1
|
Graf C, Fuhrmann L, Lutz T, Stephan C, Knecht G, Gute P, Bickel M, Peiffer KH, Finkelmeier F, Dultz G, Mondorf A, Wetzstein N, Filmann N, Herrmann E, Zeuzem S, Beerenwinkel N, Dietz J, Sarrazin C. Expanding epidemic of recently acquired HCV in HIV-coinfected patients over a period of 10 years. JHEP Rep 2023; 5:100701. [PMID: 37305441 PMCID: PMC10250927 DOI: 10.1016/j.jhepr.2023.100701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 01/12/2023] [Accepted: 02/01/2023] [Indexed: 06/13/2023] Open
Abstract
Background & Aims Ongoing transmission of HCV infections is associated with risk factors such as drug injection, needlestick injuries, and men who have sex with men (MSM). Ways of transmission, the course of acute infection, changes of virologic features, and incidence over time are not well known. Methods Over a period of 10 years, n = 161 patients with recently acquired HCV infection (RAHC) (median follow-up 6.8 years) were prospectively enrolled. NS5B sequencing was performed to re-evaluate the HCV genotype (GT) and for phylogenetic analyses. Results Patients with RAHC were mainly male (92.5%), MSM (90.1%), and HIV-coinfected (86.3%). Transmission risk factors for MSM and non-MSM were sexual risk behaviour (100 and 6.3%, respectively), injection drug use (9.7 and 37.5%, respectively), and nasal drug use (15.2 and 0%, respectively). Spontaneous and interferon- or direct-acting antiviral-based clearance rates were 13.6, 84.3 and 93.4%, respectively. Mean RAHC declined from 19.8 in the first to 13.2 in the past five study years. Although the majority of infections was caused by HCV GT1a, the frequency of HCV GT4d and slightly HCV GT3a increased over time. No relevant clustering of HCV isolates was observed in non-MSM. However, 45% of HCV GT1a and 100% of HCV GT4d MSM cases clustered with MSM isolates from other countries. Travel-associated infections were supported by personal data in an MSM subgroup. No international clustering was detected in MSM with HCV GT1b or HCV GT3a. Conclusions RAHCs were mainly diagnosed in HIV-coinfected MSM patients and were associated with sexual risk behaviour. Spontaneous clearance rates were low, and phylogenetic clusters were observed in the majority of patients. Impact and Implications We evaluated the occurrence and transmission of recently acquired HCV infections (RAHCs) over a period of 10 years. Our data demonstrate that the presence of RAHC was mainly found in HIV-coinfected MSM, with internationally connected transmission networks being observed in the majority of patients. Spontaneous clearance rates were low, and reinfection rates increased mainly driven by a small subset of MSM patients with high-risk behaviour.
Collapse
Affiliation(s)
- Christiana Graf
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt, Germany
| | - Lara Fuhrmann
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | | | - Christoph Stephan
- HIVCENTER, Department of Infectious Diseases, University Hospital, Goethe University, Frankfurt, Germany
| | | | | | | | - Kai-Henrik Peiffer
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt, Germany
| | - Fabian Finkelmeier
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt, Germany
| | - Georg Dultz
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt, Germany
| | - Antonia Mondorf
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt, Germany
| | - Nils Wetzstein
- HIVCENTER, Department of Infectious Diseases, University Hospital, Goethe University, Frankfurt, Germany
| | - Natalie Filmann
- Institute of Biostatistics and Mathematical Modeling, Goethe University, Frankfurt, Germany
| | - Eva Herrmann
- Institute of Biostatistics and Mathematical Modeling, Goethe University, Frankfurt, Germany
| | - Stefan Zeuzem
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt, Germany
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Julia Dietz
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt, Germany
| | - Christoph Sarrazin
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt, Germany
- Medizinische Klinik II, St. Josefs-Hospital, Wiesbaden, Germany
| |
Collapse
|
2
|
Salazar-Vizcaya L, Kouyos RD, Metzner KJ, Caraballo Cortes K, Böni J, Shah C, Fehr J, Braun DL, Bernasconi E, Mbunkah HA, Hoffmann M, Labhardt N, Cavassini M, Rougemont M, Günthard HF, Keiser O, Rauch A. Changing Trends in International Versus Domestic HCV Transmission in HIV-Positive Men Who Have Sex With Men: A Perspective for the Direct-Acting Antiviral Scale-Up Era. J Infect Dis 2020; 220:91-99. [PMID: 30759225 PMCID: PMC6548898 DOI: 10.1093/infdis/jiz069] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/11/2019] [Indexed: 12/29/2022] Open
