Hepatitis B Virus Genotype Study in West Africa Reveals an Expanding Clade of Subgenotype A4

Hepatitis B virus (HBV) classification comprises up to 10 genotypes with specific geographical distribution worldwide, further subdivided into 40 subgenotypes, which have different impacts on liver disease outcome. Though extensively studied, the classification of subgenotype A sequences remains ambiguous. This study aimed to characterize HBV isolates from West African patients and propose a more advanced classification of subgenotype A. Fourteen HBV full-length genome sequences isolated from patients from The Gambia and Senegal were obtained and phylogenetically analyzed. Phylogenetic analysis of HBV genotype A sequences isolated from Senegalese and Gambian patients exhibited separate clusters from the other known and confirmed subgenotypes A (A1, A2, A6). Most of the sequences (10/14) clustered with an isolate from Cuba, reported as subgenotype A4 (supported by maximal bootstrap value). Four isolates from The Gambia and Senegal clustered separately from all other subgenotypes and samples sequenced in the study. Three of which from The Gambia, designated as an expanding clade of subgenotype A4, exhibited a mean inter-subgenotypic nucleotide divergence over the entire genome sequence higher than 4% in comparison with the other subgenotypes and the other isolates sequenced in the study, except with subgenotype A4 isolates (3.9%), and this was supported by a maximal bootstrap value. The last one from Senegal seemed to be an expanding subgenotype close to the new clade of A4. Amino acid analysis unveiled a novel motif specific to these isolates. This study revealed an expanding evolution of HBV subgenotype A and novel amino acid motifs. It also highlighted the need for a consensus regarding the analysis and classification of HBV sequences.

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Analysis of the entire nucleotide sequence of hepatitis B virus genotype B in the Philippines reveals a new subgenotype of genotype B

Journal of General Virology ◽

10.1099/vir.0.81525-0 ◽

2006 ◽

Vol 87 (5) ◽

pp. 1175-1180 ◽

Cited By ~ 23

Author(s):

Futoshi Nagasaki ◽

Hirofumi Niitsuma ◽

Julieta G. Cervantes ◽

Masanori Chiba ◽

Shan Hong ◽

...

Keyword(s):

Hepatitis B Virus ◽

Hepatitis B ◽

Genetic Distances ◽

The Philippines ◽

Nucleotide Sequences ◽

Virus Genotype ◽

Hbv Genotype ◽

Phylogenetic Tree Analysis ◽

Entire Genome ◽

B Virus

The entire nucleotide sequences were determined for hepatitis B virus (HBV) genotype B (HBV/B) genomes extracted from five patients in the Philippines and designated GenBank AB219426, AB219427, AB219428, AB219429 and AB219430. The serotype of the first four isolates was ayw and that of GenBank AB219430 was adw. Divergences of entire sequences were 1·0–2·0 % between the first four isolates and 3·8–4·2 % between these four and GenBank AB219430. Phylogenetic-tree analysis revealed that, worldwide, HBV/B comprises five subgenotypes: B1, B2, B3, B4 and the new Philippines group, designated B5. Divergences of the entire genome sequences between four isolates in subgenotype B5 and isolates from other countries (subgenotypes) were 4·4–4·8 % with Vietnam (B4), 2·9–3·5 % with Indonesia (B3), 4·7–5·1 % with China (B2) and 5·4–6·0 % with Japan (B1). Similarly, GenBank AB219430 showed the lowest divergences: 3·4 % with the isolate from Indonesia (B3), 5·0 % with Vietnam (B4), 5·4 % with China (B2) and 6·1 % with Japan (B1). This is the first report of entire nucleotide sequences of HBV/B from the Philippines and the results show that these sequences belong to a new subgenotype, B5. The present study identified that HBV/B isolates throughout the world are divided genetically into five subgenotypes, the relationships between geographical distances and the genetic distances of HBV/B being well-correlated.

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Complete Genome Sequence of a Precore-Defective Hepatitis B Virus Genotype D2 Strain Isolated in Bangladesh

Microbiology Resource Announcements ◽

10.1128/mra.00083-20 ◽

2020 ◽

Vol 9 (11) ◽

Author(s):

Md Golzar Hossain ◽

Md Muket Mahmud ◽

Md Arifur Rahman ◽

Sharmin Akter ◽

K. H. M. Nazmul Hussain Nazir ◽

...

Keyword(s):

Hepatitis B Virus ◽

Nucleotide Sequence ◽

Hepatitis B ◽

Complete Genome Sequence ◽

Complete Nucleotide Sequence ◽

Mutational Analysis ◽

Limited Information ◽

Virus Genotype ◽

Hbv Genotype ◽

B Virus

Hepatitis B virus (HBV) genomic mutations affect viral replication, disease progression, and diagnostic and vaccination efficiency. There is limited information regarding characterization and mutational analysis of HBV isolated in Bangladesh. Here, we report the complete nucleotide sequence of a precore-defective HBV genotype D2 strain isolated in Bangladesh.

