance to protease, reverse transcriptase and integrase inhibitors. This high-throughput and sensitive assay could significantly improve access to drug resistance genotyping worldwide. Electronic supplementary material The online version of this article (doi:10.1186/s12977-014-0122-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dawn M Dudley
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
| | - Adam L Bailey
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
| | - Shruti H Mehta
- Department of Epidemiology, Epidemiology and Oncology, Johns Hopkins University, Baltimore, MD, USA.
| | - Austin L Hughes
- Department of Biology, University of South Carolina, Columbia, South Carolina, USA.
| | - Gregory D Kirk
- Departments of Medicine, Epidemiology and Oncology, Johns Hopkins University, Baltimore, MD, USA.
| | - Ryan P Westergaard
- Department of Medicine, Division of Infectious Disease, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
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40
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Ram D, Leshkowitz D, Gonzalez D, Forer R, Levy I, Chowers M, Lorber M, Hindiyeh M, Mendelson E, Mor O. Evaluation of GS Junior and MiSeq next-generation sequencing technologies as an alternative to Trugene population sequencing in the clinical HIV laboratory. J Virol Methods 2014; 212:12-6. [PMID: 25445792 DOI: 10.1016/j.jviromet.2014.11.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 11/02/2014] [Accepted: 11/04/2014] [Indexed: 01/20/2023]
Abstract
Population HIV-1 sequencing is currently the method of choice for the identification and follow-up of HIV-1 antiretroviral drug resistance. It has limited sensitivity and results in a consensus sequence showing the most prevalent nucleotide per position. Moreover concomitant sequencing and interpretation of the results for several samples together is laborious and time consuming. In this study, the practical use of GS Junior and MiSeq bench-top next generation sequencing (NGS) platforms as an alternative to Trugene Sanger-based population sequencing in the clinical HIV laboratory was assessed. DeepChek(®)-HIV TherapyEdge software was used for processing all the protease and reverse transcriptase sequences and for resistance interpretation. Plasma samples from nine HIV-1 carriers, representing the major HIV-1 subtypes in Israel, were compared. The total number of amino acid substitutions identified in the nine samples by GS Junior (232 substitutions) and MiSeq (243 substitutions) was similar and higher than Trugene (181 substitutions), emphasizing the advantage of deep sequencing on population sequencing. More than 80% of the identified substitutions were identical between the GS Junior and MiSeq platforms, most of which (184 of 199) at similar frequency. Low abundance substitutions accounted for 20.9% of the MiSeq and 21.9% of the GS Junior output, the majority of which were not detected by Trugene. More drug resistance mutations were identified by both the NGS platforms, primarily, but not only, at low abundance. In conclusion, in combination with DeepChek, both GS Junior and MiSeq were found to be more sensitive than Trugene and adequate for HIV-1 resistance analysis in the clinical HIV laboratory.
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Affiliation(s)
- Daniela Ram
- National HIV Reference Laboratory, Central Virology Laboratory, Ministry of Health, Tel-Hashomer, Ramat-Gan, Israel.
| | - Dena Leshkowitz
- Bioinformatics Unit, The Nancy and Stephen Grand National Center for Personalized Medicine, Weizmann Institute, Rehovot, Israel.
| | | | | | - Itzchak Levy
- Infectious Disease Unit, Sheba Medical Center, Tel-Hashomer, Ramat-Gan, Israel.
| | - Michal Chowers
- Infectious Disease Unit, Meir Medical Center, Kfar Saba, Israel.
| | - Margalit Lorber
- Autoimmune Disease Unit, Rambam Medical Center, Haifa, Israel.
| | - Musa Hindiyeh
- National HIV Reference Laboratory, Central Virology Laboratory, Ministry of Health, Tel-Hashomer, Ramat-Gan, Israel; Tel-Aviv University, Tel-Aviv, Israel.
| | - Ella Mendelson
- National HIV Reference Laboratory, Central Virology Laboratory, Ministry of Health, Tel-Hashomer, Ramat-Gan, Israel; Tel-Aviv University, Tel-Aviv, Israel.
| | - Orna Mor
- National HIV Reference Laboratory, Central Virology Laboratory, Ministry of Health, Tel-Hashomer, Ramat-Gan, Israel.
