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

Schneider, Adriano de Bernardi; Osiowy, Carla; Hostager, Reilly; Krarup, Henrik; Børresen, Malene Landbo; Tanaka, Yasuhito; Morriseau, Taylor; Wertheim, Joel O.

doi:10.3389/fmicb.2020.602296

Cited by 6 publications

(6 citation statements)

References 49 publications

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“…Most viral genotypes/subgenotypes/subclades are based on whole-genome nucleotide divergence of a specific percentage, usually determined by phylogeny showing clades/lineages of a defined 'high' statistical support (>70% bootstrap) [60,61]. Hepatitis B viruses, for example, are classified into genotypes and subgenotypes based on their monophyly, amino acid signatures, and genetic distance [62]. In HIV, major distinct clades are classified as major genetic groups, with multiple subtypes within the genetic groups [63].…”

Section: Discussionmentioning

confidence: 99%

Dynamic Molecular Epidemiology Reveals Lineage-Associated Single-Nucleotide Variants That Alter RNA Structure in Chikungunya Virus

Spicher

Delitz

Schneider

et al. 2021

Genes

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Chikungunya virus (CHIKV) is an emerging Alphavirus which causes millions of human infections every year. Outbreaks have been reported in Africa and Asia since the early 1950s, from three CHIKV lineages: West African, East Central South African, and Asian Urban. As new outbreaks occurred in the Americas, individual strains from the known lineages have evolved, creating new monophyletic groups that generated novel geographic-based lineages. Building on a recently updated phylogeny of CHIKV, we report here the availability of an interactive CHIKV phylodynamics dataset, which is based on more than 900 publicly available CHIKV genomes. We provide an interactive view of CHIKV molecular epidemiology built on Nextstrain, a web-based visualization framework for real-time tracking of pathogen evolution. CHIKV molecular epidemiology reveals single nucleotide variants that change the stability and fold of locally stable RNA structures. We propose alternative RNA structure formation in different CHIKV lineages by predicting more than a dozen RNA elements that are subject to perturbation of the structure ensemble upon variation of a single nucleotide.

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Section: Discussionmentioning

confidence: 99%

Dynamic Molecular Epidemiology Reveals Lineage-Associated Single-Nucleotide Variants That Alter RNA Structure in Chikungunya Virus

Spicher

Delitz

Schneider

et al. 2021

Genes

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“…Genotypes comprise several subgenotypes having a pairwise divergence of 4% to 7.5%. Over the years, the discovery of new subgenotypes has been extensively described [6][7][8][9][10], but there have been many debates about the possible misclassification of some of them [11]. In the absence of an ICTV classification, several attempts have been made to standardize the ICTV classification system [12][13][14][15].…”

Section: Introductionmentioning

confidence: 99%

Phylogeography of hepatitis B virus: The role of Portugal in the early dissemination of HBV worldwide

Marcelino

Ezeonwumelu

Janeiro³

et al. 2022

PLoS ONE

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In Portugal, the genetic diversity, origin of HBV and the Portuguese role in the dissemination of HBV worldwide were never investigated. In this work, we studied the epidemic history and transmission dynamics of HBV genotypes that are endemic in Portugal. HBV pol gene was sequenced from 130 patients followed in Lisbon. HBV genotype A was the most prevalent (n = 54, 41.5%), followed by D (n = 44, 33.8%), and E (n = 32, 24.6%). Spatio-temporal evolutionary dynamics was reconstructed in BEAST using a Bayesian Markov Chain Monte Carlo method, with a GTR nucleotide substitution model, an uncorrelated lognormal relaxed molecular clock model, a Bayesian skyline plot, and a continuous diffusion model. HBV subgenotype D4 was the first to be introduced in Portugal around 1857 (HPD 95% 1699–1931) followed by D3 and A2 a few decades later. HBV genotype E and subgenotype A1 were introduced in Portugal later, almost simultaneously. Our results indicate a very important role of Portugal in the exportation of subgenotypes D4 and A2 to Brazil and Cape Verde, respectively, in the beginning of the XX century. This work clarifies the epidemiological history of HBV in Portugal and provides new insights in the early and global epidemic history of this virus.

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“…These genotypes have distinct geographic distribution [19], as do their sub-genotypes, characterized by >3%-4% genomic nucleotide divergence [6,20]. Accordingly, infection with different HBV genotypes and their related clinical outcomes are often highly associated with different ethnic populations [21][22][23].…”

Section: Discussionmentioning

confidence: 99%

“…There are 10 genotypes described for HBV, A–J, that are differentiated based on 7.5% or greater nucleotide divergence throughout the complete genome [5]. These genotypes have distinct geographic distribution [19], as do their sub‐genotypes, characterized by >3%–4% genomic nucleotide divergence [6, 20]. Accordingly, infection with different HBV genotypes and their related clinical outcomes are often highly associated with different ethnic populations [21–23].…”

Section: Discussionmentioning

confidence: 99%

Hepatitis B virus genotype surveillance in Canadian blood donors and a referred patient population, 2016–2021

Osiowy,

Giles,

Lowe

et al. 2023

Vox Sanguinis

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Background and ObjectivesHepatitis B virus (HBV) genotypes (A–H) have a distinct geographic distribution and are highly associated with the country of birth. Canada has experienced increased immigration over the past decade, primarily from regions where HBV is endemic. This study investigated the proportions and trends of HBV genotypes within blood donor and clinical populations of Canada over the period 2016–2021.Materials and MethodsStudy samples involved two cohorts: (1) Canadian blood donors (n = 246) deferred from donation due to HBV test positivity and (2) chronic HBV patients from across Canada (clinically referred population, n = 3539). Plasma or serum was extracted, and the surface antigen and/or polymerase‐coding region was amplified and sequenced to determine genotype by phylogenetic analysis.ResultsSix (A–E, G) and eight (A–H) HBV genotypes were detected among deferred blood donors and the clinically referred population, respectively. Differences in HBV genotype proportions between the two cohorts were observed across Canada. Males comprised most of the referred population among genotypes A–E (p < 0.0001), except for genotypes B and C. The median age was younger among blood donors (36 years [range 17–72]) compared with the referred population (41 years [range 0–99]). Distinct trends of increasing (E, referred; B, blood donor) and decreasing genotype prevalence were observed over the study period.ConclusionHBV genotypes in Canada are highly diverse, suggesting a large immigrant population. Observed trends in genotype prevalence and proportional differences among cohorts imply shifts among the HBV‐infected population of Canada, which warrants continued surveillance.

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

Cited by 6 publications

References 49 publications

Dynamic Molecular Epidemiology Reveals Lineage-Associated Single-Nucleotide Variants That Alter RNA Structure in Chikungunya Virus

Dynamic Molecular Epidemiology Reveals Lineage-Associated Single-Nucleotide Variants That Alter RNA Structure in Chikungunya Virus

Phylogeography of hepatitis B virus: The role of Portugal in the early dissemination of HBV worldwide

Hepatitis B virus genotype surveillance in Canadian blood donors and a referred patient population, 2016–2021

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