Abstract
Background Scale-up of direct-acting antiviral therapy is expected to abate hepatitis C virus (HCV) incidence among human immunodeficiency virus (HIV)-positive men who have sex with men (MSM). International transmission could influence this process. We classified HCV infections in HIV-positive MSM as either domestically or internationally acquired, and estimated how this classification changed over time. Methods HCV subtype 1a (the most frequent subtype among MSM) genomes from 99 persons enrolled in the Swiss HIV Cohort Study and diagnosed with replicating HCV infections, were sequenced. Sixty-six of these sequences were from MSM. We inferred maximum-likelihood phylogenetic trees and time trees containing a fragment of the NS5B region of these and 374 circulating strains. We inferred transmission clusters from these trees and used the country composition of such clusters to attribute infections to domestic or international transmission. Results Of HCV transmissions, 50% to 80% were classified as domestic depending on the classification criterion. Between 2000 and 2007, the fraction attributable to domestic transmission was 54% (range 0–75%). It increased to 85% (range 67%–100%) between 2008 and 2016. Conclusions International and domestic transmission have played major roles in this epidemic. While international transmission persists, local transmission has established as the main source of infections.
Collapse
Affiliation(s)
- Luisa Salazar-Vizcaya
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Kamila Caraballo Cortes
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Poland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Cyril Shah
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Jan Fehr
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland
| | - Dominique L Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Lugano Regional Hospital, Switzerland
| | - Herbert A Mbunkah
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Matthias Hoffmann
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, Switzerland
| | - Niklaus Labhardt
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Switzerland
| | - Matthias Cavassini
- Infectious Diseases Service, Department of Medicine, University Hospital of Lausanne, Switzerland
| | - Mathieu Rougemont
- Division of Infectious Diseases, University Hospital Geneva, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Olivia Keiser
- Institute of Global Health, University of Geneva, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | | |
Collapse
|
3
|
Caro-Pérez N, Martínez-Rebollar M, Gregori J, Quer J, González P, Gambato M, García-González N, González-Candelas F, Costa J, Esteban JI, Mallolas J, Forns X, Laguno M, Pérez-Del-Pulgar S. Phylogenetic analysis of an epidemic outbreak of acute hepatitis C in HIV-infected patients by ultra-deep pyrosequencing. J Clin Virol 2017; 92:42-47. [PMID: 28521213 DOI: 10.1016/j.jcv.2017.05.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/29/2017] [Accepted: 05/06/2017] [Indexed: 01/18/2023]
Abstract
BACKGROUND The incidence of acute hepatitis C (AHC) among HIV-infected men who have sex with men (MSM) has increased significantly in the last 10 years. Several studies point to a social and sexual network of HIV-positive MSM that extends internationally. OBJECTIVES The aim of our study was to investigate the dynamics of HCV transmission in an outbreak of AHC in HIV-infected MSM in Barcelona by ultra-deep pyrosequencing. STUDY DESIGN Between 2008 and 2013, 113 cases of AHC in HIV-infected MSM were diagnosed in the Infectious Diseases Unit, Hospital Clínic, Barcelona. Massive sequencing was performed using the Roche 454 GS Junior platform. To define possible transmission networks, maximum likelihood phylogenetic trees were constructed, and levels of genetic diversity within and among patients were compared. RESULTS Among the 70 cases analyzed, we have identified 16 potential clusters of transmission: 8 for genotype 1a (23 cases involved), 1 for genotype 1b (3 cases) and 7 for genotype 4d (27 cases). Although the initial phylogenetic reconstruction suggested a local transmission cluster of HCV gt4d, our approach based on low genetic differentiation did not corroborate it. Indeed, gt4d strains formed 4 independent groups related to patients from other countries. CONCLUSIONS Frequent clustering of HIV-positive MSM shows that HCV infection has spread through a local network in Barcelona. This outbreak is related to a large international HCV transmission network among MSM. Public health efforts are needed to reduce HCV transmission among this high-risk group.