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Novel Hepatitis B Virus Genotype A Subtyping Assay That Distinguishes Subtype Aa from Ae and Its Application in Epidemiological Studies

Journal of Virology ◽

10.1128/jvi.78.14.7575-7581.2004 ◽

2004 ◽

Vol 78 (14) ◽

pp. 7575-7581 ◽

Cited By ~ 15

Author(s):

Izumi Hasegawa ◽

Yasuhito Tanaka ◽

Anna Kramvis ◽

Takanobu Kato ◽

Fuminaka Sugauchi ◽

...

Keyword(s):

Hepatitis B Virus ◽

Hepatitis B ◽

Clinical Manifestations ◽

The United States ◽

Sub Saharan Africa ◽

Virus Genotype ◽

Hbv Genotype ◽

Specificity And Sensitivity ◽

B Virus ◽

Genotype A

ABSTRACT The eight genotypes of hepatitis B virus (HBV) have different geographical distributions, virological characteristics, and clinical manifestations. A unique subtype of HBV genotype A (HBV/A) was reported in sub-Saharan Africa, raising the possibility that patients infected with this subtype (HBV/Aa [“a” for African and Asian]) may have different clinical outcomes than other HBV/A isolates (HBV/Ae [“e” for European]). Comparison between 30 HBV/Aa and 30 HBV/Ae isolates indicated that almost all HBV/Ae isolates had G at nucleotide (nt) 1809 and C at nt 1812, whereas HBV/Aa isolates had T1809/T1812. Taking advantage of these two single nucleotide polymorphisms (SNPs), a novel subtype-specific PCR assay in the X/precore/core region was developed. This assay was combined with a restriction fragment length polymorphism assay using BglII in a different region (nt 1984 to 1989), which has a SNP distinguishing HBV/Aa from HBV/Ae, resulting in 100% specificity for the combined assay. Application of the subtyping assay using sera from 109 paid donors in the United States indicated significantly different distributions of HBV/A subtypes among races; African-Americans, Caucasians, and Hispanics had HBV/Ae, whereas Asians had mainly HBV/Aa, suggesting that the HBV/Aa isolates may have been imported by recent immigration from Asia. In conclusion, the specificity and sensitivity of the combined subtyping assay were confirmed, and its usefulness was demonstrated in a practical context.

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The dominant hepatitis B virus genotype identified in Tibet is a C/D hybrid

Journal of General Virology ◽

10.1099/0022-1317-83-11-2773 ◽

2002 ◽

Vol 83 (11) ◽

pp. 2773-2777 ◽

Cited By ~ 73

Author(s):

Chaoyin Cui ◽

Jinxiu Shi ◽

Lijian Hui ◽

Huifeng Xi ◽

Zhuoma ◽

...

Keyword(s):

Hepatitis B Virus ◽

Hepatitis B ◽

Dna Sequences ◽

The Other ◽

Virus Genotype ◽

Hbv Genotypes ◽

B Virus ◽

Genotype C ◽

Genomic Regions ◽

Positive Population

There are no reports on DNA sequences of hepatitis B virus (HBV) strains from Tibet, although this highland area has a high HBsAg-positive population. We characterized HBV isolates from sera of 26 HBsAg-positive Tibetans. To determine the HBV genotypes and their phylogenetic relationships, we sequenced two genomic regions, one including the pre-S1/pre-S2/S region and the other including the pre-C/C region. The sequences were classified into two different genotypes based on different regions of the genome, except for one isolate. To clarify this finding, two complete HBV genomes that represented the two groups of isolates were sequenced. From the sequencing results, we concluded that HBV strains in Tibet may be classified as genotype C, and there are at least two subgroups. The dominant subgroup is a C/D hybrid with serotype ayw2, and the other is genotype C with serotype adw. This is the first report of complete nucleotide sequences of HBV from Tibet. These results contribute to the investigation of recombinant HBV strains throughout the world and should encourage further study of genotypes and recombination in HBV from this particular region.

