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Journal of Clinical Microbiology, September 2002, p. 3140-3145, Vol. 40, No. 9
0095-1137/02/$04.00+0 DOI: 10.1128/JCM.40.9.3140-3145.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.
Department of Gastroenterology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
Received 22 June 2001/ Returned for modification 17 November 2001/ Accepted 13 June 2002
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An RNA virus associated with non-A to E hepatitis named GB virus C (GBV-C)/hepatitis G virus (HGV) and a DNA virus named TT virus (TTV) were recently cloned (6, 8, 11, 12, 17). However, previous studies showed that GBV-C/HGV and TTV are unlikely to be major etiologic agents of non-B, non-C HCC, and they have not yet been confirmed to be hepatotropic (1-5, 7, 9, 10, 24).
A novel DNA virus named SEN virus (SEN-V) was also recently cloned from the plasma of a patient with posttransfusion hepatitis. This patient had elevated transaminase levels but did not have viral markers for hepatitis type A to E viruses or hepatitis G virus (19). SEN-V is a circular 3,900-nucleotide DNA virus. There are eight SEN-V genotypes, called A to H. SEN-V was classified into the same group as TTV variants (including SANBAN and TUS01). Prototype TTV, TTV YONBAN, and TTV PMV formed an outer group of SEN-V (19). Of the eight genotypes, genotypes D and H (or genotype C) have been reported to be related to liver dysfunction (19). Although SEN-V has been observed in patients with acute and chronic liver disease (CLD) of unknown etiology, the role of SEN-V in the pathogenesis of liver disease is not yet known (15, 21, 22). We screened patients with non-B, non-C CLD and patients without liver disease for SEN-V DNA to determine the possible role of SEN-V in the pathogenesis of liver disease and in the development of HCC, especially in patients with non-B, non-C chronic hepatitis and HCC.
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Detection of SEN-V DNA. DNA was extracted from 50 µl of serum with the SepaGene kit (Sanko Junyaku, Tokyo, Japan) according to the manufacturer's instructions. The extracted DNA was dissolved in 20 µl of Tris-HCl buffer (10 mM; pH 8.0) containing 1 mM EDTA, heated to 95°C for 15 min, and quickly chilled on ice. The total amount of extracted DNA was subjected to nested PCR with Ready-To-Go PCR beads (Pharmacia Biotech, Uppsala, Sweden). The first round of PCR was performed with primer sets specific for each genotype. The sense primers specific for genotypes A to D and H were as follows: SEA-S, SEB-S, SEC-S, SED-S, and SEH-S, respectively (Table 1). The antisense primers specific for genotypes A to D and H were as follows: SEA-AS, SEB-AS, SEC-AS, SED-AS, and SEH-AS, respectively (Table 1). These primers were used to amplify 336-, 444-, 619-, 510-, and 830-bp fragments from genotypes A to D and H, respectively. The reaction was run in microtubes with the GeneAmp PCR system 9600 (Perkin-Elmer Applied Biosystems, Foster City, Calif.). Amplification was performed for 35 cycles, with each cycle consisting of denaturation at 94°C for 1 min, annealing at 54°C for 1 min, and elongation at 72°C for 1 min. A 10-min final hold at 72°C was used to complete strand synthesis. The second round of PCR was carried out with sense and antisense primers specific for genotypes A to D and H. The sense primers were as follows: SEA-S2, SEB-S2, SEC-S2, SED-S2, and SEH-S2, respectively (Table 1). The antisense primers specific for genotypes A to D and H were as follows: SEA-AS2, SEB-AS2, SEC-AS2, SED-AS2, and SEH-AS2, respectively (Table 1). These primers were used to amplify 288-, 396-, 577-, 459-, and 783-bp fragments from genotypes A to D and H, respectively. The amplification was performed for 30 cycles, with each cycle consisting of denaturation at 94°C for 1 min, annealing at 54°C for 1 min, and elongation at 72°C for 1 min, followed by a final hold at 72°C for 7 min. The amplified products were electrophoresed on 1.5% agarose gels, stained with ethidium bromide, and observed under UV light.