Collapse
Affiliation(s)
- Noelia Caro-Pérez
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, Universitat de Barcelona, Barcelona, Spain.
| | | | - Josep Gregori
- Liver Unit, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron, CIBERehd, Barcelona, Spain; Roche Diagnostics SL, Sant Cugat del Vallès, Barcelona, Spain.
| | - Josep Quer
- Liver Unit, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron, CIBERehd, Barcelona, Spain.
| | - Patricia González
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, Universitat de Barcelona, Barcelona, Spain.
| | - Martina Gambato
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, Universitat de Barcelona, Barcelona, Spain.
| | - Neris García-González
- Joint Research Unit Infección y Salud Pública, FISABIO-Universitat de València, I2SysBio, CIBERESP, Valencia, Spain.
| | - Fernando González-Candelas
- Joint Research Unit Infección y Salud Pública, FISABIO-Universitat de València, I2SysBio, CIBERESP, Valencia, Spain.
| | - Josep Costa
- Microbiology Department, Centre Diagnòstic Biomèdic, Hospital Clínic, CIBERehd, Barcelona, Spain.
| | - Juan Ignacio Esteban
- Liver Unit, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron, CIBERehd, Barcelona, Spain.
| | - Josep Mallolas
- Infectious Diseases Unit, Hospital Clínic, IDIBAPS, Barcelona, Spain.
| | - Xavier Forns
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, Universitat de Barcelona, Barcelona, Spain.
| | - Montse Laguno
- Infectious Diseases Unit, Hospital Clínic, IDIBAPS, Barcelona, Spain.
| | - Sofía Pérez-Del-Pulgar
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, Universitat de Barcelona, Barcelona, Spain.
| |
Collapse
|
4
|
Hamad HA, Thurston J, Teague T, Ackad E, Yousef MS. The NS4A Cofactor Dependent Enhancement of HCV NS3 Protease Activity Correlates with a 4D Geometrical Measure of the Catalytic Triad Region. PLoS One 2016; 11:e0168002. [PMID: 27936126 PMCID: PMC5148068 DOI: 10.1371/journal.pone.0168002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 11/24/2016] [Indexed: 12/22/2022] Open
Abstract
We are developing a 4D computational methodology, based on 3D structure modeling and molecular dynamics simulation, to analyze the active site of HCV NS3 proteases, in relation to their catalytic activity. In our previous work, the 4D analyses of the interactions between the catalytic triad residues (His57, Asp81, and Ser139) yielded divergent, gradual and genotype-dependent, 4D conformational instability measures, which strongly correlate with the known disparate catalytic activities among genotypes. Here, the correlation of our 4D geometrical measure is extended to intra-genotypic alterations in NS3 protease activity, due to sequence variations in the NS4A activating cofactor. The correlation between the 4D measure and the enzymatic activity is qualitatively evident, which further validates our methodology, leading to the development of an accurate quantitative metric to predict protease activity in silico. The results suggest plausible “communication” pathways for conformational propagation from the activation subunit (the NS4A cofactor binding site) to the catalytic subunit (the catalytic triad). The results also strongly suggest that the well-sampled (via convergence quantification) structural dynamics are more connected to the divergent catalytic activity observed in HCV NS3 proteases than to rigid structures. The method could also be applicable to predict patients’ responses to interferon therapy and better understand the innate interferon activation pathway.
