Novel genotypes of hepatitis C virus in Thailand

Sugiyama, Kazuo; Kato, Naoya; Nakazawa, Takahiro; Yonemura, Yutaka; Phornphutkul, Kannika; Kunakorn, Mongkol; Petchclai, B; Shimotohno, Kunitada

doi:10.1099/0022-1317-76-9-2323

Cited by 18 publications

(11 citation statements)

References 20 publications

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“…The use of the BK core protein in all the constructs implied that the sequence of position 9–11 in the core region was GAA (typical of genotype 1 and 2) and not ACT (characteristic of genotype 3) [3]. These nucleotide changes are the same (and in the same position) as those observed for the TH33 strain of HCV [28], whose possible domain IV structure had already been calculated, and which was predicted to minimally alter the structure of the stem‐loop [6].…”

Section: Discussionmentioning

confidence: 99%

In vivo translational efficiency of different hepatitis C virus 5′‐UTRs

Buratti¹,

Gerotto²,

Pontisso³

et al. 1997

FEBS Letters

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Initiation of translation in hepatitis C virus (HCV) is dependent on the presence of an internal ribosome entry site (IRES) contained in its 341‐nt‐long 5′‐untranslated region (UTR). This region is very conserved among different isolates and has been used to classify HCV isolates in six different genotypes. These genotypes differ in nucleotide sequence that generally preserve the IRES structure. However, the small differences seen may be biologically and clinically significant as the HCV strains seem to differ from each other in several important ways, such as the behaviour of the viral infection and the response to interferon therapy. Therefore, differences in translational initiation efficiency amongst the various genotypes could provide an explanation for these phenomena. Using a bicistronic expression system we have compared the in vivo translational ability of the three most common European genotypes of HCV (1, 2, and 3). The results show that genotype 3 is less able than 1 and 2 to promote translation initiation. In addition, by site‐directed mutagenesis of the sequence of the IRES domain III apical stem loop structure, we have shown that the conservation of the primary nucleotide sequence and not only the structure, is important for the conservation of IRES function.

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Section: Discussionmentioning

confidence: 99%

In vivo translational efficiency of different hepatitis C virus 5′‐UTRs

Buratti¹,

Gerotto²,

Pontisso³

et al. 1997

FEBS Letters

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“…Some variants from South East Asia are phylogenetically related to type 3 or type 6 but are more divergent from other subtypes of types 3 or 6 than are subtypes of other HCV types. At present, it is unclear whether these divergent subtypes should be considered as divergent subtypes of types 3 and 6 (Mellor et al 1995;Doi et al 1996;Mizokami et al 1996;Simmonds et al 1996), or as distinct virus types (Tokita et al 1994a(Tokita et al ,b, 1995(Tokita et al , 1996Sugiyama et al 1995). Evidence tacherjee et al 1995;Dhaliwal et al 1996) and sensitivity to interferon treatment (Davis 1994), but similar differences have not yet been demonstrated between virus subtypes.…”

Section: Introductionmentioning

confidence: 93%

Characteristics of Nucleotide Substitution in the Hepatitis C Virus Genome: Constraints on Sequence Change in Coding Regions at Both Ends of the Genome

1997

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Comparison of complete genome sequences for different variants of hepatitis C virus (HCV) reveals several different constraints on sequence change. Synonymous changes are suppressed in coding regions at both 5' and 3' ends of the genome. No evidence was found for the existence of alternative reading frames or for a lower mutation frequency in these regions. Instead, suppression may be due to constraints imposed by RNA secondary structures identified within the core and NS5b genes. Nonsynonymous substitutions are less frequent than synonymous ones except in the hypervariable region of E2 and, to a lesser extent, in E1, NS2, and NS5b. Transitions are more frequent than transversions, particularly at the third position of codons where the bias is 16:1. In addition, nucleotide substitutions may not occur symmetrically since there is a bias toward G or C at the third position of codons, while T left and right arrow C transitions were twice as frequent as A left and right arrow G transitions. These different biases do not affect the phylogenetic analysis of HCV variants but need to be taken into account in interpreting sequence change in longitudinal studies.

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“…[3], with the latter gaining greater acceptance. In the Simmonds scheme, HCV can be divided into six major genotypes (1)(2)(3)(4)(5)(6). which can be further divided into more closely related subtypes.…”

Section: Introductionmentioning

confidence: 99%

Hepatitis C virus genotypes in Australia

McCaw

Moaven

Locarnini

et al. 1997

Journal of Viral Hepatitis

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The relative distribution of Australian hepatitis C virus (HCV) genotypes was determined for 500 isolates. Genotyping was performed using a commercial reverse phase hybridization assay after amplification of the 5' untranslated region of HCV by the polymerase chain reaction. Australian isolates comprised, predominantly, genotype 1 (55%) and genotype 3 (38%) with genotype 2 accounting for only 7%. Genotype 3a was the most common subtype. When the major risk groups of injecting drug users or transfusion-acquired hepatitis C were compared, there was a significantly higher incidence of genotype 1b in the transfusion-acquired group (P < 0.03). When the age of the patients was analysed, genotype 3a was more prevalent in the 21-40-year age group than the 41-60-year age group (P < 0.05). There was no significant difference in genotype distribution between males and females. HCV genotypes 1, 2 and 3 are most often found in developed countries but the relatively high prevalence of genotype 3a in Australia is unusual.

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Novel genotypes of hepatitis C virus in Thailand

Cited by 18 publications

References 20 publications

In vivo translational efficiency of different hepatitis C virus 5′‐UTRs

In vivo translational efficiency of different hepatitis C virus 5′‐UTRs

Characteristics of Nucleotide Substitution in the Hepatitis C Virus Genome: Constraints on Sequence Change in Coding Regions at Both Ends of the Genome

Hepatitis C virus genotypes in Australia

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