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Raghwani J, Rose R, Sheridan I, Lemey P, Suchard MA, Santantonio T, Farci P, Klenerman P, Pybus OG. Exceptional Heterogeneity in Viral Evolutionary Dynamics Characterises Chronic Hepatitis C Virus Infection. PLoS Pathog 2016; 12:e1005894. [PMID: 27631086 PMCID: PMC5025083 DOI: 10.1371/journal.ppat.1005894] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 08/24/2016] [Indexed: 12/14/2022] Open
Abstract
The treatment of HCV infection has seen significant progress, particularly since the approval of new direct-acting antiviral drugs. However these clinical achievements have been made despite an incomplete understanding of HCV replication and within-host evolution, especially compared with HIV-1. Here, we undertake a comprehensive analysis of HCV within-host evolution during chronic infection by investigating over 4000 viral sequences sampled longitudinally from 15 HCV-infected patients. We compare our HCV results to those from a well-studied HIV-1 cohort, revealing key differences in the evolutionary behaviour of these two chronic-infecting pathogens. Notably, we find an exceptional level of heterogeneity in the molecular evolution of HCV, both within and among infected individuals. Furthermore, these patterns are associated with the long-term maintenance of viral lineages within patients, which fluctuate in relative frequency in peripheral blood. Together, our findings demonstrate that HCV replication behavior is complex and likely comprises multiple viral subpopulations with distinct evolutionary dynamics. The presence of a structured viral population can explain apparent paradoxes in chronic HCV infection, such as rapid fluctuations in viral diversity and the reappearance of viral strains years after their initial detection. Our knowledge of HCV within-host evolution is substantially limited, which is surprising given that highly successful therapies against the virus have been developed. Key aspects of HCV infection, such as rapid fluctuations in viral diversity and the reappearance of viral strains years after their initial detection, remain unexplained. To better understand this problem, we analyse viral sequences from HCV-infected patients sampled over several years. Our findings suggest that the replication dynamics during chronic HCV infection are distinct from those of HIV-1, and dominated by the co-circulation of multiple viral strains. Although a major difference between the two chronic-infecting viruses is the level of recombination, our results indicate that HCV within-host evolution is most likely to be shaped by a structured viral population. Crucially, our study shows that HCV sampled from blood does not fully represent the within-host viral population at that time. This may have important implications for HCV treatment, especially in patients that have seemingly cleared the virus, as well as for molecular epidemiology studies investigating HCV transmission.
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Affiliation(s)
- Jayna Raghwani
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- * E-mail: (JR); (OGP)
| | - Rebecca Rose
- BioInfoExperts, Thibodaux, Los Angeles, California, United States of America
| | - Isabelle Sheridan
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven–University of Leuven, Leuven, Belgium
| | - Marc A. Suchard
- Departments of Biomathematics, Biostatistics, Human Genetics, University of California, Los Angeles, California, United States of America
| | | | - Patrizia Farci
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- * E-mail: (JR); (OGP)
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2
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Tarr AW, Khera T, Hueging K, Sheldon J, Steinmann E, Pietschmann T, Brown RJP. Genetic Diversity Underlying the Envelope Glycoproteins of Hepatitis C Virus: Structural and Functional Consequences and the Implications for Vaccine Design. Viruses 2015; 7:3995-4046. [PMID: 26193307 PMCID: PMC4517138 DOI: 10.3390/v7072809] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 06/19/2015] [Accepted: 07/08/2015] [Indexed: 12/13/2022] Open
Abstract
In the 26 years since the discovery of Hepatitis C virus (HCV) a major global research effort has illuminated many aspects of the viral life cycle, facilitating the development of targeted antivirals. Recently, effective direct-acting antiviral (DAA) regimens with >90% cure rates have become available for treatment of chronic HCV infection in developed nations, representing a significant advance towards global eradication. However, the high cost of these treatments results in highly restricted access in developing nations, where the disease burden is greatest. Additionally, the largely asymptomatic nature of infection facilitates continued transmission in at risk groups and resource constrained settings due to limited surveillance. Consequently a prophylactic vaccine is much needed. The HCV envelope glycoproteins E1 and E2 are located on the surface of viral lipid envelope, facilitate viral entry and are the targets for host immunity, in addition to other functions. Unfortunately, the extreme global genetic and antigenic diversity exhibited by the HCV glycoproteins represents a significant obstacle to vaccine development. Here we review current knowledge of HCV envelope protein structure, integrating knowledge of genetic, antigenic and functional diversity to inform rational immunogen design.