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TABLE 1. Primers used to detect or sequence SEN-V
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Genetic analysis of SEN-V DNA. Nucleotide sequencing of detectable SEN-V DNA was performed with an autosequencer (Perkin-Elmer Applied Biosystems, Foster City, Calif.) and the dye termination method as described previously (20). The direct sequencing reactions were carried out with primers specific for genotypes D and H: SED-S3 and SEH-S3, respectively (Table 1). The sequences of SEN-V types D and H were compared to the prototype sequences of SEN-V (SEN-V type D, nucleotides 528 to 677; SEN-V type H, nucleotides 402 to 551) or the reported sequence of TTV (TTV nucleotides 701 to 850 and TTV nucleotides 401 to 550). A phylogenetic tree was constructed by the unweighted pair group method with the arithmetic mean with the computer software package GENETYX-MAC (Software Development Co., Ltd., Tokyo, Japan). Nucleotide sequence homologies among the SEN-V DNAs obtained from patients and controls were calculated and analyzed. In order to identify the full-length nucleotide sequence, fragments of SEN-V types D and H were amplified with the following PCR primer sets: SED Full F and SED(1) R, SED S2 and SED AS2, SED(3) F and SED(3) R, SED(4) F and SED(4) R, SED(5) F and SED(5) R, and SED(6) F and SED Full R and primer sets SEH Full F and SEH(1) R, SEH S2 and SEH AS2, SEH(3) F and SEH(3) R, SEH(4) F and SEH(4) R, SEH(5) F and SEH(5) R, and SEH(6) F and SEH Full R (Table 1). Each primer set was designed to amplify one of six fragments from SEN-V type D (nucleotides 1 to 553, 495 to 953, 868 to 1589, 1439 to 2082, 1990 to 2688, and 2632 to 3264) or one of six fragments from SEN-V type H (nucleotides 1 to 446, 381 to 1163, 904 to 1593, 1376 to 2163, 1975 to 2558, and 2480 to 3292). The full-length nucleotide sequence was identified by direct sequencing with each set of sense and antisense primers. The codon distributions and hydrophobicities of the polyproteins encoded by the open reading frames (ORFs) of SEN-V types D and H were analyzed.
Statistical analysis. The results are expressed as the means ± standard deviations. Comparisons were performed by Student's t test and the chi-square test. Fisher's exact probability test was used to examine the relationship between HCC and SEN-V. A P value of less than 0.05 was considered statistically significant.
Nucleotide sequence accession numbers. The two full-length nucleotide sequences of SEN-V identified from a CLD patient (type D) and a control (type H) have been submitted to the DDBJ database and given accession numbers AB059532 and AB059353, respectively.
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Clinical features of SEN-V-positive chronic hepatitis and HCC patients.
The clinical features of the patients with HCC and the patients with CLD but without HCC with respect to SEN-V infection status are shown in Table 2. The clinical features included age; sex; serum albumin, total bilirubin, and transaminase levels; the results of the ICG R15 test; platelet count; blood transfusion history; and a history of heavy alcohol intake. There were no statistically significant differences in these clinical features between SEN-V-positive and SEN-V-negative patients. There were no significant differences in tumor markers, such as
-fetoprotein and des-gamma-carboxyprothrombin levels, or in tumor factors (size, tumor-node-metastasis classification) between SEN-V-positive and SEN-V-negative HCC patients (data not shown).
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TABLE 2. Clinical features of patientsa
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Both the serum and the WBCs of only one of four SEN-V-positive patients and controls were SEN-V type D positive. However, the WBCs of none of the patients or controls who were SEN-V negative were SEN-V positive.
Genetic analysis of SEN-V DNA. Most of the SEN-V DNA sequences varied between patients, to the extent that we examined them (Fig. 1). D1-13 and H11-18 were SEN-V DNAs obtained from the sera of controls, D15-30 and H20-45 were from the sera of HCC patients, and D31-59 and H53-66 were from the sera of CLD patients without HCC. There were no specific regions where mutations accumulated. All the samples from SEN-V type D- and H-positive patients that were sequenced were classified by genotype according to the genetic analysis shown in the phylogenetic tree. Each genotype-specific primer worked as expected (Fig. 2). All of the clones of SEN-V types D and H obtained were classified as closely related to the TTV family (Fig. 2). The nucleotide sequence homologies among the SEN-V DNAs obtained from patients and controls were calculated. The nucleotide sequence homologies were 80 to 100% (mean ± standard deviation, 93% ± 5%) among SEN-V type D DNAs and 85 to 97% (91% ± 4%) among SEN-V type H DNAs. Two SEN-V type D genomes and one SEN-V type H genome showed comparatively low levels of homology with other sequences, but there were no significant differences among the sequences of SEN-V DNA from controls, HCC patients, and CLD patients without HCC.
