Variability in molecular characteristics of Hepatitis E virus quasispecies could modify viral surface properties and transmission
Cédric Hartard
Laboratoire de Virologie, CHRU de Nancy Brabois, Vandoeuvre-lès-Nancy, France
Université de Lorraine, CNRS, LCPME, Nancy, France
Search for more papers by this authorHonorine Fenaux
Laboratoire de Virologie, CHRU de Nancy Brabois, Vandoeuvre-lès-Nancy, France
Université de Lorraine, CNRS, LCPME, Nancy, France
Search for more papers by this authorAlexis Gentilhomme
Laboratoire de Virologie, CHRU de Nancy Brabois, Vandoeuvre-lès-Nancy, France
Search for more papers by this authorJohn M. Murray
School of Mathematics and Statistics, UNSW Sydney, Sydney, NSW, Australia
Search for more papers by this authorElma Akand
School of Mathematics and Statistics, UNSW Sydney, Sydney, NSW, Australia
Search for more papers by this authorElodie Laugel
Laboratoire de Virologie, CHRU de Nancy Brabois, Vandoeuvre-lès-Nancy, France
Université de Lorraine, CNRS, LCPME, Nancy, France
Search for more papers by this authorSibel Berger
Laboratoire de Virologie, CHRU de Nancy Brabois, Vandoeuvre-lès-Nancy, France
Search for more papers by this authorArmand Maul
LIEC (Laboratoire Interdisciplinaire des Environnements Continentaux), Université de Lorraine, CNRS, Metz, France
Search for more papers by this authorAlexis de Rougemont
CHU de Dijon, Centre national de référence des virus entériques, Dijon, France
Search for more papers by this authorHélène Jeulin
Laboratoire de Virologie, CHRU de Nancy Brabois, Vandoeuvre-lès-Nancy, France
Université de Lorraine, CNRS, LCPME, Nancy, France
Search for more papers by this authorThomas Remen
DRCI, Délégation à la Recherche Clinique et à l'Innovation, Unité de Méthodologie, Data Management et Statistique, CHRU de Nancy Brabois, Vandoeuvre-lès-Nancy, France
Search for more papers by this authorMouni Bensenane
Service d'hépato-gastro-entérologie, CHRU de Nancy Brabois, Vandoeuvre-lès-Nancy, France
Search for more papers by this authorJean-Pierre Bronowicki
Service d'hépato-gastro-entérologie, CHRU de Nancy Brabois, Vandoeuvre-lès-Nancy, France
Search for more papers by this authorChristophe Gantzer
Université de Lorraine, CNRS, LCPME, Nancy, France
Search for more papers by this authorIsabelle Bertrand
Université de Lorraine, CNRS, LCPME, Nancy, France
Search for more papers by this authorCorresponding Author
Evelyne Schvoerer
Laboratoire de Virologie, CHRU de Nancy Brabois, Vandoeuvre-lès-Nancy, France
Université de Lorraine, CNRS, LCPME, Nancy, France
Correspondence
Evelyne Schvoerer, Laboratoire de Virologie-CHRU de Nancy Brabois, Rue Morvan, 54511 Vandoeuvre-lès-Nancy, France.