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Affiliation(s)
- Alexander W Tarr
- School of Life Sciences, Nottingham Digestive Diseases Biomedical Research Unit, University of Nottingham, Nottingham NG7 2RD, UK.
| | - Tanvi Khera
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centrefor Infection Research (HZI), Hannover D-30625, Germany.
| | - Kathrin Hueging
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centrefor Infection Research (HZI), Hannover D-30625, Germany.
| | - Julie Sheldon
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centrefor Infection Research (HZI), Hannover D-30625, Germany.
| | - Eike Steinmann
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centrefor Infection Research (HZI), Hannover D-30625, Germany.
| | - Thomas Pietschmann
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centrefor Infection Research (HZI), Hannover D-30625, Germany.
- German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig 38124, Germany.
| | - Richard J P Brown
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centrefor Infection Research (HZI), Hannover D-30625, Germany.
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Analysis of the evolution and structure of a complex intrahost viral population in chronic hepatitis C virus mapped by ultradeep pyrosequencing. J Virol 2014; 88:13709-21. [PMID: 25231312 DOI: 10.1128/jvi.01732-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
UNLABELLED Hepatitis C virus (HCV) causes chronic infection in up to 50% to 80% of infected individuals. Hypervariable region 1 (HVR1) variability is frequently studied to gain an insight into the mechanisms of HCV adaptation during chronic infection, but the changes to and persistence of HCV subpopulations during intrahost evolution are poorly understood. In this study, we used ultradeep pyrosequencing (UDPS) to map the viral heterogeneity of a single patient over 9.6 years of chronic HCV genotype 4a infection. Informed error correction of the raw UDPS data was performed using a temporally matched clonal data set. The resultant data set reported the detection of low-frequency recombinants throughout the study period, implying that recombination is an active mechanism through which HCV can explore novel sequence space. The data indicate that polyvirus infection of hepatocytes has occurred but that the fitness quotients of recombinant daughter virions are too low for the daughter virions to compete against the parental genomes. The subpopulations of parental genomes contributing to the recombination events highlighted a dynamic virome where subpopulations of variants are in competition. In addition, we provide direct evidence that demonstrates the growth of subdominant populations to dominance in the absence of a detectable humoral response. IMPORTANCE Analysis of ultradeep pyrosequencing data sets derived from virus amplicons frequently relies on software tools that are not optimized for amplicon analysis, assume random incorporation of sequencing errors, and are focused on achieving higher specificity at the expense of sensitivity. Such analysis is further complicated by the presence of hypervariable regions. In this study, we made use of a temporally matched reference sequence data set to inform error correction algorithms. Using this methodology, we were able to (i) detect multiple instances of hepatitis C virus intrasubtype recombination at the E1/E2 junction (a phenomenon rarely reported in the literature) and (ii) interrogate the longitudinal quasispecies complexity of the virome. Parallel to the UDPS, isolation of IgG-bound virions was found to coincide with the collapse of specific viral subpopulations.
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de Amorim RMS, Coelho A, Lampe E, Raiol T, Martins RMB. Genetic diversity of hepatitis C virus quasispecies in chronic renal failure patients in Midwest Brazil. Arch Virol 2014; 159:1917-25. [PMID: 24562426 DOI: 10.1007/s00705-014-1994-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 11/21/2013] [Indexed: 11/28/2022]
Abstract
Hepatitis C virus (HCV) quasispecies constitute a dynamic population in a continuous process of variation and selection. To investigate effect of the immune system on the genetic variability of HCV, we compared the hypervariable region 1 (HVR1) of immunosuppressed patients with chronic renal failure (CRF group) to immunocompetent patients with HCV chronic infection (control group). The HVR1 from ten samples of each group was amplified, cloned and sequenced. The HCV quasispecies from the control group had a higher frequency of variable sites in HVR1 (83.9 % vs 59.3 %, p < 0.05), as well as a greater diversity within (intra-patient) and between samples, compared to the CRF group. The clustering of the majority of the quasispecies of the CRF group in the phylogenetic tree also showed the limited diversity of the quasispecies in immunosuppressed patients. Moreover, a higher variability of amino acids at positions 384, 386, 391, 394, 397, 398, 400, 405 and 410 was observed in the control group than in the CRF group, which showed a greater variability only at position 388 (p < 0.05). These data corroborates the hypothesis that the major selective pressure factor is the immune system, which promotes a high degree of diversity in the viral progeny and contributes to a constant evolution of HCV.