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Rawson JMO, Mansky LM. Retroviral vectors for analysis of viral mutagenesis and recombination. Viruses 2014; 6:3612-42. [PMID: 25254386 PMCID: PMC4189041 DOI: 10.3390/v6093612] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 09/15/2014] [Accepted: 09/17/2014] [Indexed: 12/29/2022] Open
Abstract
Retrovirus population diversity within infected hosts is commonly high due in part to elevated rates of replication, mutation, and recombination. This high genetic diversity often complicates the development of effective diagnostics, vaccines, and antiviral drugs. This review highlights the diverse vectors and approaches that have been used to examine mutation and recombination in retroviruses. Retroviral vectors for these purposes can broadly be divided into two categories: those that utilize reporter genes as mutation or recombination targets and those that utilize viral genes as targets of mutation or recombination. Reporter gene vectors greatly facilitate the detection, quantification, and characterization of mutants and/or recombinants, but may not fully recapitulate the patterns of mutagenesis or recombination observed in native viral gene sequences. In contrast, the detection of mutations or recombination events directly in viral genes is more biologically relevant but also typically more challenging and inefficient. We will highlight the advantages and disadvantages of the various vectors and approaches used as well as propose ways in which they could be improved.
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Affiliation(s)
- Jonathan M O Rawson
- Institute for Molecular Virology, University of Minnesota, Moos Tower 18-242, 515 Delaware St SE, Minneapolis, MN 55455, USA.
| | - Louis M Mansky
- Institute for Molecular Virology, University of Minnesota, Moos Tower 18-242, 515 Delaware St SE, Minneapolis, MN 55455, USA.
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Leung RKK, Dong ZQ, Sa F, Chong CM, Lei SW, Tsui SKW, Lee SMY. Quick, sensitive and specific detection and evaluation of quantification of minor variants by high-throughput sequencing. MOLECULAR BIOSYSTEMS 2014; 10:206-14. [PMID: 24264059 DOI: 10.1039/c3mb70334g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Minor variants have significant implications in quasispecies evolution, early cancer detection and non-invasive fetal genotyping but their accurate detection by next-generation sequencing (NGS) is hampered by sequencing errors. We generated sequencing data from mixtures at predetermined ratios in order to provide insight into sequencing errors and variations that can arise for which simulation cannot be performed. The information also enables better parameterization in depth of coverage, read quality and heterogeneity, library preparation techniques, technical repeatability for mathematical modeling, theory development and simulation experimental design. We devised minor variant authentication rules that achieved 100% accuracy in both testing and validation experiments. The rules are free from tedious inspection of alignment accuracy, sequencing read quality or errors introduced by homopolymers. The authentication processes only require minor variants to: (1) have minimum depth of coverage larger than 30; (2) be reported by (a) four or more variant callers, or (b) DiBayes or LoFreq, plus SNVer (or BWA when no results are returned by SNVer), and with the interassay coefficient of variation (CV) no larger than 0.1. Quantification accuracy undermined by sequencing errors could neither be overcome by ultra-deep sequencing, nor recruiting more variant callers to reach a consensus, such that consistent underestimation and overestimation (i.e. low CV) were observed. To accommodate stochastic error and adjust the observed ratio within a specified accuracy, we presented a proof of concept for the use of a double calibration curve for quantification, which provides an important reference towards potential industrial-scale fabrication of calibrants for NGS.
