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Rodrigo C, Walker MR, Leung P, Eltahla AA, Grebely J, Dore GJ, Applegate T, Page K, Dwivedi S, Bruneau J, Morris MD, Cox AL, Osburn W, Kim AY, Schinkel J, Shoukry NH, Lauer GM, Maher L, Hellard M, Prins M, Luciani F, Lloyd AR, Bull RA. Limited naturally occurring escape in broadly neutralizing antibody epitopes in hepatitis C glycoprotein E2 and constrained sequence usage in acute infection. INFECTION GENETICS AND EVOLUTION 2017; 49:88-96. [PMID: 28065804 DOI: 10.1016/j.meegid.2017.01.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 12/07/2016] [Accepted: 01/03/2017] [Indexed: 12/12/2022]
Abstract
Broadly neutralizing antibodies have been associated with spontaneous clearance of the hepatitis C infection as well as viral persistence by immune escape. Further study of neutralizing antibody epitopes is needed to unravel pathways of resistance to virus neutralization, and to identify conserved regions for vaccine design. All reported broadly neutralizing antibody (BNAb) epitopes in the HCV Envelope (E2) glycoprotein were identified. The critical contact residues of these epitopes were mapped onto the linear E2 sequence. All publicly available E2 sequences were then downloaded and the contact residues within the BNAb epitopes were assessed for the level of conservation, as well as the frequency of occurrence of experimentally-proven resistance mutations. Epitopes were also compared between two sequence datasets obtained from samples collected at well-defined time points from acute (<180days) and chronic (>180days) infections, to identify any significant differences in residue usage. The contact residues for all BNAbs were contained within 3 linear regions of the E2 protein sequence. An analysis of 1749 full length E2 sequences from public databases showed that only 10 out of 29 experimentally-proven resistance mutations were present at a frequency >5%. Comparison of subtype 1a viral sequences obtained from samples collected during acute or chronic infection revealed significant differences at positions 610 and 655 with changes in residue (p<0.05), and at position 422 (p<0.001) with a significant difference in variability (entropy). The majority of experimentally-described escape variants do not occur frequently in nature. The observed differences between acute and chronically isolated sequences suggest constraints on residue usage early in infection.
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Affiliation(s)
- Chaturaka Rodrigo
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
| | - Melanie R Walker
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Preston Leung
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Auda A Eltahla
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Jason Grebely
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Gregory J Dore
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Tanya Applegate
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Kimberly Page
- Department of Epidemiology and Biostatistics, University of New Mexico, Albuquerque, NM, USA
| | - Sunita Dwivedi
- Department of Epidemiology and Biostatistics, University of New Mexico, Albuquerque, NM, USA
| | - Julie Bruneau
- CRCHUM, Université de Montréal, Montreal, QC, Canada
| | - Meghan D Morris
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Andrea L Cox
- Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - William Osburn
- Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | | | - Janke Schinkel
- Department of Internal Medicine, Division of Infectious Diseases, Tropical Medicine and AIDS, Center for Infection and Immunity Amsterdam, Academic Medical Center, Meibergdreef, Amsterdam, The Netherlands
| | | | | | - Lisa Maher
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Margaret Hellard
- Burnet Institute, Melbourne, VIC, Australia; Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Australia
| | - Maria Prins
- Department of Internal Medicine, Division of Infectious Diseases, Tropical Medicine and AIDS, Center for Infection and Immunity Amsterdam, Academic Medical Center, Meibergdreef, Amsterdam, The Netherlands; GGD Public Health Service of Amsterdam, Amsterdam, The Netherlands
| | - Fabio Luciani
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Andrew R Lloyd
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia; The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Rowena A Bull
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
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Palmer BA, Fanning LJ. Synonymous Co-Variation across the E1/E2 Gene Junction of Hepatitis C Virus Defines Virion Fitness. PLoS One 2016; 11:e0167089. [PMID: 27880830 PMCID: PMC5120871 DOI: 10.1371/journal.pone.0167089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 11/07/2016] [Indexed: 11/18/2022] Open
Abstract
Hepatitis C virus is a positive-sense single-stranded RNA virus. The gene junction partitioning the viral glycoproteins E1 and E2 displays concurrent sequence evolution with the 3'-end of E1 highly conserved and the 5'-end of E2 highly heterogeneous. This gene junction is also believed to contain structured RNA elements, with a growing body of evidence suggesting that such structures can act as an additional level of viral replication and transcriptional control. We have previously used ultradeep pyrosequencing to analyze an amplicon library spanning the E1/E2 gene junction from a treatment naïve patient where samples were collected over 10 years of chronic HCV infection. During this timeframe maintenance of an in-frame insertion, recombination and humoral immune targeting of discrete virus sub-populations was reported. In the current study, we present evidence of epistatic evolution across the E1/E2 gene junction and observe the development of co-varying networks of codons set against a background of a complex virome with periodic shifts in population dominance. Overtime, the number of codons actively mutating decreases for all virus groupings. We identify strong synonymous co-variation between codon sites in a group of sequences harbouring a 3 bp in-frame insertion and propose that synonymous mutation acts to stabilize the RNA structural backbone.
