Genetic drift of hepatitis C virus during an 8.2-year infection in a chimpanzee: Variability and stability

Okamoto, Hiroaki; Kojima, M.; Okada, Shunichi; Yamada, Hiroshi; Iizuka, Hisao; Tanaka, Takeshi; Muchmore, Elizabeth; Peterson, David A.; Ito, Yukio; Mishiro, Shunji

doi:10.1016/0042-6822(92)90933-g

Cited by 375 publications

(211 citation statements)

References 12 publications

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“…Dideoxy DNA sequencing was performed by the dye termination method in an ABI automated DNA sequencer (Applied Biosystems, Foster City, California) with the BigDye Terminator Cycle Sequence Ready Reaction (Applied Biosystems) as specified by the manufacturers. HCV 5Ј HPCJ 483 was used as a standard strain of the virus (Okamoto et al, 1992).…”

Section: Methodsmentioning

confidence: 99%

Hepatitis C Virus from the Hearts of Patients with Myocarditis and Cardiomyopathy

Matsumori

Yutani

Ikeda

et al. 2000

Laboratory Investigation

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SUMMARY:The myocardium may be the target of several types of viral infections. The importance of hepatitis C virus (HCV) infection has been recently noted in patients with myocarditis and in patients with dilated or hypertrophic cardiomyopathy. The present study sought to detect HCV genomes in formalin-fixed paraffin sections of autopsied hearts from patients with myocarditis and patients with dilated or hypertrophic cardiomyopathy. Paraffin sections were deparaffinized, RNA was extracted, and the positive and negative strands of HCV RNA were detected by performing reverse transcription and nested polymerase chain reaction. The polymerase chain reaction products were cloned and sequenced. ␤-actin gene was used as a control for the successful amplification of a housekeeping gene. Among 106 hearts examined, ␤-actin gene was amplified in 61 hearts (57.5%). Among the latter, HCV RNA was detected in 13 hearts (21.3%), and negative strands in 4 hearts (6.6%). HCV RNA was found in 4 hearts (33.3%) with myocarditis, in 3 hearts (11.5%) with dilated cardiomyopathy, and in 6 hearts (26.0%) with hypertrophic cardiomyopathy. The sequences recovered from nine patients were highly homologous to the standard strain of HCV. HCV genomes were not found in either 35 hearts from patients with myocardial infarction or 20 hearts from patients with noncardiac diseases. These HCV RNA positive samples were obtained from 1 heart in 1979, 7 hearts between 1980 and 1989, and 5 hearts since 1990, indicating that HCV RNA can be amplified from paraffin-embedded hearts preserved for many years. This method of detecting HCV genomes in formalin-fixed paraffin cardiac specimens has enabled us to widen our research into HCV infection and has been helpful in identifying the presence of HCV infection in cardiac myopathic disorders. (Lab Invest 2000, 80:1137-1142.

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Section: Methodsmentioning

confidence: 99%

Hepatitis C Virus from the Hearts of Patients with Myocarditis and Cardiomyopathy

Matsumori

Yutani

Ikeda

et al. 2000

Laboratory Investigation

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“…The expected sizes of the PCR products were 259 bp and 189 bp, respectively. Nt positions are according to Okamoto et al (Okamoto et al, 1992).…”

Section: Amplification Of Hcv Genomic Regionsmentioning

confidence: 99%

Assessment of Genotype and Molecular Evolution of Hepatitis C Virus in Formalin-Fixed Paraffin-Embedded Liver Tissue from Patients With Chronic Hepatitis C Virus Infection

Soguero

Campo

Ribalta

et al. 2000

Laboratory Investigation

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SUMMARY:Drawbacks of hepatitis C virus (HCV) RNA detection in paraffin-embedded liver tissue have satisfactorily been solved by RT-PCR amplification of the 5Јnon-coding region (5ЈNCR). However, detection of this highly conserved region does not provide information on epidemiological or pathogenetic aspects of HCV infection. This study explores whether other functionally important genetic regions of HCV, such as the hypervariable region 1 (HVR-1) and the interferon sensitivity-determining region (ISDR), can be retrieved from paraffin-embedded liver specimens by RT-PCR, and whether the amplified material is suitable for further molecular analyses. RT-PCR amplification of 5ЈNCR, HVR-1, and ISDR was assessed in RNA extracted from 50 formalin-fixed, paraffin-embedded liver specimens, including 23 needle liver biopsies (11 from patients with non-A, non-B chronic hepatitis diagnosed between 1971 and 1985, 8 from subjects with normal liver histology and 4 from sequential biopsies from a patient with HCV recurrence after liver transplantation), and 27 liver explants from patients undergoing transplantation between 1988 and 1996 (16 with HCV-related cirrhosis and 11 with other disorders). The 5ЈNCR was successfully amplified in 8 of 11 (73%) non-A, non-B chronic hepatitis biopsies and in all of the specimens from patients with serological documentation of HCV infection. There were no false-positive results. HCV genotype was identified by RFLP analysis of the 5ЈNCR in the 13 cases analyzed. HVR-1 and ISDR were amplified in 24 of 28 (86%) samples, which were positive for the 5ЈNCR. Efficient amplification was inversely related to the time of storage. The evolutionary changes of HVR-1 and ISDR were successfully analyzed by direct sequencing of amplificates from the explanted liver and from the sequential liver biopsies in a patient with HCV infection recurrence after transplantation. These observations indicate that paraffin-embedded liver tissue, even when stored for more than 20 years, is appropriate for advanced studies on the molecular biology of HCV. (Lab Invest 2000, 80:851-856).

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“…Conserved secondary structures are recognized within a Y-terminal region of 300 nt of the HCV genome, and (Okamoto et al, 1992c), HC-J6 of genotype III/2a (Okamoto et al, 1991), HC-J8 of genotype IV/2b (Okamoto et al, 1992b) and NZL1 of genotype V/3a , as well as for the five HCV isolates from Nepal classifiable into subgroups of group 3 (3b to 3f). In-phase stop codons are shaded.…”

mentioning

confidence: 99%

“…"~ The four HCV isolates of different genotypes with the entire sequence known are HC-J1 (Okamoto et aL, 1992a), HC-J4/83 (Okamoto et aL, 1992c), HC-J6 (Okamoto et aL, 1991) and HC-J8 (Okamoto et al, 1992 b) with database accession nos. D 10749, DO 1217, D00944 and D01221, respectively.…”

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

Journal of General Virology

104

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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.

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Genetic drift of hepatitis C virus during an 8.2-year infection in a chimpanzee: Variability and stability

Cited by 375 publications

References 12 publications

Hepatitis C Virus from the Hearts of Patients with Myocarditis and Cardiomyopathy

Hepatitis C Virus from the Hearts of Patients with Myocarditis and Cardiomyopathy

Assessment of Genotype and Molecular Evolution of Hepatitis C Virus in Formalin-Fixed Paraffin-Embedded Liver Tissue from Patients With Chronic Hepatitis C Virus Infection

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

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