Collapse
Affiliation(s)
- Hamzah A. Hamad
- Department of Physics, College of Arts and Sciences, Southern Illinois University Edwardsville, Illinois, United States of America
| | - Jeremy Thurston
- Department of Physics, College of Arts and Sciences, Southern Illinois University Edwardsville, Illinois, United States of America
| | - Thomas Teague
- Department of Physics, College of Arts and Sciences, Southern Illinois University Edwardsville, Illinois, United States of America
| | - Edward Ackad
- Department of Physics, College of Arts and Sciences, Southern Illinois University Edwardsville, Illinois, United States of America
| | - Mohammad S. Yousef
- Department of Physics, College of Arts and Sciences, Southern Illinois University Edwardsville, Illinois, United States of America
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
- * E-mail:
| |
Collapse
|
5
|
Dietz J, Lutz T, Knecht G, Gute P, Berkowski C, Lange CM, Khaykin P, Stephan C, Brodt HR, Herrmann E, Zeuzem S, Sarrazin C. Evolution and function of the HCV NS3 protease in patients with acute hepatitis C and HIV coinfection. Virology 2015; 485:213-22. [PMID: 26295281 DOI: 10.1016/j.virol.2015.06.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 06/12/2015] [Accepted: 06/26/2015] [Indexed: 01/03/2023]
Abstract
Little is known about the importance of the hepatitis C virus (HCV) NS3 protease in acute hepatitis C. In this prospective study, 82 consecutive patients with acute hepatitis C and human immunodeficiency virus (HIV) coinfection were enrolled. Individuals were infected with highly related HCV strains and the baseline NS3 quasispecies diversity and complexity was higher compared to a chronic hepatitis C control group (P<0.0001). Both parameters were comparable in patients with spontaneous clearance (n=6) versus treatment-induced SVR (n=5) or development of chronic hepatitis C (n=9). Longitudinal NS3 quasispecies kinetics showed a trend to a decreasing diversity and complexity (P<0.05) within 4 weeks in patients with spontaneous clearance compared to the other groups. The innate immune signalling protein CARDIF was cleaved to a similar extent independent of the outcome. Together with a more pronounced viral load decline (P<0.05), an early decreasing NS3 quasispecies evolution indicates spontaneous clearance of acute hepatitis C.
Collapse
Affiliation(s)
- Julia Dietz
- Department of Internal Medicine 1, J.W. Goethe University Hospital, Frankfurt, Germany
| | | | | | | | - Caterina Berkowski
- Department of Internal Medicine 1, J.W. Goethe University Hospital, Frankfurt, Germany
| | | | - Pavel Khaykin
- Department of Internal Medicine 2, J.W. Goethe University Hospital, Frankfurt, Germany
| | - Christoph Stephan
- Department of Internal Medicine 2, J.W. Goethe University Hospital, Frankfurt, Germany
| | - Hans-Reinhard Brodt
- Department of Internal Medicine 2, J.W. Goethe University Hospital, Frankfurt, Germany
| | - Eva Herrmann
- Institute of Biostatistics and Mathematical Modeling, J.W. Goethe University, Frankfurt, Germany
| | - Stefan Zeuzem
- Department of Internal Medicine 1, J.W. Goethe University Hospital, Frankfurt, Germany
| | - Christoph Sarrazin
- Department of Internal Medicine 1, J.W. Goethe University Hospital, Frankfurt, Germany.