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Gismondi MI, Díaz Carrasco JM, Valva P, Becker PD, Guzmán CA, Campos RH, Preciado MV. Dynamic changes in viral population structure and compartmentalization during chronic hepatitis C virus infection in children. Virology 2013; 447:187-96. [PMID: 24210114 DOI: 10.1016/j.virol.2013.09.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 09/03/2013] [Indexed: 12/17/2022]
Abstract
Classic phylogenetic and modern population-based clustering methods were used to analyze hepatitis C virus (HCV) evolution in plasma and to assess viral compartmentalization within peripheral blood mononuclear cells (PBMCs) in 6 children during 3.2-9.6yr of follow-up. Population structure analysis of cloned amplicons encompassing hypervariable region 1 led to the distinction of two evolutionary patterns, one highly divergent and another one genetically homogeneous. Viral adaptability was reflected by co-evolution of viral communities switching rapidly from one to another in the context of divergence and stability associated with highly homogeneous communities which were replaced by new ones after long periods. Additionally, viral compartmentalization of HCV in PBMCs was statistically demonstrated, suggesting their role as a pool of genetic variability. Our results support the idea of a community-based structure of HCV viral populations during chronic infection and highlight a role of the PBMC compartment in the persistence of such structure.
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Affiliation(s)
- María Inés Gismondi
- Laboratorio de Biología Molecular, División Patología, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina.
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Affiliation(s)
- Rebecca R. Gray
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Marco Salemi
- Department of Pathology, Immunology & Laboratory Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- * E-mail:
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Li H, Atkins E, Bruckner J, McArdle S, Qiu WC, Thomassen LV, Scott J, Shuhart MC, Livingston S, Townshend-Bulson L, McMahon BJ, Harris M, Griffin S, Gretch DR. Genetic and functional heterogeneity of the hepatitis C virus p7 ion channel during natural chronic infection. Virology 2012; 423:30-7. [DOI: 10.1016/j.virol.2011.11.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 08/01/2011] [Accepted: 11/11/2011] [Indexed: 01/19/2023]
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Abstract
The nucleotide sequence diversity present among hepatitis C virus (HCV) isolates allows rapid adjustment to exterior forces including host immunity and drug therapy. This viral response reflects a combination of a high rate of replication together with an error-prone RNA-dependent RNA polymerase, providing for the selection and proliferation of the viruses with the highest fitness. We examined HCV subtype 1a whole-genome sequences to identify positions contributing to genotypic and phenotypic diversity. Phylogenetic tree reconstructions showed two distinct clades existing within the 1a subtype with each clade having a star-like tree topology and lacking definite correlation between time or place of isolation and phylogeny. Identification of significant phylogenetically informative sites at the nucleotide level revealed positions not only contributing to clade differentiation, but which are located at or proximal to codons associated with resistance to protease inhibitors (NS3 Q41) or polymerase inhibitors (NS5B S368). Synonymous/nonsynonymous substitution mutation analyses revealed that the majority of nucleotide mutations yielded synonymous amino acids, indicating the presence of purifying selection pressure across the polyprotein with pockets of positive selection also being detected. Despite evidence for divergence at several loci, certain 1a characteristics were preserved including the length of the alternative reading frame/F protein (ARF/F) gene, and a subtype 1a-specific phosphorylation site in NS5A (S349). Our analysis suggests that there may be strain-specific differences in the development of antiviral resistance to viruses infecting patients who are dependent on the genetic variation separating these two clades.
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Affiliation(s)
- B E Pickett
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
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Li H, Hughes AL, Bano N, McArdle S, Livingston S, Deubner H, McMahon BJ, Townshend-Bulson L, McMahan R, Rosen HR, Gretch DR. Genetic diversity of near genome-wide hepatitis C virus sequences during chronic infection: evidence for protein structural conservation over time. PLoS One 2011; 6:e19562. [PMID: 21573177 PMCID: PMC3088699 DOI: 10.1371/journal.pone.0019562] [Citation(s) in RCA: 22] [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: 09/07/2010] [Accepted: 04/09/2011] [Indexed: 01/06/2023] Open
Abstract
Infection with hepatitis C virus (HCV) is one of the leading causes of chronic hepatitis, liver cirrhosis and end-stage liver disease worldwide. The genetics of HCV infection in humans and the disease course of chronic hepatitis C are both remarkably variable. Although the response to interferon treatment is largely dependent on HCV genotypes, whether or not a relationship exists between HCV genome variability and clinical course of hepatitis C disease still remains unknown. To more thoroughly understand HCV genome evolution over time in association with disease course, near genome-wide HCV genomes present in 9 chronically infected participants over 83 total study years were sequenced. Overall, within HCV genomes, the number of synonymous substitutions per synonymous site (d(S)) significantly exceeded the number of non-synonymous substitutions per site (d(N)). Although both d(S) and d(N) significantly increased with duration of chronic infection, there was a highly significant decrease in d(N)/d(S) ratio in HCV genomes over time. These results indicate that purifying selection acted to conserve viral protein structure despite persistence of high level of nucleotide mutagenesis inherent to HCV replication. Based on liver biopsy fibrosis scores, HCV genomes from participants with advanced fibrosis had significantly greater d(S) values and lower d(N)/d(S) ratios compared to participants with mild liver disease. Over time, viral genomes from participants with mild disease had significantly greater annual changes in d(N), along with higher d(N)/d(S) ratios, compared to participants with advanced fibrosis. Yearly amino acid variations in the HCV p7, NS2, NS3 and NS5B genes were all significantly lower in participants with severe versus mild disease, suggesting possible pathogenic importance of protein structural conservation for these viral gene products.
