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Colson P, Bader W, Fantini J, Dudouet P, Levasseur A, Pontarotti P, Devaux C, Raoult D. From viral democratic genomes to viral wild bunch of quasispecies. J Med Virol 2023; 95:e29209. [PMID: 37937701 DOI: 10.1002/jmv.29209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/05/2023] [Accepted: 10/19/2023] [Indexed: 11/09/2023]
Abstract
The tremendous majority of RNA genomes from pathogenic viruses analyzed and deposited in databases are consensus or "democratic" genomes. They represent the genomes most frequently found in the clinical samples of patients but do not account for the huge genetic diversity of coexisting genomes, which is better described as quasispecies. A viral quasispecies is defined as the dynamic distribution of nonidentical but closely related mutants, variants, recombinant, or reassortant viral genomes. Viral quasispecies have collective behavior and dynamics and are the subject of internal interactions that comprise interference, complementation, or cooperation. In the setting of SARS-CoV-2 infection, intrahost SARS-CoV-2 genetic diversity was recently notably reported for immunocompromised, chronically infected patients, for patients treated with monoclonal antibodies targeting the viral spike protein, and for different body compartments of a single patient. A question that deserves attention is whether such diversity is generated postinfection from a clonal genome in response to selection pressure or is already present at the time of infection as a quasispecies. In the present review, we summarize the data supporting that hosts are infected by a "wild bunch" of viruses rather than by multiple virions sharing the same genome. Each virion in the "wild bunch" may have different virulence and tissue tropisms. As the number of viruses replicated during host infections is huge, a viral quasispecies at any time of infection is wide and is also influenced by host-specific selection pressure after infection, which accounts for the difficulty in deciphering and predicting the appearance of more fit variants and the evolution of epidemics of novel RNA viruses.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Wahiba Bader
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Jacques Fantini
- INSERM UMR_S 1072, Aix-Marseille Université, Marseille, France
| | - Pierre Dudouet
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Pierre Pontarotti
- IHU Méditerranée Infection, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS)-SNC5039, Marseille, France
| | - Christian Devaux
- IHU Méditerranée Infection, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS)-SNC5039, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
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Lapointe HR, Dong W, Dong WWY, Kirkby D, Woods C, Poon AFY, Howe AYM, Harrigan PR, Brumme CJ. Validation of a Genotype-Independent Hepatitis C Virus Near-Whole Genome Sequencing Assay. Viruses 2021; 13:v13091721. [PMID: 34578305 PMCID: PMC8473162 DOI: 10.3390/v13091721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/17/2021] [Accepted: 08/26/2021] [Indexed: 11/16/2022] Open
Abstract
Despite the effectiveness of direct-acting antiviral agents in treating hepatitis C virus (HCV), cases of treatment failure have been associated with the emergence of resistance-associated substitutions. To better guide clinical decision-making, we developed and validated a near-whole-genome HCV genotype-independent next-generation sequencing strategy. HCV genotype 1-6 samples from direct-acting antiviral agent treatment-naïve and -treated HCV-infected individuals were included. Viral RNA was extracted using a NucliSens easyMAG and amplified using nested reverse transcription-polymerase chain reaction. Libraries were prepared using Nextera XT and sequenced on the Illumina MiSeq sequencing platform. Data were processed by an in-house pipeline (MiCall). Nucleotide consensus sequences were aligned to reference strain sequences for resistance-associated substitution identification and compared to NS3, NS5a, and NS5b sequence data obtained from a validated in-house assay optimized for HCV genotype 1. Sequencing success rates (defined as achieving >100-fold read coverage) approaching 90% were observed for most genotypes in samples with a viral load >5 log10 IU/mL. This genotype-independent sequencing method resulted in >99.8% nucleotide concordance with the genotype 1-optimized method, and 100% agreement in genotype assignment with paired line probe assay-based genotypes. The assay demonstrated high intra-run repeatability and inter-run reproducibility at detecting substitutions above 2% prevalence. This study highlights the performance of a freely available laboratory and bioinformatic approach for reliable HCV genotyping and resistance-associated substitution detection regardless of genotype.
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Affiliation(s)
- Hope R. Lapointe
- Department of Medicine, Division of Social Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (H.R.L.); (P.R.H.)
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (W.W.Y.D.); (D.K.); (C.W.)
| | - Weiyan Dong
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (W.W.Y.D.); (D.K.); (C.W.)
| | - Winnie W. Y. Dong
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (W.W.Y.D.); (D.K.); (C.W.)
| | - Don Kirkby
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (W.W.Y.D.); (D.K.); (C.W.)
| | - Conan Woods
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (W.W.Y.D.); (D.K.); (C.W.)
| | - Art F. Y. Poon
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
| | - Anita Y. M. Howe
- British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4, Canada;
| | - P. Richard Harrigan
- Department of Medicine, Division of Social Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (H.R.L.); (P.R.H.)
| | - Chanson J. Brumme
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (W.W.Y.D.); (D.K.); (C.W.)