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Affiliation(s)
- Brendan A. Palmer
- Molecular Virology Diagnostic & Research Laboratory, Department of Medicine, University College Cork, Cork, Ireland
- * E-mail: (LJF); (BAP)
| | - Liam J. Fanning
- Molecular Virology Diagnostic & Research Laboratory, Department of Medicine, University College Cork, Cork, Ireland
- * E-mail: (LJF); (BAP)
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Sequence and functional analysis of the envelope glycoproteins of hepatitis C virus variants selectively transmitted to a new host. J Virol 2013; 87:13609-18. [PMID: 24109215 DOI: 10.1128/jvi.02119-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Hepatitis C virus (HCV) remains a challenging public health problem worldwide. The identification of viral variants establishing de novo infections and definition of the phenotypic requirements for transmission would facilitate the design of preventive strategies. We explored the transmission of HCV variants in three cases of acute hepatitis following needlestick accidents. We used single-genome amplification of glycoprotein E1E2 gene sequences to map the genetic bottleneck upon transmission accurately. We found that infection was likely established by a single variant in two cases and six variants in the third case. Studies of donor samples showed that the transmitted variant E1E2 amino acid sequences were identical or closely related to those of variants from the donor virus populations. The transmitted variants harbored a common signature site at position 394, within hypervariable region 1 of E2, together with additional signature amino acids specific to each transmission pair. Surprisingly, these E1E2 variants conferred no greater capacity for entry than the E1E2 derived from nontransmitted variants in lentiviral pseudoparticle assays. Mutants escaping the antibodies of donor sera did not predominate among the transmitted variants either. The fitness parameters affecting the selective outgrowth of HCV variants after transmission in an immunocompetent host may thus be more complex than those suggested by mouse models. Human antibodies directed against HCV envelope effectively cross-neutralized the lentiviral particles bearing E1E2 derived from transmitted variants. These findings provide insight into the molecular mechanisms underlying HCV transmission and suggest that viral entry is a potential target for the prevention of HCV infection.
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Guan M, Wang W, Liu X, Tong Y, Liu Y, Ren H, Zhu S, Dubuisson J, Baumert TF, Zhu Y, Peng H, Aurelian L, Zhao P, Qi Z. Three different functional microdomains in the hepatitis C virus hypervariable region 1 (HVR1) mediate entry and immune evasion. J Biol Chem 2012; 287:35631-35645. [PMID: 22927442 PMCID: PMC3471721 DOI: 10.1074/jbc.m112.382341] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 08/22/2012] [Indexed: 12/29/2022] Open
Abstract
High genetic heterogeneity is an important characteristic of hepatitis C virus (HCV) that contributes to its ability to establish persistent infection. The hypervariable region 1 (HVR1) that includes the first 27 amino acid residues of the E2 envelope glycoprotein is the most variable region within the HCV polyprotein. HVR1 plays a major role in both HCV cell entry and immune evasion, but the respective contribution of specific amino acid residues is still unclear. Our mutagenesis analyses of HCV pseudoparticles and cell culture-derived HCV using the H77 isolate indicate that five residues at positions 14, 15, and 25-27 mediate binding of the E2 protein to the scavenger receptor class B, type I receptor, and any residue herein is indispensable for HCV cell entry. The region spanning positions 16-24 contains the sole neutralizing epitope and is dispensable for HCV entry, but it is involved in heparan binding. More importantly, this region is necessary for the enhancement of HCV entry by high density lipoprotein and interferes with virus neutralization by E2-neutralizing antibodies. Residues at positions 1-13 are also dispensable for HCV entry, but they can affect HCV infectivity by modulating binding of the envelope protein to scavenger receptor class B, type I. Mutations occurring at this site may confer resistance to HVR1 antibodies. These findings further our understanding about the mechanisms of HCV cell entry and the significance of HVR1 variation in HCV immune evasion. They have major implications for the development of HCV entry inhibitors and prophylactic vaccines.
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Affiliation(s)
- Mo Guan
- Department of Microbiology, Second Military Medical University, Shanghai 200433, China
| | - Wenbo Wang
- Department of Microbiology, Second Military Medical University, Shanghai 200433, China
| | - Xiaoqing Liu
- Department of Microbiology, Second Military Medical University, Shanghai 200433, China
| | - Yimin Tong
- Department of Microbiology, Second Military Medical University, Shanghai 200433, China
| | - Yuan Liu
- Department of Microbiology, Second Military Medical University, Shanghai 200433, China
| | - Hao Ren
- Department of Microbiology, Second Military Medical University, Shanghai 200433, China
| | - Shiying Zhu
- Department of Microbiology, Second Military Medical University, Shanghai 200433, China
| | - Jean Dubuisson
- Inserm U1019, CNRS UMR8204, Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Université Lille Nord de France, F-59021 Lille, France
| | - Thomas F Baumert
- Unité Inserm U.748, Université de Strasbourg, Nouvel Hôpital Civil, 3 Rue Koeberlé, F-67000 Strasbourg, France
| | - Yongzhe Zhu
- Department of Microbiology, Second Military Medical University, Shanghai 200433, China
| | - Haoran Peng
- Department of Microbiology, Second Military Medical University, Shanghai 200433, China
| | - Laure Aurelian
- Department of Pharmacology and Experimental Therapeutics, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Ping Zhao
- Department of Microbiology, Second Military Medical University, Shanghai 200433, China.
| | - Zhongtian Qi
- Department of Microbiology, Second Military Medical University, Shanghai 200433, China.
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