Sequence variability in the 5' non-coding region of hepatitis C virus: identification of a new virus type and restrictions on sequence diversity

Self Cite

391

285

A method is described for identifying different genotypes of hepatitis C virus (HCV) by restriction endonuclease cleavage of sequences amplified by PCR from the 5' non-coding region. Using the enzymes HaeIII-RsaI and HinfI-MvaI, followed by cleavage with BstU1 or ScrFI, it was possible to identify and distinguish HCV genotypes la, lb, 2a, 2b, 3a, 3b, 4, 5 and 6. The method was used to investigate the prevalence of these genotypes in 723 blood donors in 15 countries, the largest survey to date, and one which covered a wide range of geographical regions (Europe, America, Africa and Asia). These results, combined with a review of the existing literature, indicate the existence of several distinct regional patterns of HCV genotype distribution, and provide the framework for future detailed epidemiological investigations of HCV transmission.

Section: Far-east and South-east Asiamentioning

confidence: 99%

Section: Far-east and South-east Asiamentioning

confidence: 99%

Survey of major genotypes and subtypes of hepatitis C virus using RFLP of sequences amplified from the 5' non-coding region

Davidson

Simmonds²,

Ferguson³

et al. 1995

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391

285

“…Consequently, an A-G mismatch is produced for all type 2 sequences and weak G U pairs for types 3b, 4, 5 and 6 and some type 1 sequences. An alternative structure for this region juxtaposes positions -159/-128 (Simmonds et al, 1993b;Fig. 6) resulting in the creation of a U-A pair for sequences having a U substitution at -159, while covariance in all type 2 sequences produces an A-U pairing.…”

Section: Structural Implications Of 5"ncr Sequence Variationmentioning

confidence: 99%

Variation of the hepatitis C virus 5' non-coding region: implications for secondary structure, virus detection and typing

Smith

Mellor²,

Jarvis³

et al. 1995

Self Cite

220

160

Variation in the 5' non-coding region (5'NCR) of hepatitis C virus (HCV) was investigated in detail by comparing 314 5'NCR sequences of viruses ofgenotypes 1 to 6. Evidence was obtained for the existence of associations between particular 5'NCR sequence motifs and virus types and subtypes. No recombination was observed between the 5'NCR and coding regions of different genotypes, implying that the sequence of subgenomic regions such as the 5'NCR can be used to deduce virus genotype. The distribution of polymorphic sites within the 5'NCR is used to propose improved oligonucleotide primers for virus detection and quantification that would be equally efficient in detecting RNA of different virus genotypes. The accuracy of two different genotyping methods (RFLP and the line probe assay) based on analysis of sequence polymorphisms in the 5'NCR is predicted from the sequences surveyed to be 97 % and 83 % respectively for types 1 to 6, with higher accuracies for distinguishing between subtypes la/lb, 2a/2b or 3a/3b. Several sites of genotype-specific polymorphism were covariant and maintained the base pairings required for a secondary structure model of the 5"NCR. Other sites of variation suggest minor modifications to this model and have implications for the probable functions of the 5"NCR

“…The five isolates from Nepal shared only 77"0 to 82.6 % of a core gene sequence of 242 or 226 nt with HCV isolates from Egypt, which are proposed to be of type 4 by Simmonds et al (1993). They showed a similarity of 90.9 to 94.6 % in a 5' UTR sequence to HCV isolates of unclassified genotypes from various areas of the world (Bukh et al, 1992), which is substantially less than the value of 95.8 to 98.8 % among themselves.…”

mentioning

confidence: 99%

“…D166t4 and D16615. Simmonds et al, 1993;Stuyver et al, 1993). Genotype I corresponds to la, II to lb, III to 2a, IV to 2b, V to 3a and VI to 3b.…”

mentioning

confidence: 99%

Hepatitis C virus variants from Nepal with novel genotypes and their classification into the third major group

Tokita

Okamoto

Sakamoto

et al. 1994

104

Five isolates of hepatitis C virus (HCV) RNA from patients with chronic liver disease in Nepal were not classifiable into the known genotypes I/la, II/lb, II1/2a, IV/2b or V/3a using PCR with type-specific primers deduced from the HCV core gene. Their nucleotide sequences were determined for the 5'-terminal 1.5 kilobases and 3'-terminal 1.2 kilobases, covering 30 % of the entire genome, and compared with each other and with reported sequences of HCV isolates of various genotypes. They were more similar to a reported HCV isolate (NZL1) of genotype V/3a (in 81.6 to 84.1% of their nucleotides and 85"7 to 88.7% of the deduced amino acid sequence) compared with the genotypes I/la to IV/2b (in 69.3 to 74.7% and 72'3 to 77.4%, respectively). Hence they were considered to be variants of the third major group (group 3). The five HCV isolates shared 81.3 to 85.2% of nucleotide sequence and 85.4 to 89.3 % of deduced amino acid sequence. Thus they were substantially different from each other. One of them was classified as genotype Vl/3b due to an 88-2 % similarity in nucleotide sequence to that of the reported HCV isolates of this genotype, whereas the remaining four were classified into provisional genotypes 3c, 3d, 3e and 3f. These HCV variants have evolved and remained in Nepal, and have not been observed in the other areas of the world.