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Genogeography and Immune Epitope Characteristics of Hepatitis B Virus Genotype C Reveals Two Distinct Types: Asian and Papua-Pacific.

Thedja MD, Muljono DH, Ie SI, Sidarta E - PLoS ONE (2015)

Bottom Line: Based on phylogenetic tree and geographical origins of isolates, two major groups of HBV/C isolates--East-Southeast Asia and Papua-Pacific--were identified.Analysis of core and surface immune epitopes supported these findings with several amino acid substitutions distinguishing the East-Southeast Asia isolates from the Papua-Pacific isolates.A west-to-east gradient of HBsAg subtype distribution was observed with adrq+ prominent in the East and Southeast Asia and adrq- in the Pacific, with several adrq-indeterminate subtypes observed in Papua and Papua New Guinea (PNG).

View Article: PubMed Central - PubMed

Affiliation: Eijkman Institute for Molecular Biology, Jakarta, Indonesia; Eijkman Winkler Institute, University Medical Centre (UMC) Utrecht, Utrecht, The Netherlands.

ABSTRACT
Distribution of hepatitis B virus (HBV) genotypes/subgenotypes is geographically and ethnologically specific. In the Indonesian archipelago, HBV genotype C (HBV/C) is prevalent with high genome variability, reflected by the presence of 13 of currently existing 16 subgenotypes. We investigated the association between HBV/C molecular characteristics with host ethnicity and geographical distribution by examining various subgenotypes of HBV/C isolates from the Asia and Pacific region, with further analysis on the immune epitope characteristics of the core and surface proteins. Phylogenetic tree was constructed based on complete HBV/C genome sequences from Asia and Pacific region, and genetic distance between isolates was also examined. HBV/C surface and core immune epitopes were analyzed and grouped by comparing the amino acid residue characteristics and geographical origins. Based on phylogenetic tree and geographical origins of isolates, two major groups of HBV/C isolates--East-Southeast Asia and Papua-Pacific--were identified. Analysis of core and surface immune epitopes supported these findings with several amino acid substitutions distinguishing the East-Southeast Asia isolates from the Papua-Pacific isolates. A west-to-east gradient of HBsAg subtype distribution was observed with adrq+ prominent in the East and Southeast Asia and adrq- in the Pacific, with several adrq-indeterminate subtypes observed in Papua and Papua New Guinea (PNG). This study indicates that HBV/C isolates can be classified into two types, the Asian and the Papua-Pacific, based on the virus genome diversity, immune epitope characteristics, and geographical distribution, with Papua and PNG as the molecular evolutionary admixture region in the switching from adrq+ to adrq-.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree of HBV/C isolates from different countries in East and Southeast Asia, and Papua-Pacific.A Bayesian phylogenetic tree analysis based on complete genome sequences showed that isolates from various subgenotypes (C1-C16) are clearly grouped into two major clusters, consistent with their geographical origins. Seven HBV/C subgenotypes (C1, C2, C5, C7, C8, C9, and C10) from East and Southeast Asia, and one (C14) from Papua (light highlight) were well-separated from those six subgenotypes (C6, C11, C12, C13, C15, and C16) from Papua, and from one subgenotype (C3) from Pacific, the more east region of the Papua (dark highlight). Although the root of subgenotype C3 phylogenetically is distanced from the subgenotypes of Papua, the isolate geographic origin, the immune epitope characteristics of surface and core proteins, and the HBsAg subtype gradient distribution showed these HBV/C3 isolates to be close to Papua subgenotypes. Therefore, the Papua and the Pacific subgenotypes are classified together into Papua-Pacific type. The diversification of the Asian type from the Papua-Pacific type started from Papua of Indonesia to the east. The other subgenotype, HBV/C4, was distanced from other subgenotypes. In this analysis, one strain (GQ358157) from Papua reported as C6 in our previous study [23] grouped into C12. We redefine this strain as a member of HBV/C12.
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pone.0132533.g001: Phylogenetic tree of HBV/C isolates from different countries in East and Southeast Asia, and Papua-Pacific.A Bayesian phylogenetic tree analysis based on complete genome sequences showed that isolates from various subgenotypes (C1-C16) are clearly grouped into two major clusters, consistent with their geographical origins. Seven HBV/C subgenotypes (C1, C2, C5, C7, C8, C9, and C10) from East and Southeast Asia, and one (C14) from Papua (light highlight) were well-separated from those six subgenotypes (C6, C11, C12, C13, C15, and C16) from Papua, and from one subgenotype (C3) from Pacific, the more east region of the Papua (dark highlight). Although the root of subgenotype C3 phylogenetically is distanced from the subgenotypes of Papua, the isolate geographic origin, the immune epitope characteristics of surface and core proteins, and the HBsAg subtype gradient distribution showed these HBV/C3 isolates to be close to Papua subgenotypes. Therefore, the Papua and the Pacific subgenotypes are classified together into Papua-Pacific type. The diversification of the Asian type from the Papua-Pacific type started from Papua of Indonesia to the east. The other subgenotype, HBV/C4, was distanced from other subgenotypes. In this analysis, one strain (GQ358157) from Papua reported as C6 in our previous study [23] grouped into C12. We redefine this strain as a member of HBV/C12.