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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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Sequence Analysis of PreS2 Region of Hepatitis B Virus Genotype D Isolates

NUST Journal of Natural Sciences ◽

10.53992/njns.v3i1.10 ◽

2021 ◽

Vol 3 (1) ◽

pp. 5-11

Author(s):

Amania Anwar ◽

Sheeba Murad ◽

Hajra Sadia

Keyword(s):

Hepatocellular Carcinoma ◽

Hepatitis B Virus ◽

Hepatitis B ◽

Point Mutations ◽

Cell Permeability ◽

Serum Samples ◽

Virus Genotype ◽

Hbv Genotype ◽

Hbv Genotypes ◽

B Virus

Hepatitis B virus (HBV) is a well known agent of liver diseases. HBV disease burden varies across theglobe with regions from low to high endemicity. Pakistan lies in the intermediate endemic zone, withhigh rate of mortality due to liver disease, cirrhosis and hepatocellular carcinoma. There is a wide rangeof heterogeneity in relation to HBV genotypes and sub-genotypes and in their patterns of pathogenesis,virulence and response to antiviral therapy. A large number of HBV genomic variations are associatedwith clinical outcomes such as hepatocellular carcinoma and liver cirrhosis. Thus, the present study aimsto analyze PreS2 gene sequences from HBV isolates and their phylogeny. To investigate this, a study wasconducted on twenty one HBV chronically infected individuals, serum samples were subjected to PCRwith specific primers for PreS2 region of HBV genotype D and then sequenced. Point mutations: A39V,P41H and L42I were found in cell permeability domain of PreS2 protein. However, MHC class I and IIepitopes were conserved in all sequences. Phylogenetic analysis was carried out by comparing thenucleotide sequence with 22 reference sequences of HBV sub-genotype D retrieved from the GeneBank.Phylogenetic analysis showed that two of our isolates, ASAB1 (2266) and ASAB3 (PIMS 7) sharedcluster 1 with China D1, Pakistan D1, Iran D1 and Turkey D1. Meanwhile, ASAB2 (HF2) was grouped incluster 2 with Lebanese D2 and Brazil D2.

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Hepatitis B virus genotype G epidemiology and co-infection with genotype A in Canada

Journal of General Virology ◽

10.1099/vir.0.2008/005124-0 ◽

2008 ◽

Vol 89 (12) ◽

pp. 3009-3015 ◽

Cited By ~ 56

Author(s):

Carla Osiowy ◽

Diane Gordon ◽

Jamie Borlang ◽

Elizabeth Giles ◽

Jean-Pierre Villeneuve

Keyword(s):

Hepatitis B Virus ◽

Hepatitis B ◽

Sequence Divergence ◽

Virus Genotype ◽

Hbv Genotype ◽

B Virus ◽

Average Sequence Divergence ◽

Unusual Variant ◽

Average Sequence ◽

Genotype A

Hepatitis B virus (HBV) genotype G (HBV/G) is an unusual variant, and little is known about its epidemiology and natural history, particularly the requirement for a co-infecting HBV genotype and their relationship during infection. This study investigated the quasispecies nature of co-infecting genotypes in 39 samples collected over a 6 year period from 13 HBV/G-infected patients. HBV/G infections were found to occur predominantly in males (92 %) and were primarily associated with male homosexual sex (67 %). All patients were infected with HBV/G and HBV/A, or a recombinant HBV/A/G strain. Co-infecting genotypic prevalence was often observed to fluctuate over time, with periods of HBV/G monoinfection in some patients. The average sequence divergence among Canadian HBV/G strains was 1.57±0.62 %. Thus, all HBV/G infections in Canada occur in the context of co-infection or recombination with HBV/A, and strains display increased sequence divergence compared with all known HBV/G sequences described to date.

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The Global Hepatitis B Virus Genotype Distribution Approximated from Available Genotyping Data

Genes ◽

10.3390/genes9100495 ◽

2018 ◽

Vol 9 (10) ◽

pp. 495 ◽

Cited By ~ 13

Author(s):

Stoyan Velkov ◽

Jördis Ott ◽

Ulrike Protzer ◽

Thomas Michler

Keyword(s):

Hepatitis B Virus ◽

Hepatitis B ◽

Treatment Strategies ◽

Population Data ◽

Genotype Distribution ◽

Virus Genotype ◽

Hbv Genotype ◽

B Virus ◽

Chronic Hbv ◽

The Individual

Hepatitis B virus (HBV) is divided into nine genotypes, A to I. Currently, it remains unclear how the individual genotypes contribute to the estimated 250 million chronic HBV infections. We performed a literature search on HBV genotyping data throughout the world. Over 900 publications were assessed and data were extracted from 213 records covering 125 countries. Using previously published HBV prevalence, and population data, we approximated the number of infections with each HBV genotype per country and the genotype distribution among global chronic HBV infections. We estimated that 96% of chronic HBV infections worldwide are caused by five of the nine genotypes: genotype C is most common (26%), followed by genotype D (22%), E (18%), A (17%) and B (14%). Genotypes F to I together cause less than 2% of global chronic HBV infections. Our work provides an up-to-date analysis of global HBV genotyping data and an initial approach to estimate how genotypes contribute to the global burden of chronic HBV infection. Results highlight the need to provide HBV cell culture and animal models that cover at least genotypes A to E and represent the vast majority of global HBV infections to test novel treatment strategies.

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