| |
Collapse
|
6
|
Similarities between Human Immunodeficiency Virus Type 1 and Hepatitis C Virus Genetic and Phenotypic Protease Quasispecies Diversity. J Virol 2015; 89:9758-64. [PMID: 26178979 DOI: 10.1128/jvi.01097-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 07/09/2015] [Indexed: 12/16/2022] Open
Abstract
UNLABELLED Human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) are two highly variable RNA viruses that cause chronic infections in humans. Although HCV likely preceded the AIDS epidemic by some decades, the global spread of both viruses is a relatively recent event. Nevertheless, HCV global diversity is higher than that of HIV-1. To identify differences in mutant diversity, we compared the HIV-1 protease and HCV NS3 protease quasispecies. Three protease gene quasispecies samples per virus, isolated from a total of six infected patients, were genetically and phenotypically analyzed at high resolution (HIV-1, 308 individual clones; HCV, 299 clones). Single-nucleotide variant frequency did not differ between quasispecies from the two viruses (HIV-1, 2.4 × 10(-3) ± 0.4 × 10(-3); HCV, 2.1 × 10(-3) ± 0.5 × 10(-3)) (P = 0.1680). The proportion of synonymous substitutions to potential synonymous sites was similar (3.667 ± 0.6667 and 2.183 ± 0.9048, respectively) (P = 0.2573), and Shannon's entropy values did not differ between HIV-1 and HCV (0.84 ± 0.02 and 0.83 ± 0.12, respectively) (P = 0.9408). Of note, 65% (HIV-1) and 67% (HCV) of the analyzed enzymes displayed detectable protease activity, suggesting that both proteases have a similar mutational robustness. In both viruses, there was a rugged protease enzymatic activity landscape characterized by a sharp peak, representing the master sequence, surrounded by a collection of diverse variants present at lower frequencies. These results indicate that nucleotide quasispecies diversification during chronic infection is not responsible for the higher worldwide genetic diversity observed in HCV. IMPORTANCE HCV global diversity is higher than that of HIV-1. We asked whether HCV genetic diversification during infection is responsible for the higher worldwide genetic diversity observed in HCV. To this end, we analyzed and compared the genotype and enzymatic activities of HIV-1 and HCV protease quasispecies existing in infected individuals. Our results indicate that HIV-1 and HCV protease quasispecies have very similar genetic diversity and comparable rugged enzymatic activity landscapes. Therapy for HCV has expanded, with new therapeutic agents such as the direct-acting antivirals (DAAs). DAAs, which target HCV NS3 protease and other virus proteins, have improved cure rates. However, major questions remain to be elucidated regarding the virologic correlates of HCV eradication. The findings shown here may help our understanding of the different therapeutic responses observed during chronic HCV infection.
Collapse
|
7
|
Identification, molecular cloning, and analysis of full-length hepatitis C virus transmitted/founder genotypes 1, 3, and 4. mBio 2015; 6:e02518. [PMID: 25714714 PMCID: PMC4358020 DOI: 10.1128/mbio.02518-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Hepatitis C virus (HCV) infection is characterized by persistent replication of a complex mixture of viruses termed a “quasispecies.” Transmission is generally associated with a stringent population bottleneck characterized by infection by limited numbers of “transmitted/founder” (T/F) viruses. Characterization of T/F genomes of human immunodeficiency virus type 1 (HIV-1) has been integral to studies of transmission, immunopathogenesis, and vaccine development. Here, we describe the identification of complete T/F genomes of HCV by single-genome sequencing of plasma viral RNA from acutely infected subjects. A total of 2,739 single-genome-derived amplicons comprising 10,966,507 bp from 18 acute-phase and 11 chronically infected subjects were analyzed. Acute-phase sequences diversified essentially randomly, except for the poly(U/UC) tract, which was subject to polymerase slippage. Fourteen acute-phase subjects were productively infected by more than one genetically distinct virus, permitting assessment of recombination between replicating genomes. No evidence of recombination was found among 1,589 sequences analyzed. Envelope sequences of T/F genomes lacked transmission signatures that could distinguish them from chronic infection viruses. Among chronically infected subjects, higher nucleotide substitution rates were observed in the poly(U/UC) tract than in envelope hypervariable region 1. Fourteen full-length molecular clones with variable poly(U/UC) sequences corresponding to seven genotype 1a, 1b, 3a, and 4a T/F viruses were generated. Like most unadapted HCV clones, T/F genomes did not replicate efficiently in Huh 7.5 cells, indicating that additional cellular factors or viral adaptations are necessary for in vitro replication. Full-length T/F HCV genomes and their progeny provide unique insights into virus transmission, virus evolution, and virus-host interactions associated with immunopathogenesis. Hepatitis C virus (HCV) infects 2% to 3% of the world’s population and exhibits extraordinary genetic diversity. This diversity is mirrored by HIV-1, where characterization of transmitted/founder (T/F) genomes has been instrumental in studies of virus transmission, immunopathogenesis, and vaccine development. Here, we show that despite major differences in genome organization, replication strategy, and natural history, HCV (like HIV-1) diversifies essentially randomly early in infection, and as a consequence, sequences of actual T/F viruses can be identified. This allowed us to capture by molecular cloning the full-length HCV genomes that are responsible for infecting the first hepatocytes and eliciting the initial immune responses, weeks before these events could be directly analyzed in human subjects. These findings represent an enabling experimental strategy, not only for HCV and HIV-1 research, but also for other RNA viruses of medical importance, including West Nile, chikungunya, dengue, Venezuelan encephalitis, and Ebola viruses.