Email: [email protected]
Search for more papers by this authorCédric Hartard
Laboratoire de Virologie, CHRU de Nancy Brabois, Vandoeuvre-lès-Nancy, France
Université de Lorraine, CNRS, LCPME, Nancy, France
Search for more papers by this authorHonorine Fenaux
Laboratoire de Virologie, CHRU de Nancy Brabois, Vandoeuvre-lès-Nancy, France
Université de Lorraine, CNRS, LCPME, Nancy, France
Search for more papers by this authorAlexis Gentilhomme
Laboratoire de Virologie, CHRU de Nancy Brabois, Vandoeuvre-lès-Nancy, France
Search for more papers by this authorJohn M. Murray
School of Mathematics and Statistics, UNSW Sydney, Sydney, NSW, Australia
Search for more papers by this authorElma Akand
School of Mathematics and Statistics, UNSW Sydney, Sydney, NSW, Australia
Search for more papers by this authorElodie Laugel
Laboratoire de Virologie, CHRU de Nancy Brabois, Vandoeuvre-lès-Nancy, France
Université de Lorraine, CNRS, LCPME, Nancy, France
Search for more papers by this authorSibel Berger
Laboratoire de Virologie, CHRU de Nancy Brabois, Vandoeuvre-lès-Nancy, France
Search for more papers by this authorArmand Maul
LIEC (Laboratoire Interdisciplinaire des Environnements Continentaux), Université de Lorraine, CNRS, Metz, France
Search for more papers by this authorAlexis de Rougemont
CHU de Dijon, Centre national de référence des virus entériques, Dijon, France
Search for more papers by this authorHélène Jeulin
Laboratoire de Virologie, CHRU de Nancy Brabois, Vandoeuvre-lès-Nancy, France
Université de Lorraine, CNRS, LCPME, Nancy, France
Search for more papers by this authorThomas Remen
DRCI, Délégation à la Recherche Clinique et à l'Innovation, Unité de Méthodologie, Data Management et Statistique, CHRU de Nancy Brabois, Vandoeuvre-lès-Nancy, France
Search for more papers by this authorMouni Bensenane
Service d'hépato-gastro-entérologie, CHRU de Nancy Brabois, Vandoeuvre-lès-Nancy, France
Search for more papers by this authorJean-Pierre Bronowicki
Service d'hépato-gastro-entérologie, CHRU de Nancy Brabois, Vandoeuvre-lès-Nancy, France
Search for more papers by this authorChristophe Gantzer
Université de Lorraine, CNRS, LCPME, Nancy, France
Search for more papers by this authorIsabelle Bertrand
Université de Lorraine, CNRS, LCPME, Nancy, France
Search for more papers by this authorCorresponding Author
Evelyne Schvoerer
Laboratoire de Virologie, CHRU de Nancy Brabois, Vandoeuvre-lès-Nancy, France
Université de Lorraine, CNRS, LCPME, Nancy, France
Correspondence
Evelyne Schvoerer, Laboratoire de Virologie-CHRU de Nancy Brabois, Rue Morvan, 54511 Vandoeuvre-lès-Nancy, France.
Email: [email protected]
Search for more papers by this authorCédric Hartard and Honorine Fenaux contributed equally to this work.
Abstract
Hepatitis E virus (HEV) usually causes self-limited liver diseases but can also result in severe cases. Genotypes 1 (G1) and 2 circulate in developing countries are human-restricted and waterborne, while zoonotic G3 and G4 circulating in industrialized countries preferentially infect human through consumption of contaminated meat. Our aims were to identify amino acid patterns in HEV variants that could be involved in pathogenicity or in transmission modes, related to their impact on antigenicity and viral surface hydrophobicity. HEV sequences from human (n = 37) and environmental origins (wild boar [n = 3], pig slaughterhouse effluent [n = 6] and urban wastewater [n = 2]) were collected for the characterization of quasispecies using ultra-deep sequencing (ORF2/ORF3 overlap). Predictive and functional assays were carried out to investigate viral particle antigenicity and hydrophobicity. Most quasispecies showed a major variant while a mixture was observed in urban wastewater and in one chronically infected patient. Amino acid signatures were identified, as a rabbit-linked HEV pattern in two infected patients, or the S68L (ORF2) / H81C (ORF3) residue mostly identified in wild boars. By comparison with environmental strains, molecular patterns less likely represented in humans were identified. Patterns impacting viral hydrophobicity and/or antigenicity were also observed, and the higher hydrophobicity of HEV naked particles compared with the enveloped forms was demonstrated. HEV variants isolated from human and environment present molecular patterns that could impact their surface properties as well as their transmission. These molecular patterns may concern only one minor variant of a quasispecies and could emerge under selective pressure.
CONFLICT OF INTEREST
All authors report no conflicts of interest.
Open Research
DATA AVAILABILITY STATEMENT
The data that support the findings of this study are available from the corresponding author upon reasonable request.