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Affiliation(s)
- Hui Li
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, United States of America
| | - Austin L. Hughes
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America
| | - Nazneen Bano
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, United States of America
| | - Susan McArdle
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, United States of America
| | - Stephen Livingston
- Liver Disease and Hepatitis Program, Alaska Native Tribal Health Consortium, Anchorage, Alaska, United States of America
| | - Heike Deubner
- Department of Pathology, University of Washington Medical Center, Seattle, Washington, United States of America
| | - Brian J. McMahon
- Liver Disease and Hepatitis Program, Alaska Native Tribal Health Consortium, Anchorage, Alaska, United States of America
| | - Lisa Townshend-Bulson
- Liver Disease and Hepatitis Program, Alaska Native Tribal Health Consortium, Anchorage, Alaska, United States of America
| | - Rachel McMahan
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Hugo R. Rosen
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - David R. Gretch
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, United States of America
- Department of Medicine, University of Washington Medical Center, Seattle, Washington, United States of America
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Xiu BS, Feng XY, He J, Wang GH, Zhang XY, Zhang HQ, Song XG, Chen K, Ling SG, Zhu CX, Wei L, Rao HY. Evaluation of cross-reactive antibody response to HVR1 in chronic hepatitis C. World J Gastroenterol 2010; 16:4460-6. [PMID: 20845515 PMCID: PMC2941071 DOI: 10.3748/wjg.v16.i35.4460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
AIM: To evaluate the presence and cross-reactive antibodies against hypervariable region 1 (HVR1) in hepatitis C virus (HCV) infected patients and its relationship with the progression of the disease.
METHODS: Sixteen representative HVR1 proteins selected from a unique set of 1600 natural sequences were used to semiquantitate the cross-reactivity of HVR1 antibodies in the sera of HCV patients. Fifty-five chronic HCV patients including 23 with asymptomatic mild hepatitis, 18 with chronic hepatitis and 16 with liver cirrhosis patients were studied.
RESULTS: The degree of the cross-reactivity of anti-HVR1 antibodies in 23 patients with mild asymptomatic hepatitis was 3.09 ± 2.68, which was significantly lower than in those with chronic hepatitis (5.44 ± 3.93, P < 0.05) and liver cirrhosis (7.44 ± 3.90, P < 0.01). No correlation was observed between the broadness of the cross-reactivity anti-HVR1 antibodies and patient’s age, infection time, serum alanine aminotransferase activity, or serum HCV-RNA concentration. It was the breath of cross-reactivity rather than the presence of anti-HVR1 antibody in HCV sera that was associated with the progression of liver disease.
CONCLUSION: The broadly cross-reactive HVR1 antibodies generated in natural HCV patients can not neutralize the virus, which results in persistent infection in patients with chronic hepatitis.
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Li H, Sullivan DG, Feuerborn N, McArdle S, Bekele K, Pal S, Yeh M, Carithers RL, Perkins JD, Gretch DR. Genetic diversity of hepatitis C virus predicts recurrent disease after liver transplantation. Virology 2010; 402:248-55. [PMID: 20400171 DOI: 10.1016/j.virol.2010.03.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Revised: 03/15/2010] [Accepted: 03/23/2010] [Indexed: 01/07/2023]
Abstract
Approximately 20% of patients receiving liver transplants for end-stage hepatitis C rapidly develop severe allograph fibrosis within the first 24 months after transplant. Hepatitis C virus (HCV) variants were studied in 56 genotype-1-infected subjects with end-stage hepatitis C disease at the time before and 12 months after liver transplant, and post-transplant outcome was followed with serial liver biopsies. In 15 cases, pre-transplant HCV genetic diversity was studied in detail in liver (n=15), serum (n=15), peripheral blood mononuclear cells (n=13), and perihepatic lymph nodes (n=10). Our results revealed that pre-transplant HCV genetic diversity predicted the histological outcome of recurrent hepatitis C disease after transplant. Mild disease recurrence after transplant was significantly associated with higher genetic diversity and greater diversity changes between the pre- and post-transplant time points (p=0.004). Meanwhile, pre-transplant genetic differences between serum and liver were related to a higher likelihood of development of mild recurrent disease after transplant (p=0.039).
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Affiliation(s)
- Hui Li
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
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