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Affiliation(s)
- Ross Ka-Kit Leung
- Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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Al-Mawsawi LQ, Wu NC, De La Cruz J, Shi VC, Wu TT, Daar ES, Lewis MJ, Yang OO, Sun R. Short communication: HIV-1 gag genetic variation in a single acutely infected participant defined by high-resolution deep sequencing. AIDS Res Hum Retroviruses 2014; 30:806-11. [PMID: 24914638 DOI: 10.1089/aid.2014.0097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Acute HIV-1 infection is characterized by the rapid generation of highly diverse genetic variants to adapt to the new host environment. Understanding the dynamics of viral genetic variation at this stage of infection is critical for vaccine design efforts and early drug treatment. Here, using a high-resolution deep sequencing approach targeting the HIV-1 gag region, we reveal very early immune pressure with dramatic subpopulation shifts in a single acutely infected participant providing further insight into the genetic dynamics of acute HIV-1 infection.
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Affiliation(s)
- Laith Q Al-Mawsawi
- 1 Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at University of California , Los Angeles, Los Angeles, California
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Quiñones-Mateu ME, Avila S, Reyes-Teran G, Martinez MA. Deep sequencing: becoming a critical tool in clinical virology. J Clin Virol 2014; 61:9-19. [PMID: 24998424 DOI: 10.1016/j.jcv.2014.06.013] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/12/2014] [Accepted: 06/14/2014] [Indexed: 02/07/2023]
Abstract
Population (Sanger) sequencing has been the standard method in basic and clinical DNA sequencing for almost 40 years; however, next-generation (deep) sequencing methodologies are now revolutionizing the field of genomics, and clinical virology is no exception. Deep sequencing is highly efficient, producing an enormous amount of information at low cost in a relatively short period of time. High-throughput sequencing techniques have enabled significant contributions to multiples areas in virology, including virus discovery and metagenomics (viromes), molecular epidemiology, pathogenesis, and studies of how viruses to escape the host immune system and antiviral pressures. In addition, new and more affordable deep sequencing-based assays are now being implemented in clinical laboratories. Here, we review the use of the current deep sequencing platforms in virology, focusing on three of the most studied viruses: human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus.
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Affiliation(s)
- Miguel E Quiñones-Mateu
- University Hospital Translational Laboratory, University Hospitals Case Medical Center, Cleveland, OH, USA; Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Santiago Avila
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico
| | - Gustavo Reyes-Teran
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico
| | - Miguel A Martinez
- Fundació irsicaixa, Universitat Autònoma de Barcelona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
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Comparison of quasispecies diversity of HCV between chronic hepatitis c and hepatocellular carcinoma by Ultradeep pyrosequencing. BIOMED RESEARCH INTERNATIONAL 2014; 2014:853076. [PMID: 24999482 PMCID: PMC4066718 DOI: 10.1155/2014/853076] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/01/2014] [Indexed: 02/07/2023]
Abstract
Backgrounds. Hepatitis C virus (HCV) exists as population of closely related genetic variants known as quasispecies. HCV quasispecies diversity is strongly influenced by host immune pressure on virus. Quasispecies diversity is expected to decline as host immune response to HCV decreases over natural course of progressing from chronic hepatitis C (CHC) to hepatocellular carcinoma (HCC). Methods. Ultradeep pyrosequencing (UDPS) was used to evaluate degree of quasispecies diversity in 49 patients infected with HCV including 26 with CHC and 23 with HCC. Whole structural protein of HCV genome was subjected to UDPS. Results. Shannon's indices for quasispecies diversity in HCV E1 were significantly lower in patients with HCC than in those with CHC. 14 amino acid positions differed significantly between two groups. Area under curve of ROC analysis for differentiating HCC from CHC was >0.8 for all of 14 amino acid positions. Conclusion. HCV quasispecies diversity as indicator of declining host immune functions was easily assessed by UDPS technology. Shannon's indices in 14 amino acid positions were found to differentiate between patients with CHC and those with HCC. Our data propose that degree of HCV quasispecies measured by UDPS might be useful to predict progression of HCC in chronic HCV patients.