Supporting Information
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| jvh13513-sup-0001-DataS1.pngPNG image, 449.8 KB | Data S1 |
| jvh13513-sup-0002-DataS2.pngPNG image, 157.4 KB | Data S2 |
| jvh13513-sup-0003-DataS2bis.pngPNG image, 169 KB | Data S2bis |
| jvh13513-sup-0004-DataS2quat.pngPNG image, 109.1 KB | Data S2quat |
| jvh13513-sup-0005-DataS2ter.pngPNG image, 157.8 KB | Data S2ter |
| jvh13513-sup-0006-DataS3TREE.tifTIFF image, 7 MB | Data S3TREE |
| jvh13513-sup-0007-DataS4.pngPNG image, 182.5 KB | Data S4 |
| jvh13513-sup-0008-DataS5.pngPNG image, 231.6 KB | Data S5 |
| jvh13513-sup-0009-legends.docxWord document, 12.4 KB | Supplementary Material |
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REFERENCES
- 1Balayan MS, Andjaparidze AG, Savinskayay SS, et al. Evidence for a virus in non-A, non-B hepatitis transmitted via the fecal-oral route. Intervirology. 1983; 20: 23-31. https://doi.org/10.1159/000149370
- 2Colson P, Raoult D. Autochthonous hepatitis E: a common and fatal but neglected emerging disease in France. Clin Microbiol Infect. 2017; 23(12): 898-899. https://doi.org/10.1016/j.cmi.2017.06.027
- 3Izopet J, Tremeaux P, Marion O, et al. Hepatitis E virus infections in Europe. J Clin Virol. 2019; 120: 20-26. https://doi.org/10.1016/j.jcv.2019.09.004
- 4Kumar H, Kamar N, Kumar D. Hepatitis E: current status in India and other Asian countries. J Pure Appl Microbiol. 2019; 13(1): 141-159. https://doi.org/10.22207/JPAM.13.1.15
- 5Nimgaonkar I, Ding Q, Schwartz RE, Ploss A. Hepatitis E virus: advances and challenges. Nat Rev Gastroenterol Hepatol. 2017; 15(2): 96-110. https://doi.org/10.1038/nrgastro.2017.150
- 6Khuroo MS, Khuroo MS, Khuroo NS. Hepatitis E: discovery, global impact, control and cure. World J Gastroenterol. 2016; 22(31): 7030-7045. https://doi.org/10.3748/wjg.v22.i31.7030
- 7Dalton HR, Izopet J. Transmission and epidemiology of hepatitis E Virus genotype 3 and 4 infections. Cold Spring Harb Perspect Med. 2018; 8(11):a032144. https://doi.org/10.1101/cshperspect.a032144
- 8Lee G-H, Tan B-H, Chi-Yuan Teo E, et al. Chronic infection with camelid hepatitis E virus in a liver transplant recipient who regularly consumes camel meat and milk. Gastroenterology. 2016; 150(2): 355-357.e3. https://doi.org/10.1053/j.gastro.2015.10.048
- 9Cao D, Meng X-J. Molecular biology and replication of hepatitis E virus. Emerg Microbes Infect. 2012; 1(1): 1-10. https://doi.org/10.1038/emi.2012.7
- 10He M, Wang M, Huang Y, et al. The ORF3 protein of genotype 1 hepatitis E virus suppresses TLR3-induced NF-κB signaling via TRADD and RIP1. Sci Rep. 2016; 6: 1-13. https://doi.org/10.1038/srep27597
- 11Kenney SP, Wentworth JL, Heffron CL, Meng X-J. Replacement of the hepatitis E virus ORF3 protein PxxP motif with heterologous late domain motifs affects virus release via interaction with TSG101. Virology. 2015; 486(3): 198-208. https://doi.org/10.1016/j.virol.2015.09.012
- 12Ankcorn MJ, Tedder RS. Hepatitis E: the current state of play. Transfus Med. 2017; 27(2): 84-95. https://doi.org/10.1111/tme.12405
- 13Pischke S, Hartl J, Pas SD, Lohse AW, Jacobs BC, Van der Eijk AA. Hepatitis E virus: infection beyond the liver? J Hepatol. 2017; 66(5): 1082-1095. https://doi.org/10.1016/j.jhep.2016.11.016
- 14van Tong H, Hoan NX, Wang B, Wedemeyer H, Bock C-T, Velavan TP. Hepatitis E virus mutations: functional and clinical relevance. EBioMedicine. 2016; 11: 31-42. https://doi.org/10.1016/j.ebiom.2016.07.039
- 15Borkakoti J, Ahmed G, Rai A, Kar P. Report of novel H105R, D29N, V27A mutations in the methyltransferase region of the HEV genome in patients with acute liver failure. J Clin Virol. 2017; 91: 1-4. https://doi.org/10.1016/j.jcv.2017.03.017