Collapse
|
8
|
Franco S, Tural C, Nevot M, Moltó J, Rockstroh JK, Clotet B, Martinez MA. Detection of a sexually transmitted hepatitis C virus protease inhibitor-resistance variant in a human immunodeficiency virus-infected homosexual man. Gastroenterology 2014; 147:599-601.e1. [PMID: 24859204 DOI: 10.1053/j.gastro.2014.05.010] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 04/16/2014] [Accepted: 05/09/2014] [Indexed: 01/30/2023]
Abstract
There is an international epidemic of hepatitis C virus (HCV) infection among human immunodeficiency virus-infected men who have sex with men. Transmission of HCV variants that are resistant to recently approved direct-acting antivirals (DAAs) could be an important clinical and public health problem. We document a case of transmission of a DAA-resistant variant of HCV from a patient who was treated with telaprevir to his sexual partner. The transmission of HCV DAA-resistant variants could impair therapeutic regimens that include DAAs.
Collapse
Affiliation(s)
| | - Cristina Tural
- Department of Internal Medicine, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; Universitat Autònoma de Barcelona (UAB), Spain; Universitat de Vic (UVic) Barcelona, Spain; Fundació Lluita contra la SIDA, Badalona, Spain
| | | | - José Moltó
- Department of Internal Medicine, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; Universitat Autònoma de Barcelona (UAB), Spain; Universitat de Vic (UVic) Barcelona, Spain; Fundació Lluita contra la SIDA, Badalona, Spain
| | | | - Bonaventura Clotet
- Fundació irsiCaixa, Badalona, Spain; Department of Internal Medicine, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; Universitat Autònoma de Barcelona (UAB), Spain; Universitat de Vic (UVic) Barcelona, Spain; Fundació Lluita contra la SIDA, Badalona, Spain
| | | |
Collapse
|
9
|
Abstract
A central question in protein molecular evolution is whether an amino acid that occurs at a given site makes an independent contribution to fitness or whether its contribution depends on other amino acid sites in the protein sequence, a phenomenon known as intragenic epistasis. In the absence of intragenic epistasis, natural selection acts on a protein mutation independent of its genetic background, and the experimentally determined fitness for a mutation should be the same across all genetic backgrounds. We tested this hypothesis by using site-directed mutagenesis to introduce a well-characterized deleterious single amino acid substitution in 56 different hepatitis C virus NS3 protease variants. The catalytic efficiency of the mutated proteases was determined and compared with the corresponding wild-type protein. Fitness effects ranged from lethality to significantly beneficial. Although primarily deleterious and lethal effects were observed (41 and 5 out of 56 tested variants, respectively), deleterious effects ranged from near neutral (-26.7% reduction of fitness) to near lethal (-98.5%). Our findings demonstrate that the introduced amino acid substitution has different fitness effects in different protein variants and provide independent support for the relevant role of intragenic epistasis in protein evolution.
Collapse
Affiliation(s)
- Mariona Parera
- Fundació irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Miguel Angel Martinez
- Fundació irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| |
Collapse
|