Analysis of genomic-length HBV sequences to determine genotype and subgenotype reference sequences

The Journal of General Virology
Anna McNaughtonM. Azim Ansari

Abstract

Hepatitis B virus (HBV) is a diverse, partially double-stranded DNA virus, with 9 genotypes (A-I), and a putative 10th genotype (J), characterized thus far. Given the broadening interest in HBV sequencing, there is an increasing requirement for a consistent, unified approach to HBV genotype and subgenotype classification. We set out to generate an updated resource of reference sequences using the diversity of all genomic-length HBV sequences available in public databases. We collated and aligned genomic-length HBV sequences from public databases and used maximum-likelihood phylogenetic analysis to identify genotype clusters. Within each genotype, we examined the phylogenetic support for currently defined subgenotypes, as well as identifying well-supported clades and deriving reference sequences for them. Based on the phylogenies generated, we present a comprehensive set of HBV reference sequences at the genotype and subgenotype level. All of the generated data, including the alignments, phylogenies and chosen reference sequences, are available online (https://doi.org/10.6084/m9.figshare.8851946) as a simple open-access resource.

References

May 18, 2005·The Journal of Infectious Diseases·Henry L Y ChanJoseph J Y Sung
Nov 25, 2005·Journal of Virology·Peter Simmonds, Sofie Midgley
Apr 14, 2006·Systematic Biology·T Heath Ogden, Michael S Rosenberg
Jul 19, 2006·Journal of Medical Virology·Maria MakuwaFrançois Simon
Dec 8, 2006·The Journal of Infectious Diseases·Stephen E LivingstonVladimir P Chulanov
Apr 28, 2007·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Tsuyoshi HatakeyamaKazuaki Chayama
Dec 22, 2007·Journal of Medical Virology·Dildora AvazovaMasashi Mizokami
Nov 4, 2008·Emerging Infectious Diseases·Christophe M OlingerClaude P Muller
Apr 22, 2009·Journal of Medical Virology·Lolita CavintaStephan Schaefer
Sep 16, 2009·Emerging Infectious Diseases·Iris E AndernachClaude P Muller
Sep 30, 2009·Intervirology·Stephan SchaeferHelene Norder
Oct 28, 2009·Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology·Mahmoud Reza PourkarimMarc Van Ranst
Jan 22, 2010·Journal of Virology·Hurng-Yi WangDing-Shinn Chen
Feb 16, 2010·Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology·Mahmoud Reza PourkarimMarc Van Ranst
Jun 29, 2010·Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology·Zhihui XuDongping Xu
Sep 17, 2010·Journal of Clinical Microbiology·Sumantra GhoshSimanti Datta
Nov 10, 2010·Antiviral Therapy·Stephen Locarnini, Fabien Zoulim
Jan 14, 2011·Journal of Gastroenterology and Hepatology·Chih-Lin Lin, Jia-Horng Kao
Jan 26, 2011·Journal of Medical Virology·Cuong Hung NguyenHiroshi Ichimura
Aug 29, 2012·BMC Gastroenterology·Weifeng ShiZhong Zhang
Sep 18, 2012·Hepatology Research : the Official Journal of the Japan Society of Hepatology·Mukhlid Yousif, Anna Kramvis
Sep 19, 2012·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Dimitrios ParaskevisAngelos Hatzakis
Nov 6, 2012·Nucleic Acids Research·Juliette HayerChristophe Combet
Mar 30, 2013·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Weifeng ShiDesmond G Higgins
Jun 26, 2013·Antiviral Therapy·Sebastián MarcianoAdrián C Gadano

❮ Previous
Next ❯

Citations

Feb 2, 2021·Frontiers in Microbiology·Adriano de Bernardi SchneiderJoel O Wertheim
Apr 4, 2021·Microorganisms·Rayana Maryse ToyéIsabelle Chemin
Sep 10, 2020·JHEP Reports : Innovation in Hepatology·Damien CohenIsabelle Chemin
Jul 31, 2021·The Journal of General Virology·Fazle Rabbi ChowdhuryPhilippa C Matthews

❮ Previous
Next ❯

Datasets Mentioned

BETA
EU670263
KF170740

Methods Mentioned

BETA
genotyping

Software Mentioned

Geno2pheno
HBVdb
blast
RAxML
mafft

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

The Brazilian Journal of Infectious Diseases : an Official Publication of the Brazilian Society of Infectious Diseases
Silvana Gama Florencio ChacháAna de Lourdes Candolo Martinelli
Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology
Henry Lik-Yuen ChanTony Shu-Kam Mok
Revista española de quimioterapia : publicación oficial de la Sociedad Española de Quimioterapia
J J CostaA Aguilera
© 2021 Meta ULC. All rights reserved