- 16Todt D, Gisa A, Radonic A, et al. In vivo evidence for ribavirin-induced mutagenesis of the hepatitis E virus genome. Gut. 2016; 65(10): 1733-1743. https://doi.org/10.1136/gutjnl-2015-311000
- 17Lhomme S, Abravanel F, Dubois M, et al. Characterization of the polyproline region of the hepatitis E virus in immunocompromised patients. J Virol. 2014; 88(20): 12017-12025. https://doi.org/10.1128/JVI.01625-14
- 18Johne R, Reetz J, Ulrich RG, et al. An ORF1-rearranged hepatitis E virus derived from a chronically infected patient efficiently replicates in cell culture. J Viral Hepat. 2014; 21(6): 447-456. https://doi.org/10.1111/jvh.12157
- 19Kamar N, Izopet J, Cintas P, et al. Hepatitis E virus-induced neurological symptoms in a kidney-transplant patient with chronic hepatitis. Am J Transplant. 2010; 10(5): 1321-1324. https://doi.org/10.1111/j.1600-6143.2010.03068.x
- 20Xing L, Li TC, Mayazaki N, et al. Structure of hepatitis E virion-sized particle reveals an RNA-dependent viral assembly pathway. J Biol Chem. 2010; 285(43): 33175-33183. https://doi.org/10.1074/jbc.M110.106336
- 21Aggarwal R, Shukla R, Jameel S, et al. T-cell epitope mapping of ORF2 and ORF3 proteins of human hepatitis E virus. J Viral Hepat. 2007; 14(4): 283-292. https://doi.org/10.1111/j.1365-2893.2006.00796.x
- 22Zafrullah M, Ozdener MH, Panda SK, Jameel S. The ORF3 protein of hepatitis E virus is a phosphoprotein that associates with the cytoskeleton. J Virol. 1997; 71(12): 9045-9053. https://doi.org/10.1128/jvi.71.12.9045-9053.1997
- 23Nan Y, Wu C, Zhao Q, Sun Y, Zhang Y-J, Zhou E-M. Vaccine development against zoonotic hepatitis E virus: open questions and remaining challenges. Front Microbiol. 2018; 9: 1-16. https://doi.org/10.3389/fmicb.2018.00266.
- 24Osterman A, Vizoso Pinto M, Haase R, et al. Systematic screening for novel, serologically reactive Hepatitis E Virus epitopes. Virol J. 2012; 9(1): 28. https://doi.org/10.1186/1743-422X-9-28
- 25Fenaux H, Chassaing M, Berger S, et al. Molecular features of hepatitis E virus circulation in environmental and human samples. J Clin Virol. 2018; 103: 63-70. https://doi.org/10.1016/j.jcv.2018.04.003
- 26Clemente-Casares P, Pina S, Buti M, et al. Hepatitis E virus epidemiology in industrialized countries. Emerg Infect Dis. 2003; 9(4): 448-454. https://doi.org/10.3201/eid0904.020351
- 27Smith DB, Paddy JO, Simmonds P. The use of human sewage screening for community surveillance of hepatitis E virus in the UK. J Med Virol. 2016; 88(5): 915-918. https://doi.org/10.1002/jmv.24403
- 28Boudaud N, Machinal C, David F, et al. Removal of MS2, Qβ and GA bacteriophages during drinking water treatment at pilot scale. Water Res. 2012; 46(8): 2651-2664. https://doi.org/10.1016/j.watres.2012.02.020
- 29Brié A, Bertrand I, Meo M, Boudaud N, Gantzer C. The Effect of heat on the physicochemical properties of bacteriophage MS2. Food Environ Virol. 2016; 8(4): 251-261. https://doi.org/10.1007/s12560-016-9248-2
- 30Dika C, Ly-Chatain MH, Francius G, Duval JFL, Gantzer C. Non-DLVO adhesion of F-specific RNA bacteriophages to abiotic surfaces: importance of surface roughness, hydrophobic and electrostatic interactions. Colloids Surfaces A Physicochem Eng Asp. 2013; 435: 178-187. https://doi.org/10.1016/j.colsurfa.2013.02.045
- 31Xing L, Wang JC, Li T-C, et al. Spatial configuration of hepatitis E virus antigenic domain. J Virol. 2011; 85(2): 1117-1124. https://doi.org/10.1128/JVI.00657-10
