Establishment of reference sequences of hepatitis B virus genotype B subgenotypes

Hepatitis B virus (HBV) has been classified into ten genotypes (A-J). Genotype B (HBV/B) is divided into nine subgenotypes (B1-B9), each with specific geographical predominance. Some reference sequence of HBV/B subgenotypes are currently in use, but these sequences have defects, being insufficient to represent the reference of individual subgenotype. The aim of this study was to establish a more representative reference of HBV/B subgenotypes in different regions. Full genomic sequences of HBV/B were obtained from GenBank and compartmentalized into genomic subtypes. The homology between our established HBV/B subgenotype references was evaluated at the nucleotide level. We established reference strains for B1-Japan, B2-China, B3-Indonesia, B4-Vietnam, B6-North America, B7-Indonesia and B9-Southeast Asia. Fractional significant mutation sites of the strains that were established were observed in the BCP/Pre-C regions. We calculated the genetic divergence time from the most recent common ancestor of HBV/B pedigree. The reference sequences established in the study provide reference standards for studies on molecular characterization, virology and pathogenesis of HBV/B.

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Molecular Evolution of Hepatitis B Virus Genotype F in Latin America

10.21203/rs.3.rs-875996/v1 ◽

2021 ◽

Author(s):

Jonas Wolf ◽

Thiago Kastell Mazeto ◽

Vagner Reinaldo Zingalli Bueno Pereira ◽

Daniel Simon ◽

Vagner Ricardo Lunge

Keyword(s):

Latin America ◽

Hepatitis B Virus ◽

Molecular Evolution ◽

Hepatitis B ◽

Recent Common Ancestor ◽

Virus Genotype ◽

Hbv Genotype ◽

Most Recent Common Ancestor ◽

B Virus ◽

Genotype F

Abstract Hepatitis B virus (HBV) genotype F evolution is not completely understood in Latin America. This study aims to evaluate the molecular evolution of HBV-F in Latin America by comparing 224 whole-genome sequences. Bayesian coalescent analysis was performed to estimate the time to the most recent common ancestor. Four main clades were formed dated back between 1245 and 1730. Also, four subclades were identified dated back between 1705 and 1801. HBV-F overall effective population size grew in the 18th century and showed an initial circulation of HBV-F from Venezuela to other countries from Latin America.

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Analysis of Hepatitis B virus genotype D in Greenland suggests presence of a novel subgenotype

10.1101/2020.06.06.20123968 ◽

2020 ◽

Author(s):

Adriano de Bernardi Schneider ◽

Reilly Hostager ◽

Henrik Krarup ◽

Malene Børresen ◽

Yasuhito Tanaka ◽

...

Keyword(s):

Hepatitis B Virus ◽

Hepatitis B ◽

Recent Common Ancestor ◽

Virus Genotype ◽

Most Recent Common Ancestor ◽

Hbv Genotypes ◽

Sister Clade ◽

B Virus ◽

Inuit Population ◽

Circumpolar Arctic

A disproportionate amount of Greenland’s Inuit population is chronically infected with Hepatitis B virus (HBV; 5-10%). HBV genotypes B and D are most prevalent in the circumpolar Arctic. Here, we report 39 novel HBV/D sequences from individuals residing in southwestern Greenland. We performed phylodynamic analyses with ancient HBV DNA calibrators to investigate the origin and relationship of these taxa to other HBV sequences. We inferred a substitution rate of 1.4×10−5 [95% HPD 8.8×10−6, 2.0×10−5] and a time to the most recent common ancestor of 629 CE [95% HPD 37-1138 CE]. The Greenland taxa form a sister clade to HBV/D2 sequences, specifically New Caledonian and Indigenous Taiwanese samples. The Greenland sequences share amino acid signatures with subgenotypes D1 and D2, and approximately 98% sequence identity. Our results suggest the classification of these novel sequences does not fit within the current nomenclature. Thus, we propose these taxa be a novel subgenotype.

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Analysis of Hepatitis B Virus Genotype D in Greenland Suggests the Presence of a Novel Quasi-Subgenotype

Frontiers in Microbiology ◽

10.3389/fmicb.2020.602296 ◽

2021 ◽

Vol 11 ◽

Cited By ~ 2

Author(s):

Adriano de Bernardi Schneider ◽

Carla Osiowy ◽

Reilly Hostager ◽

Henrik Krarup ◽

Malene Børresen ◽

...

Keyword(s):

Hepatitis B Virus ◽

Hepatitis B ◽

Recent Common Ancestor ◽

Virus Genotype ◽

Most Recent Common Ancestor ◽

Hbv Genotypes ◽

B Virus ◽

Disproportionate Number ◽

Inuit Population ◽

Circumpolar Arctic

A disproportionate number of Greenland's Inuit population are chronically infected with Hepatitis B virus (HBV; 5–10%). HBV genotypes B and D are most prevalent in the circumpolar Arctic. Here, we report 39 novel HBV/D sequences from individuals residing in southwestern Greenland. We performed phylodynamic analyses with ancient HBV DNA calibrators to investigate the origin and relationship of these taxa to other HBV sequences. We inferred a substitution rate of 1.4 × 10−5 [95% HPD 8.8 × 10−6, 2.0 × 10−5] and a time to the most recent common ancestor of 629 CE [95% HPD 37–1138 CE]. The Greenland taxa form a sister clade to HBV/D2 sequences, specifically New Caledonian and Indigenous Taiwanese sequences. The Greenland sequences share amino acid signatures with subgenotypes D1 and D2 and ~97% sequence identity. Our results suggest the classification of these novel sequences does not fit within the current nomenclature. Thus, we propose these taxa be considered a novel quasi-subgenotype.

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