TY - JOUR
T1 - A novel hepatitis B virus recombinant genotype D4/E identified in a South African population
AU - Matlou, Mmatsatsi K.
AU - Gaelejwe, Lucinda R.
AU - Musyoki, Andrew Munyalo
AU - Rakgole, Jonny Nare
AU - Selabe, Selokela Gloria
AU - Amponsah-Dacosta, Edina
N1 - Funding Information:
This work was supported by grants from the Poliomyelitis Research Foundation (PRF) [grant numbers: 11/74 and 15/37 ] and the National Health Laboratory Service (NHLS) [grant number: GRANT004_94329 ].
Publisher Copyright:
© 2019
Copyright:
Copyright 2019 Elsevier B.V., All rights reserved.
PY - 2019/4/1
Y1 - 2019/4/1
N2 - © 2019 Background: Genetic diversity is a characteristic trait of the hepatitis B virus (HBV) and has been associated with different clinical outcomes. In South Africa, HBV infection is a major public health concern. Most HBV infections are caused by genotype A strains. However rare cases of infection with HBV genotype D have been reported. The purpose of this study was to investigate the molecular characteristics of a rare HBV subgenotype D4 isolate. Methods: The full-length genome of isolate ZADGM6964 was amplified in a one-step polymerase chain reaction. The amplified product was purified and cloned into a pGEM®-T Easy Vector System to investigate the genetic diversity of the viral quasi-populations. The primary isolate and clones were then directly sequenced and analysed using an array of bioinformatics software. Results: Phylogenetic analysis showed that the primary isolate and cloned sequences formed a monophyletic cluster away from subgenotype D4 reference strains. Further recombination analysis revealed that isolate ZADGM6964 was in fact a D4/E recombinant strain with breakpoints identified within the X and overlapping pre-Core/Core open reading frames with a >70% bootstrap confidence level. The recombinant genotype D4/E was found to be unique from other D/E strains archived in the genetic database, GenBank. Conclusion: This study represents the first ever report on the isolation and molecular characterization of an HBV D4/E recombinant strain in South Africa. The findings provide evidence of further HBV genetic diversity in South Africa than has been previously reported.
AB - © 2019 Background: Genetic diversity is a characteristic trait of the hepatitis B virus (HBV) and has been associated with different clinical outcomes. In South Africa, HBV infection is a major public health concern. Most HBV infections are caused by genotype A strains. However rare cases of infection with HBV genotype D have been reported. The purpose of this study was to investigate the molecular characteristics of a rare HBV subgenotype D4 isolate. Methods: The full-length genome of isolate ZADGM6964 was amplified in a one-step polymerase chain reaction. The amplified product was purified and cloned into a pGEM®-T Easy Vector System to investigate the genetic diversity of the viral quasi-populations. The primary isolate and clones were then directly sequenced and analysed using an array of bioinformatics software. Results: Phylogenetic analysis showed that the primary isolate and cloned sequences formed a monophyletic cluster away from subgenotype D4 reference strains. Further recombination analysis revealed that isolate ZADGM6964 was in fact a D4/E recombinant strain with breakpoints identified within the X and overlapping pre-Core/Core open reading frames with a >70% bootstrap confidence level. The recombinant genotype D4/E was found to be unique from other D/E strains archived in the genetic database, GenBank. Conclusion: This study represents the first ever report on the isolation and molecular characterization of an HBV D4/E recombinant strain in South Africa. The findings provide evidence of further HBV genetic diversity in South Africa than has been previously reported.
KW - Bioinformatics
KW - Genetics
KW - Virology
UR - http://www.scopus.com/inward/record.url?scp=85063798784&partnerID=8YFLogxK
U2 - 10.1016/j.heliyon.2019.e01477
DO - 10.1016/j.heliyon.2019.e01477
M3 - Article
SN - 2405-8440
VL - 5
JO - Heliyon
JF - Heliyon
IS - 4
M1 - e01477
ER -
