In Silico Analysis of Genetic Diversity of Human Hepatitis B Virus in Southeast Asia, Australia and New Zealand

Phan, Ngoc; Faddy, Helen M.; Flower, Robert L.; Spann, Kirsten; Roulis, Eileen

doi:10.3390/v12040427

Cited by 3 publications

(5 citation statements)

References 72 publications

(103 reference statements)

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“…We found genotype C to be predominant, followed by genotypes B and D, then genotype A. This observation was consistent with previous findings that genotypes B and C are most prevalent in Australia, followed by genotypes A and D [ 17 , 47 ].…”

Section: Discussionsupporting

confidence: 92%

“…A previous study identified the polymerase and pre-surface/surface loci as the most genetically diverse regions along the HBV viral genome [ 47 ]. In this study we found two genetically diverse regions, nt103–203 and nt333–438, which appear to contain or overlap with sequences coding for two corresponding epitopes of HBsAg (AA51–70 and AA110–147 for wild-type HBsAg GQ183486) predicted by Rezaee et al (2016) [ 26 ].…”

Section: Discussionmentioning

confidence: 99%

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Low Genetic Diversity of Hepatitis B Virus Surface Gene amongst Australian Blood Donors

Phan

Faddy

Flower

et al. 2021

Viruses

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Variants in the small surface gene of hepatitis B virus (HBV), which codes for viral surface antigen (HBsAg), can affect the efficacy of HBsAg screening assays and can be associated with occult HBV infection (OBI). This study aimed to characterise the molecular diversity of the HBV small surface gene from HBV-reactive Australian blood donors. HBV isolates from 16 HBsAg-positive Australian blood donors’ plasma were sequenced and genotyped by phylogenies of viral coding genes and/or whole genomes. An analysis of the genetic diversity of eight HBV small surface genes from our 16 samples was conducted and compared with HBV sequences from NCBI of 164 international (non-Australian) blood donors. Genotypes A–D were identified in our samples. The region of HBV small surface gene that contained the sequence encoding the ‘a’ determinant had a greater genetic diversity than the remaining part of the gene. No escape mutants or OBI-related variants were observed in our samples. Variant call analysis revealed two samples with a nucleotide deletion leading to truncation of polymerase and/or large/middle surface amino acid sequences. Overall, we found that HBV small surface gene sequences from Australian donors demonstrated a lower level of genetic diversity than those from non-Australian donor population included in the study.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

Low Genetic Diversity of Hepatitis B Virus Surface Gene amongst Australian Blood Donors

Phan

Faddy

Flower

et al. 2021

Viruses

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“…Of course, this hypothesis deserves more substance and should be confirmed by undertaking well-designed longitudinal or case-control studies. It is supported, however, by the low nucleotide diversity observed by Phan and coworkers [ 20 ].…”

Section: Genetic Variations Observed On Hbv Genotype I Genomementioning

confidence: 94%

“…The proportions of te ancestral genotypes for each HBV genotype I gene and product are given in Table 1 . Concerning the overall nucleotide diversity of genotype I, Phan and coworkers observed a lower amount of diversity here than in other Australasian HBV genotypes (A, B, C, and D) except between nucleotides 2500–2600 (terminal protein domain) [ 20 ].…”

Section: Genome Architecturementioning

confidence: 99%

Concealed for a Long Time on the Marches of Empires: Hepatitis B Virus Genotype I

Marchio,

Sitbounlang,

Deharo

et al. 2023

Microorganisms

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Genotype I, the penultimate HBV genotype to date, was granted the status of a bona fide genotype only in the XXIst century after some hesitations. The reason for these hesitations was that genotype I is a complex recombinant virus formed with segments from three original genotypes, A, C, and G. It was estimated that genotype I is responsible for only an infinitesimal fraction (<1.0%) of the chronic HBV infection burden worldwide. Furthermore, most probably due to its recent discovery and rarity, the natural history of infection with genotype I is poorly known in comparison with those of genotypes B or C that predominate in their area of circulation. Overall, genotype I is a minor genotype infecting ethnic minorities. It is endemic to the Southeast Asian Massif or Eastern Zomia, a vast mountainous or hilly region of 2.5 million km2 spreading from Eastern India to China, inhabited by a little more than 100 million persons belonging primarily to ethnic minorities speaking various types of languages (Tibeto-Burman, Austroasiatic, and Tai-Kadai) who managed to escape the authority of central states during historical times. Genotype I consists of two subtypes: I1, present in China, Laos, Thailand, and Vietnam; and I2, encountered in India, Laos, and Vietnam.

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“…Several publications describe or review the clinical relevance of HBV variants [ 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 ]. However, whilst previous studies analyze the frequency of mutations in a certain genomic region, within selected populations or within specific genotypes [ 30 , 31 , 32 , 33 , 34 ], there is currently no comprehensive overview of the distribution of clinically relevant HBV variants between world regions or genotypes. However, this information could be useful to understand varying phenotypes of the different HBV genotypes and inform further optimization of diagnostic tests and treatment regimens.…”

Section: Introductionmentioning

confidence: 99%

Global Occurrence of Clinically Relevant Hepatitis B Virus Variants as Found by Analysis of Publicly Available Sequencing Data

Velkov

Protzer

Michler

2020

Viruses

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Several viral factors impact the natural course of hepatitis B virus (HBV) infection, the sensitivity of diagnostic tests, or treatment response to interferon-α and nucleos(t)ide analogues. These factors include the viral genotype and serotype but also mutations affecting the HBV surface antigen, basal core promoter/pre-core region, or reverse transcriptase. However, a comprehensive overview of the distribution of HBV variants between HBV genotypes or different geographical locations is lacking. To address this, we performed an in silico analysis of publicly available HBV full-length genome sequences. We found that not only the serotype frequency but also the majority of clinically relevant mutations are primarily associated with specific genotypes. Distinct mutations enriched in certain world regions are not explained by the local genotype distribution. Two HBV variants previously identified to confer resistance to the nucleotide analogue tenofovir in vitro were not identified, questioning their translational relevance. In summary, our work elucidates the differences in the clinical manifestation of HBV infection observed between genotypes and geographical locations and furthermore helps identify suitable diagnostic tests and therapies.

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In Silico Analysis of Genetic Diversity of Human Hepatitis B Virus in Southeast Asia, Australia and New Zealand

Cited by 3 publications

References 72 publications

Low Genetic Diversity of Hepatitis B Virus Surface Gene amongst Australian Blood Donors

Low Genetic Diversity of Hepatitis B Virus Surface Gene amongst Australian Blood Donors

Concealed for a Long Time on the Marches of Empires: Hepatitis B Virus Genotype I

Global Occurrence of Clinically Relevant Hepatitis B Virus Variants as Found by Analysis of Publicly Available Sequencing Data

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