Mentions: Phylogenetic analysis based on 69 HBV complete sequences retrieved from GenBank confirmed the clustering of eight HBV genotypes and their subgenotypes as shown in Fig 1. Interestingly, of 62 HBV/C isolates, two major clusters were observed: one of 35 isolates [C1 (10), C2 (9), C5 (7), C7 (1), C8 (4), C9 (1), C10 (1), and C14 (2)], and the other of 23 isolates [C6 (12), C11 (2), C12 (4), C13 (3), C15 (1), and C16 (1)]. The first cluster associated mainly with Southeast and East Asian countries, while the second cluster with those of Papua. Two isolates of C3 which are specific to Pacific region has distinct root with those of Asia and Papua clusters, and the remaining two C4 isolates of Northern Australia belonged to the more distinct lineage that was more distant compared to the two clusters and the Pacific isolates.


Genogeography and Immune Epitope Characteristics of Hepatitis B Virus Genotype C Reveals Two Distinct Types: Asian and Papua-Pacific.

Thedja MD, Muljono DH, Ie SI, Sidarta E - PLoS ONE (2015)

Phylogenetic tree of HBV/C isolates from different countries in East and Southeast Asia, and Papua-Pacific.A Bayesian phylogenetic tree analysis based on complete genome sequences showed that isolates from various subgenotypes (C1-C16) are clearly grouped into two major clusters, consistent with their geographical origins. Seven HBV/C subgenotypes (C1, C2, C5, C7, C8, C9, and C10) from East and Southeast Asia, and one (C14) from Papua (light highlight) were well-separated from those six subgenotypes (C6, C11, C12, C13, C15, and C16) from Papua, and from one subgenotype (C3) from Pacific, the more east region of the Papua (dark highlight). Although the root of subgenotype C3 phylogenetically is distanced from the subgenotypes of Papua, the isolate geographic origin, the immune epitope characteristics of surface and core proteins, and the HBsAg subtype gradient distribution showed these HBV/C3 isolates to be close to Papua subgenotypes. Therefore, the Papua and the Pacific subgenotypes are classified together into Papua-Pacific type. The diversification of the Asian type from the Papua-Pacific type started from Papua of Indonesia to the east. The other subgenotype, HBV/C4, was distanced from other subgenotypes. In this analysis, one strain (GQ358157) from Papua reported as C6 in our previous study [23] grouped into C12. We redefine this strain as a member of HBV/C12.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4498642&req=5