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Kijak GH, Sanders-Buell E, Harbolick EA, Pham P, Chenine AL, Eller LA, Rono K, Robb ML, Michael NL, Kim JH, Tovanabutra S. Targeted deep sequencing of HIV-1 using the IonTorrentPGM platform. J Virol Methods 2014; 205:7-16. [PMID: 24797459 DOI: 10.1016/j.jviromet.2014.04.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 04/11/2014] [Accepted: 04/25/2014] [Indexed: 10/25/2022]
Abstract
The characterization of mixed HIV-1 populations is a key question in clinical and basic research settings. This can be achieved through targeted deep sequencing (TDS), where next-generation sequencing is used to examine in depth a sub-genomic region of interest. This study explores the suitability of IonTorrent PGM(LifeTechnologies) for the TDS-based analysis of HIV-1 evolution. Using laboratory reagents and primary specimens sampled at pre-peak viremia the error rates from misincorporation and in vitro recombination were <0.5%. The sequencing error rate was 2- to 3-fold higher in/around homopolymeric tracts, and could be discerned from true polymorphism using bidirectional sequencing. The limit of detection of complex variants was further lowered by using haplotyping. The application of this system was illustrated on primary samples from an individual infected with HIV-1 followed from pre-peak viremia through six months post-acquisition. TDS provided an augmented view of the extent of genetic diversity, the covariation among polymorphisms, the evolutionary pathways, and the boundaries of the mutational space explored by the viral swarm. Based on its performance, the system can be applied for the characterization of minor viral variants in support of studies of viral evolution, which can inform the rational design of the next generation of vaccines and therapeutics.
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Affiliation(s)
- Gustavo H Kijak
- U.S. Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
| | - Eric Sanders-Buell
- U.S. Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Elizabeth A Harbolick
- U.S. Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Phuc Pham
- U.S. Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Agnes L Chenine
- U.S. Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Leigh Anne Eller
- U.S. Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Kathleen Rono
- Kenya Medical Research Institute/Walter Reed Project, Kericho, Kenya
| | - Merlin L Robb
- U.S. Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Nelson L Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Jerome H Kim
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
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McElroy K, Thomas T, Luciani F. Deep sequencing of evolving pathogen populations: applications, errors, and bioinformatic solutions. MICROBIAL INFORMATICS AND EXPERIMENTATION 2014; 4:1. [PMID: 24428920 PMCID: PMC3902414 DOI: 10.1186/2042-5783-4-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 01/07/2014] [Indexed: 12/15/2022]
Abstract
Deep sequencing harnesses the high throughput nature of next generation sequencing technologies to generate population samples, treating information contained in individual reads as meaningful. Here, we review applications of deep sequencing to pathogen evolution. Pioneering deep sequencing studies from the virology literature are discussed, such as whole genome Roche-454 sequencing analyses of the dynamics of the rapidly mutating pathogens hepatitis C virus and HIV. Extension of the deep sequencing approach to bacterial populations is then discussed, including the impacts of emerging sequencing technologies. While it is clear that deep sequencing has unprecedented potential for assessing the genetic structure and evolutionary history of pathogen populations, bioinformatic challenges remain. We summarise current approaches to overcoming these challenges, in particular methods for detecting low frequency variants in the context of sequencing error and reconstructing individual haplotypes from short reads.
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Affiliation(s)
- Kerensa McElroy
- Centre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW 2052, Australia.