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FIG. 1. Multiple-sequence alignments of SEN-V DNAs. The sequences of the samples were compared with the consensus sequence. Only the nucleotides that differed from the consensus sequence are shown. SEN-V type D nucleotides 528 to 677 and SEN-V type H nucleotides 402 to 551 are the consensus sequences. D1, D6, D8, D10, D12, D13, D15, D16, D17, D23, D25, D29, D30, D31, D32, and D59 and H11, H14, H18, H20, H22, H45, H53, and H66 are samples from patients (HCC, CLD) and controls (CNTL).
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FIG. 2. Nucleotides 528 to 677 of SEN-V type D were compared with the sequences of the same regions of SEN-V types A to H and TTV nucleotides 701 to 850. Nucleotides 402 to 551 of SEN-V type H were compared with the sequences of the same regions of SEN-V types A to H and TTV nucleotides 402 to 551. The phylogenetic tree was constructed by the unweighted pair group method with the arithmetic mean by using the computer software package GENETYX-MAC (Software Development Co., Ltd.). The sample numbers are as described in the legend to Fig. 1.
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The prevalence of SEN-V in our study group of patients with HCC or patients with CLD without HCC is similar to the prevalences reported in previous studies, in which SEN-V DNA was detected in 17 to 92% of patients with liver disease (15, 21-23). However, our study showed a high prevalence of SEN-V in controls, in contrast to the low prevalence (1 to 10%) in subjects without liver disease reported in previous studies (15, 22). The difference in the rate of detection of SEN-V DNA between this and previous reports may be due to differences in the quantity of SEN-V DNA in the sera, differences in the PCR primers used, or differences in the sensitivities of the assay systems used. According to the results of sequence analysis, the specificity of the PCR was high enough. The sensitivity of the PCR could not be determined accurately because the concentration of SEN-V DNA varied among samples. The high rate of detection of SEN-V DNA in sera from healthy controls may indicate a high prevalence of SEN-V. To eliminate the possibility that we were detecting human genome sequences, we performed PCR using WBC DNA as a template.
We also compared the detectabilities of SEN-V DNA from sera and from WBCs. WBCs from none of the SEN-V-negative patients was SEN-V DNA positive. If the SEN-V DNA detected originated in the human genome, it should mainly be detected in WBCs rather than in serum. Furthermore, the sequences of the DNAs that we amplified varied among the patients. The DNA sequences obtained from SEN-V type D- and type H-positive patients were classified by genotype, and those from SEN-V type A to C-positive and SEN-V type E to G-positive patients were classified in the phylogenetic tree. The intragenotype homologies between the sequences obtained from our patients and those reported for SEN-V DNA were at least 87% (SEN-V type D) and 90% (SEN-V type H). These results suggest that the DNA that we detected was viral DNA rather than DNA from the host genome.
We also investigated whether there was a correlation between the presence of SEN-V and the severity of CLD with concomitant HCC. Infection with SEN-V did not have a significant effect on the status of liver disease. The prevalence of SEN-V DNA viremia in our study was similar in patients with HCC (76%) and patients with CLD without HCC (69%). Thus, SEN-V does not seem to contribute to the development of CLD or the development of HCC from CLD.
The prevalence of TTV in this study was lower than that reported previously (18). The difference in the PCR primers used to detect the TTV DNA could explain the lower prevalence of TTV in our study (24).
Genetic analysis of the SEN-V DNA sequences obtained showed no differences among the control, HCC, and CLD without HCC groups. In the analysis of full-length SEN-V type D and H DNAs, we found slight differences in codon distributions and hydrophobicities. In order to estimate whether these differences are significant, we must compare more sequences from strains of the same genotypes.
On the basis of the results of this study, it is unlikely that SEN-V contributes to the incidence of liver disease or the development of HCC in Japan. However, a prospective study of the incidence of HCC in a large population of SEN-V-positive and -negative patients will be required to prove whether SEN-V contributes to the increasing tendency of chronic liver disease to progress to HCC in Japan.
Financial support was obtained from the Program for the Promotion of Fundamental Studies in the Health Sciences of the Organization for Pharmaceutical Safety and Research of Japan, Grants-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science, and Technology of Japan, and Health Sciences Research Grants for Medical Frontier Strategy Research from the Ministry of Health, Labor, and Welfare.
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