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Correspondence:
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Cuypers L, Thijssen M, Shakibzadeh A, Sabahi F, Ravanshad M, Pourkarim MR. Next-generation sequencing for the clinical management of hepatitis C virus infections: does one test fits all purposes? Crit Rev Clin Lab Sci 2019; 56:420-434. [PMID: 31317801 DOI: 10.1080/10408363.2019.1637394] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
While the prospect of viral cure is higher than ever for individuals infected with the hepatitis C virus (HCV) due to ground-breaking progress in antiviral treatment, success rates are still negatively influenced by HCV's high genetic variability. This genetic diversity is represented in the circulation of various genotypes and subtypes, mixed infections, recombinant forms and the presence of numerous drug resistant variants among infected individuals. Common misclassifications by commercial genotyping assays in combination with the limitations of currently used targeted population sequencing approaches have encouraged researchers to exploit alternative methods for the clinical management of HCV infections. Next-generation sequencing (NGS), a revolutionary and powerful tool with a variety of applications in clinical virology, can characterize viral diversity and depict viral dynamics in an ultra-wide and ultra-deep manner. The level of detail it provides makes it the method of choice for the diagnosis and clinical assessment of HCV infections. The sequence library provided by NGS is of a higher magnitude and sensitivity than data generated by conventional methods. Therefore, these technologies are helpful to guide clinical practice and at the same time highly valuable for epidemiological studies. The decreasing costs of NGS to determine genotypes, mixed infections, recombinant strains and drug resistant variants will soon make it feasible to employ NGS in clinical laboratories, to assist in the daily care of patients with HCV.
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Affiliation(s)
- Lize Cuypers
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven , Leuven , Belgium
| | - Marijn Thijssen
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven , Leuven , Belgium
| | - Arash Shakibzadeh
- Department of Medical Virology, Faculty of Medical Sciences, Tarbiat Modares University , Tehran , Iran
| | - Farzaneh Sabahi
- Department of Medical Virology, Faculty of Medical Sciences, Tarbiat Modares University , Tehran , Iran
| | - Mehrdad Ravanshad
- Department of Medical Virology, Faculty of Medical Sciences, Tarbiat Modares University , Tehran , Iran
| | - Mahmoud Reza Pourkarim
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven , Leuven , Belgium.,Health Policy Research Center, Institute of Health, Shiraz University of Medical Sciences , Shiraz , Iran.,Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine , Tehran , Iran
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Ho CKY, Raghwani J, Koekkoek S, Liang RH, Van der Meer JTM, Van Der Valk M, De Jong M, Pybus OG, Schinkel J, Molenkamp R. Characterization of Hepatitis C Virus (HCV) Envelope Diversification from Acute to Chronic Infection within a Sexually Transmitted HCV Cluster by Using Single-Molecule, Real-Time Sequencing. J Virol. 2017;91:pii: e02262-16. [PMID: 28077634 DOI: 10.1128/jvi.02262-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 12/29/2016] [Indexed: 12/18/2022] Open
Abstract
In contrast to other available next-generation sequencing platforms, PacBio single-molecule, real-time (SMRT) sequencing has the advantage of generating long reads albeit with a relatively higher error rate in unprocessed data. Using this platform, we longitudinally sampled and sequenced the hepatitis C virus (HCV) envelope genome region (1,680 nucleotides [nt]) from individuals belonging to a cluster of sexually transmitted cases. All five subjects were coinfected with HIV-1 and a closely related strain of HCV genotype 4d. In total, 50 samples were analyzed by using SMRT sequencing. By using 7 passes of circular consensus sequencing, the error rate was reduced to 0.37%, and the median number of sequences was 612 per sample. A further reduction of insertions was achieved by alignment against a sample-specific reference sequence. However, in vitro recombination during PCR amplification could not be excluded. Phylogenetic analysis supported close relationships among HCV sequences from the four male subjects and subsequent transmission from one subject to his female partner. Transmission was characterized by a strong genetic bottleneck. Viral genetic diversity was low during acute infection and increased upon progression to chronicity but subsequently fluctuated during chronic infection, caused by the alternate detection of distinct coexisting lineages. SMRT sequencing combines long reads with sufficient depth for many phylogenetic analyses and can therefore provide insights into within-host HCV evolutionary dynamics without the need for haplotype reconstruction using statistical algorithms.IMPORTANCE Next-generation sequencing has revolutionized the study of genetically variable RNA virus populations, but for phylogenetic and evolutionary analyses, longer sequences than those generated by most available platforms, while minimizing the intrinsic error rate, are desired. Here, we demonstrate for the first time that PacBio SMRT sequencing technology can be used to generate full-length HCV envelope sequences at the single-molecule level, providing a data set with large sequencing depth for the characterization of intrahost viral dynamics. The selection of consensus reads derived from at least 7 full circular consensus sequencing rounds significantly reduced the intrinsic high error rate of this method. We used this method to genetically characterize a unique transmission cluster of sexually transmitted HCV infections, providing insight into the distinct evolutionary pathways in each patient over time and identifying the transmission-associated genetic bottleneck as well as fluctuations in viral genetic diversity over time, accompanied by dynamic shifts in viral subpopulations.