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48
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Improved detection of rare HIV-1 variants using 454 pyrosequencing. PLoS One 2013; 8:e76502. [PMID: 24098517 PMCID: PMC3788733 DOI: 10.1371/journal.pone.0076502] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 08/27/2013] [Indexed: 01/21/2023] Open
Abstract
454 pyrosequencing, a massively parallel sequencing (MPS) technology, is often used to study HIV genetic variation. However, the substantial mismatch error rate of the PCR required to prepare HIV-containing samples for pyrosequencing has limited the detection of rare variants within viral populations to those present above ~1%. To improve detection of rare variants, we varied PCR enzymes and conditions to identify those that combined high sensitivity with a low error rate. Substitution errors were found to vary up to 3-fold between the different enzymes tested. The sensitivity of each enzyme, which impacts the number of templates amplified for pyrosequencing, was shown to vary, although not consistently across genes and different samples. We also describe an amplicon-based method to improve the consistency of read coverage over stretches of the HIV-1 genome. Twenty-two primers were designed to amplify 11 overlapping amplicons in the HIV-1 clade B gag-pol and env gp120 coding regions to encompass 4.7 kb of the viral genome per sample at sensitivities as low as 0.01-0.2%.
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Xu Z, Wu G, Li F, Bai J, Xing W, Zhang D, Zeng C. Positive selection signals of hepatitis B virus and their association with disease stages and viral genotypes. INFECTION GENETICS AND EVOLUTION 2013; 19:176-87. [DOI: 10.1016/j.meegid.2013.07.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 06/27/2013] [Accepted: 07/06/2013] [Indexed: 12/18/2022]
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50
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McCallum M, Oliveira M, Ibanescu RI, Kramer VG, Moisi D, Asahchop EL, Brenner BG, Harrigan PR, Xu H, Wainberg MA. Basis for early and preferential selection of the E138K mutation in HIV-1 reverse transcriptase. Antimicrob Agents Chemother 2013; 57:4681-8. [PMID: 23856772 PMCID: PMC3811420 DOI: 10.1128/aac.01029-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 07/05/2013] [Indexed: 12/13/2022] Open
Abstract
E138K, a G→A mutation in HIV-1 reverse transcriptase (RT), is preferentially selected by etravirine (ETR) and rilpivirine over other substitutions at position E138 that offer greater drug resistance. We hypothesized that there was a mutational bias for the E138K substitution and designed an allele-specific PCR to monitor the emergence of E138A/G/K/Q/R/V during ETR selection experiments. We also performed competition experiments using mutated viruses and quantified the prevalence of E138 minority species in drug-naive patients. E138K, as well as E138G, consistently emerged first during ETR selection experiments, followed by E138A and E138Q; E138R was never selected. Surprisingly, E138K was identified as a tiny minority in 23% of drug-naive subtype B patients, a result confirmed by ultradeep sequencing (UDS). This result could reflect a low fitness cost of E138K; however, E138K was one of the least fit substitutions at codon E138, even after taking into account the deoxynucleoside triphosphate pools of the cells used in competition experiments. Further UDS analysis revealed other minority species in a pattern consistent with the mutational bias of HIV RT. There was no evidence of APOBEC3-hypermutation in these selection experiments or in patients. Our results confirm the mutational bias of HIV-1 in patients and highlight the importance of G→A mutations in HIV-1 drug resistance evolution.
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Affiliation(s)
- Matthew McCallum
- McGill University AIDS Centre, Lady Davis Institute of Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Maureen Oliveira
- McGill University AIDS Centre, Lady Davis Institute of Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Ruxandra-Ilinca Ibanescu
- McGill University AIDS Centre, Lady Davis Institute of Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Victor G. Kramer
- McGill University AIDS Centre, Lady Davis Institute of Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Daniela Moisi
- McGill University AIDS Centre, Lady Davis Institute of Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Eugene L. Asahchop
- McGill University AIDS Centre, Lady Davis Institute of Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Bluma G. Brenner
- McGill University AIDS Centre, Lady Davis Institute of Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - P. Richard Harrigan
- BC Center for Excellence in HIV/AIDS, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hongtao Xu
- McGill University AIDS Centre, Lady Davis Institute of Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Mark A. Wainberg
- McGill University AIDS Centre, Lady Davis Institute of Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- Department of Experimental Medicine, McGill University, Montreal, Quebec, Canada
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