Basic Study
Copyright ©The Author(s) 2016. Published by Baishideng Publishing Group Inc. All rights reserved.
World J Virol. Nov 12, 2016; 5(4): 161-169
Published online Nov 12, 2016. doi: 10.5501/wjv.v5.i4.161
Role of RNA secondary structure in emergence of compartment specific hepatitis B virus immune escape variants
Sibnarayan Datta, Runu Chakravarty
Sibnarayan Datta, Molecular Virology Laboratory, Defence Research, Laboratory (DRDO), Tezpur 784001, Assam, India
Runu Chakravarty, Hepatitis Research Laboratory, ICMR Virus Unit (ICMR), Kolkata 700010, West Bengal, India
Author contributions: Datta S designed the study to test the hypothesis, performed predictions, analyzed the models and wrote the manuscript; Chakravarty R reviewed the results and edited the manuscript.
Supported by Fellowship and funds from University Grants Commission (UGC), Min. of Human Resource and Development, Govt. of India and Defence Research & Development Organization (DRDO) (DRDO), Min. of Defence, Govt. of India (to Sibnarayan Datta); and Indian Council of Medical Research (ICMR), Ministry of Health and Family Welfare (MoHFW) (to Runu Chakravarty).
Institutional review board statement: Not applicable.
Institutional animal care and use committee statement: Not applicable.
Conflict-of-interest statement: None of the authors have any conflict of interest to disclose.
Data sharing statement: No additional data are available.
Open-Access: This article is an open-access article which was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution Non Commercial (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:
Correspondence to: Sibnarayan Datta, PhD, Molecular Virology Laboratory, Defence Research, Laboratory (DRDO), Tezpur 784001, Assam, India.
Telephone: +91-3712-258087 Fax: +91-3712-258534
Received: June 24, 2016
Peer-review started: June 27, 2016
First decision: August 5, 2016
Revised: August 9, 2016
Accepted: August 27, 2016
Article in press: August 29, 2016
Published online: November 12, 2016

To investigate the role of subgenotype specific RNA secondary structure in the compartment specific selection of hepatitis B virus (HBV) immune escape mutations.


This study was based on the analysis of the specific observation of HBV subgenotype A1 in the serum/plasma, while subgenotype A2 with G145R mutation in the peripheral blood leukocytes (PBLs). Genetic variability found among the two subgenotypes was used for prediction and comparison of the full length pregenomic RNA (pgRNA) secondary structure and base pairings. RNA secondary structures were predicted for 37 °C using the Vienna RNA fold server, using default parameters. Visualization and detailed analysis was done using RNA shapes program.


In this analysis, using similar algorithm and conditions, entirely different pgRNA secondary structures for subgenotype A1 and subgenotype A2 were predicted, suggesting different base pairing patterns within the two subgenotypes of genotype A, specifically, in the HBV genetic region encoding the major hydrophilic loop. We observed that for subgenotype A1 specific pgRNA, nucleotide 358U base paired with 1738A and nucleotide 587G base paired with 607C. However in sharp contrast, in subgenotype A2 specific pgRNA, nucleotide 358U was opposite to nucleotide 588G, while 587G was opposite to 359U, hence precluding correct base pairing and thereby lesser stability of the stem structure. When the nucleotides at 358U and 587G were replaced with 358C and 587A respectively (as observed specifically in the PBL associated A2 sequences), these nucleotides base paired correctly with 588G and 359U, respectively.


The results of this study show that compartment specific mutations are associated with HBV subgenotype specific alterations in base pairing of the pgRNA, leading to compartment specific selection and preponderance of specific HBV subgenotype with unique mutational pattern.

Keywords: Hepatitis B, Compartmentalization, Peripheral blood leukocytes, pgRNA, RNA secondary structure, G145R

Core tip: We have previously shown that, in our study population, distribution of hepatitis B virus (HBV) subgenotypes A1 and A2 is highly biased in the serum/plasma and peripheral blood leukocyte (PBL) compartments respectively. Analysing the predicted base pairing patterns of pregenomic RNAs (pgRNAs), specific for HBV subgenotype A1 and A2, we demonstrate that the potent immune escape mutation G145R evolves specifically in the context of HBV subgenotype A2. The PBL compartment is exposed to strong anti-HBs immunity, and thus G145R is highly advantageous for the virus to persist. This explains the exclusive preponderance of subgenotype A2 in the PBL compartment, sharply contrasting the prevalence of subgenotype A1 in the serum/plasma.