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Wedemeyer H, Forns X, Hézode C, Lee SS, Scalori A, Voulgari A, Le Pogam S, Nájera I, Thommes JA. Mericitabine and Either Boceprevir or Telaprevir in Combination with Peginterferon Alfa-2a plus Ribavirin for Patients with Chronic Hepatitis C Genotype 1 Infection and Prior Null Response: The Randomized DYNAMO 1 and DYNAMO 2 Studies. PLoS One 2016; 11:e0145409. [PMID: 26752189 PMCID: PMC4713467 DOI: 10.1371/journal.pone.0145409] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 12/01/2015] [Indexed: 12/15/2022] Open
Abstract
UNLABELLED Most patients with chronic hepatitis C virus (HCV) genotype 1 infection who have had a previous null response (<2-log10 reduction in HCV RNA by treatment week 12) to peginterferon/ribavirin (PegIFN/RBV) do not achieve a sustained virological response (SVR) when re-treated with a first-generation HCV protease inhibitor (PI) administered in combination with PegIFN/RBV. We studied the incremental benefits associated with adding mericitabine (nucleoside analog inhibitor of HCV polymerase) to PI plus PegIFN alfa-2a/RBV-based therapy in two double-blind randomized multicenter phase 2 trials (with boceprevir in DYNAMO 1, and with telaprevir in DYNAMO 2). The primary endpoint in both trials was SVR, defined as HCV RNA <25 IU/mL 12 weeks after the end of treatment (SVR12). Overall, the addition of mericitabine to PI plus PegIFN alfa-2a/RBV therapy resulted in SVR12 rates of 60-70% in DYNAMO 1 and of 71-96% in DYNAMO 2. SVR12 rates were similar in patients infected with HCV genotype 1a and 1b in both trials. The placebo control arms in both studies were stopped because of high rates of virological failure. Numerically lower relapse rates were associated with longer treatment with mericitabine (24 versus 12 weeks), telaprevir-containing regimens, and regimens that included 48 weeks of PegIFN alfa-2a/RBV therapy. No mericitabine resistance mutations were identified in any patient in either trial. The addition of mericitabine did not add to the safety burden associated with either telaprevir or boceprevir-based regimens. These studies demonstrate increased SVR rates and reduced relapse rates in difficult-to-treat patients when a nucleoside polymerase inhibitor with intermediate antiviral potency is added to regimens containing a first-generation PI. TRIAL REGISTRATION ClinicalTrials.gov NCT01482403 and ClinicalTrials.gov NCT01482390.
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Affiliation(s)
- Heiner Wedemeyer
- Department of Gastroenterology, Hepatology and Endocrinology at Hannover Medical School, Hannover, Germany
| | - Xavier Forns
- Liver Unit, Hospital Clinic, IDIBAPS and CIBEREHD, Barcelona, Spain
| | - Christophe Hézode
- Department of Hepatology and Gastroenterology, Hôpital Henri Mondor, INSERM U955, Université Paris-Est, Créteil, France
| | | | - Astrid Scalori
- Global Product Development Immunology, Respiratory, Roche Products Ltd, Welwyn, United Kingdom
| | - Athina Voulgari
- Global Product Development Clinical Science, Roche Products Ltd, Welwyn, United Kingdom
| | - Sophie Le Pogam
- Clinical Development-Infectious Diseases, Genentech Inc., South San Francisco, California, United States of America
| | - Isabel Nájera
- Roche Pharma and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - James A. Thommes
- Product Development Immunology, Genentech Inc., South San Francisco, California, United States of America
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Fourati S, Pawlotsky JM. Virologic Tools for HCV Drug Resistance Testing. Viruses 2015; 7:6346-59. [PMID: 26690198 DOI: 10.3390/v7122941] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/28/2015] [Accepted: 11/30/2015] [Indexed: 12/22/2022] Open
Abstract
Recent advances in molecular biology have led to the development of new antiviral drugs that target specific steps of the Hepatitis C Virus (HCV) lifecycle. These drugs, collectively termed direct-acting antivirals (DAAs), include non-structural (NS) HCV protein inhibitors, NS3/4A protease inhibitors, NS5B RNA-dependent RNA polymerase inhibitors (nucleotide analogues and non-nucleoside inhibitors), and NS5A inhibitors. Due to the high genetic variability of HCV, the outcome of DAA-based therapies may be altered by the selection of amino-acid substitutions located within the targeted proteins, which affect viral susceptibility to the administered compounds. At the drug developmental stage, preclinical and clinical characterization of HCV resistance to new drugs in development is mandatory. In the clinical setting, accurate diagnostic tools have become available to monitor drug resistance in patients who receive treatment with DAAs. In this review, we describe tools available to investigate drug resistance in preclinical studies, clinical trials and clinical practice.
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