©The Author(s) 2020. Published by Baishideng Publishing Group Inc. All rights reserved.
Conservation and variability of hepatitis B core at different chronic hepatitis stages
Marçal Yll, Maria Francesca Cortese, Gerard Orriols, Rosario Casillas, Carolina González, Sara Sopena, Cristina Godoy, Marta Vila, David Tabernero, Ariadna Rando, Rosa Lopez-Martinez, Francisco Rodríguez-Frías, Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
Marçal Yll, Maria Francesca Cortese, Mercedes Guerrero-Murillo, Josep Gregori, Rosario Casillas, Sara Sopena, Marta Vila, Josep Quer, Francisco Rodríguez-Frías, Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
Mercedes Guerrero-Murillo, Department of Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
Josep Gregori, Cristina Godoy, David Tabernero, Josep Quer, Rafael Esteban, Mar Riveiro-Barciela, Maria Buti, Francisco Rodríguez-Frías, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, Madrid 28029, Spain
Rafael Esteban, Mar Riveiro-Barciela, Maria Buti, Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d'Hebron, Universitat Autónoma de Barcelona, Barcelona 08035, Spain
Author contributions: Rodríguez-Frías F designed the research; Cortese MF coordinated the research; Yll M and Cortese MF equally contributed to design the experiments; Yll M, Orriols G, Godoy C, Sopena S, Casillas R, González C, Vila M and Rando A performed the experiments; Yll M, Cortese MF, Gregori J and Guerrero-Murillo M analyzed data acquired during the experiments and interpreted the results; Yll M and Cortese MF drafted the manuscript; Cortese MF, Tabernero D, Lopez-Martinez R, Riveiro-Barciela M, Buti M, Quer J, Esteban R and Rodríguez-Frías F critically reviewed the manuscript.
Supported by the Instituto de Salud Carlos III, Spain, the European Regional Development Fund, No. PI18/01436.
Institutional review board statement: The study was reviewed and approved by the Clinical Research Ethics Committee of Hospital Universitari Vall d’Hebron.
Conflict-of-interest statement: Josep Gregori is an employee of Roche Diagnostics, SL.
Data sharing statement: Next-generation sequencing data were submitted to the GenBank SRA database (BioProject accession number PRJNA625435).
ARRIVE guidelines statement: The authors have read the ARRIVE guidelines, and the manuscript was prepared and revised according to the ARRIVE guidelines.
Open-Access: This article is an open-access article that was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution NonCommercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: http://creativecommons.org/licenses/by-nc/4.0/
Corresponding author: Maria Francesca Cortese, PhD, Research Scientist, Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Passeig Vall d’Hebron 119-129, Barcelona 08035, Spain. firstname.lastname@example.org
Received: February 28, 2020
Peer-review started: February 28, 2020
First decision: April 9, 2020
Revised: May 8, 2020
Accepted: May 19, 2020
Article in press: May 19, 2020
Published online: May 28, 2020
Since it is currently not possible to eradicate hepatitis B virus (HBV) infection with existing treatments, research continues to uncover new therapeutic strategies. HBV core protein, encoded by the HBV core gene (HBC), intervenes in both structural and functional processes, and is a key protein in the HBV life cycle. For this reason, both the protein and the gene could be valuable targets for new therapeutic and diagnostic strategies. Moreover, alterations in the protein sequence could serve as potential markers of disease progression.
To detect, by next-generation sequencing, HBC hyper-conserved regions that could potentially be prognostic factors and targets for new therapies.
Thirty-eight of 45 patients with chronic HBV initially selected were included and grouped according to liver disease stage [chronic hepatitis B infection without liver damage (CHB, n = 16), liver cirrhosis (LC, n = 5), and hepatocellular carcinoma (HCC, n = 17)]. HBV DNA was extracted from patients’ plasma. A region between nucleotide (nt) 1863 and 2483, which includes HBC, was amplified and analyzed by next-generation sequencing (Illumina MiSeq platform). Sequences were genotyped by distance-based discriminant analysis. General and intergroup nt and amino acid (aa) conservation was determined by sliding window analysis. The presence of nt insertion and deletions and/or aa substitutions in the different groups was determined by aligning the sequences with genotype-specific consensus sequences.
Three nt (nt 1900-1929, 2249-2284, 2364-2398) and 2 aa (aa 117-120, 159-167) hyper-conserved regions were shared by all the clinical groups. All groups showed a similar pattern of conservation, except for five nt regions (nt 1946-1992, 2060-2095, 2145-2175, 2230-2250, 2270-2293) and one aa region (aa 140-160), where CHB and LC, respectively, were less conserved (P < 0.05). Some group-specific conserved regions were also observed at both nt (2306-2334 in CHB and 1935-1976 and 2402-2435 in LC) and aa (between aa 98-103 in CHB and 28-30 and 51-54 in LC) levels. No differences in insertion and deletions frequencies were observed. An aa substitution (P79Q) was observed in the HCC group with a median (interquartile range) frequency of 15.82 (0-78.88) vs 0 (0-0) in the other groups (P < 0.05 vs CHB group).
The differentially conserved HBC and HBV core protein regions and the P79Q substitution could be involved in disease progression. The hyper-conserved regions detected could be targets for future therapeutic and diagnostic strategies.
Core tip: New tools for hepatitis B virus infection treatment and follow-up are needed. Hepatitis B virus core protein has a key role in viral replication and persistence. Analysis of viral quasispecies by next-generation sequencing can identify conserved regions in viral genes or proteins that may serve as targets for new therapeutic and diagnostic strategies. Moreover, it may help identify prognostic markers of liver disease progression. Here, we detected hyper-conserved nucleotide and amino acid regions regardless of the clinical stage. Moreover, we observed several group-specific conserved and variable regions and an amino acid substitution that could be indicative of different disease progression.