- 32Mei X, Dai F, Zou J, et al. Quasispecies dynamics of a hepatitis E virus 4 from the feces and liver biopsy of an acute hepatitis E patient during virus clearance. J Med Virol. 2020; 92(12): 3556-3562. https://doi.org/10.1002/jmv.25746
- 33Lhomme S, Abravanel F, Dubois M, et al. Hepatitis E virus quasispecies and the outcome of acute hepatitis E in solid-organ transplant patients. J Virol. 2012; 86(18): 10006-10014. https://doi.org/10.1128/JVI.01003-12
- 34Péron JM, Bureau C, Poirson H, et al. Fulminant liver failure from acute autochthonous hepatitis E in France: description of seven patients with acute hepatitis E and encephalopathy. J Viral Hepat. 2007; 14(5): 298-303. https://doi.org/10.1111/j.1365-2893.2007.00858.x
- 35Inoue J, Takahashi M, Yazaki Y, Tsuda F, Okamoto H. Development and validation of an improved RT-PCR assay with nested universal primers for detection of hepatitis E virus strains with significant sequence divergence. J Virol Methods. 2006; 137(2): 325-333. https://doi.org/10.1016/j.jviromet.2006.07.004
- 36Hartard C, Gantzer C, Bronowicki J, Schvoerer E. Emerging hepatitis E virus compared with hepatitis A virus: a new sanitary challenge. Rev Med Virol. 2019; 29(6):e2078. https://doi.org/10.1002/rmv.2078
- 37Smith DB, Simmonds P, Izopet J, et al. Proposed reference sequences for hepatitis E Virus subtypes. J Gen Virol. 2016; 97(3): 537-542. https://doi.org/10.1099/jgv.0.000393
- 38Parker JMR, Guo D, Hodges RS. New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites. Biochemistry. 1986; 25(19): 5425-5432. https://doi.org/10.1021/bi00367a013
- 39Vacic V, Iakoucheva LM, Radivojac P. Two sample logo: a graphical representation of the differences between two sets of sequence alignments. Bioinformatics. 2006; 22(12): 1536-1537. https://doi.org/10.1093/bioinformatics/btl151
- 40Norder H, Galli C, Magnil E, et al. Hepatitis E virus genotype 3 genomes from RNA-positive but serologically negative plasma donors have CUG as the start codon for ORF3. Intervirology. 2018; 61(2): 96-103. https://doi.org/10.1159/000491926
- 41Abravanel F, Lhomme S, El Costa H, et al. Rabbit hepatitis E virus infections in humans, France. Emerg Infect Dis. 2017; 23(7): 1191-1193. https://doi.org/10.3201/eid2307.170318
- 42Fenaux H, Chassaing M, Berger S, Gantzer C, Bertrand I, Schvoerer E. Transmission of hepatitis E virus by water: an issue still pending in industrialized countries. Water Res. 2019; 151: 144-157. https://doi.org/10.1016/j.watres.2018.12.014
- 43Okamoto H. Culture systems for hepatitis E virus. J Gastroenterol. 2013; 48(2): 147-158. https://doi.org/10.1007/s00535-012-0682-0
- 44Ding Q, Heller B, Capuccino JMV, et al. Hepatitis E virus ORF3 is a functional ion channel required for release of infectious particles. Proc Natl Acad Sci. 2017; 114(5): 1147-1152. https://doi.org/10.1073/pnas.1614955114
- 45Okamoto H. Hepatitis E virus cell culture models. Virus Res. 2011; 161(1): 65-77. https://doi.org/10.1016/j.virusres.2011.01.015
- 46Lhomme S, Garrouste C, Kamar N, et al. Influence of polyproline region and macro domain genetic heterogeneity on HEV persistence in immunocompromised patients. J Infect Dis. 2014; 209(2): 300-303. https://doi.org/10.1093/infdis/jit438
- 47Todt D, Meister TL, Steinmann E. Hepatitis E virus treatment and ribavirin therapy: viral mechanisms of nonresponse. Curr Opin Virol. 2018; 32: 80-87. https://doi.org/10.1016/j.coviro.2018.10.001
- 48Todt D, Walter S, Brown RJP, Steinmann E. Mutagenic effects of ribavirin on hepatitis E virus-viral extinction versus selection of fitness-enhancing mutations. Viruses. 2016; 8(10): 1-15. https://doi.org/10.3390/v8100283
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