pone.0132533.g001: Phylogenetic tree of HBV/C isolates from different countries in East and Southeast Asia, and Papua-Pacific.A Bayesian phylogenetic tree analysis based on complete genome sequences showed that isolates from various subgenotypes (C1-C16) are clearly grouped into two major clusters, consistent with their geographical origins. Seven HBV/C subgenotypes (C1, C2, C5, C7, C8, C9, and C10) from East and Southeast Asia, and one (C14) from Papua (light highlight) were well-separated from those six subgenotypes (C6, C11, C12, C13, C15, and C16) from Papua, and from one subgenotype (C3) from Pacific, the more east region of the Papua (dark highlight). Although the root of subgenotype C3 phylogenetically is distanced from the subgenotypes of Papua, the isolate geographic origin, the immune epitope characteristics of surface and core proteins, and the HBsAg subtype gradient distribution showed these HBV/C3 isolates to be close to Papua subgenotypes. Therefore, the Papua and the Pacific subgenotypes are classified together into Papua-Pacific type. The diversification of the Asian type from the Papua-Pacific type started from Papua of Indonesia to the east. The other subgenotype, HBV/C4, was distanced from other subgenotypes. In this analysis, one strain (GQ358157) from Papua reported as C6 in our previous study [23] grouped into C12. We redefine this strain as a member of HBV/C12.
Mentions: Phylogenetic analysis based on 69 HBV complete sequences retrieved from GenBank confirmed the clustering of eight HBV genotypes and their subgenotypes as shown in Fig 1. Interestingly, of 62 HBV/C isolates, two major clusters were observed: one of 35 isolates [C1 (10), C2 (9), C5 (7), C7 (1), C8 (4), C9 (1), C10 (1), and C14 (2)], and the other of 23 isolates [C6 (12), C11 (2), C12 (4), C13 (3), C15 (1), and C16 (1)]. The first cluster associated mainly with Southeast and East Asian countries, while the second cluster with those of Papua. Two isolates of C3 which are specific to Pacific region has distinct root with those of Asia and Papua clusters, and the remaining two C4 isolates of Northern Australia belonged to the more distinct lineage that was more distant compared to the two clusters and the Pacific isolates.

Bottom Line: Based on phylogenetic tree and geographical origins of isolates, two major groups of HBV/C isolates--East-Southeast Asia and Papua-Pacific--were identified.Analysis of core and surface immune epitopes supported these findings with several amino acid substitutions distinguishing the East-Southeast Asia isolates from the Papua-Pacific isolates.A west-to-east gradient of HBsAg subtype distribution was observed with adrq+ prominent in the East and Southeast Asia and adrq- in the Pacific, with several adrq-indeterminate subtypes observed in Papua and Papua New Guinea (PNG).

View Article: PubMed Central - PubMed

Affiliation: Eijkman Institute for Molecular Biology, Jakarta, Indonesia; Eijkman Winkler Institute, University Medical Centre (UMC) Utrecht, Utrecht, The Netherlands.

ABSTRACT
Distribution of hepatitis B virus (HBV) genotypes/subgenotypes is geographically and ethnologically specific. In the Indonesian archipelago, HBV genotype C (HBV/C) is prevalent with high genome variability, reflected by the presence of 13 of currently existing 16 subgenotypes. We investigated the association between HBV/C molecular characteristics with host ethnicity and geographical distribution by examining various subgenotypes of HBV/C isolates from the Asia and Pacific region, with further analysis on the immune epitope characteristics of the core and surface proteins. Phylogenetic tree was constructed based on complete HBV/C genome sequences from Asia and Pacific region, and genetic distance between isolates was also examined. HBV/C surface and core immune epitopes were analyzed and grouped by comparing the amino acid residue characteristics and geographical origins. Based on phylogenetic tree and geographical origins of isolates, two major groups of HBV/C isolates--East-Southeast Asia and Papua-Pacific--were identified. Analysis of core and surface immune epitopes supported these findings with several amino acid substitutions distinguishing the East-Southeast Asia isolates from the Papua-Pacific isolates. A west-to-east gradient of HBsAg subtype distribution was observed with adrq+ prominent in the East and Southeast Asia and adrq- in the Pacific, with several adrq-indeterminate subtypes observed in Papua and Papua New Guinea (PNG). This study indicates that HBV/C isolates can be classified into two types, the Asian and the Papua-Pacific, based on the virus genome diversity, immune epitope characteristics, and geographical distribution, with Papua and PNG as the molecular evolutionary admixture region in the switching from adrq+ to adrq-.

No MeSH data available.


Related in: MedlinePlus