A randomized controlled trial of consensus interferon with or without lactoferrin for chronic hepatitis C patients with genotype 1b and high viral load

Recently, lactoferrin has been reported to have anti-HCV effects. The aim of this study was to investigate the effect of combination therapy using consensus interferon (CIFN) and lactoferrin in patients with chronic hepatitis C. Twenty-one patients with chronic HCV infection, who were positive for HCV-RNA genotype 1b with serum viral loads from 100 to 700KIU/ml, were randomly assigned to two groups; the CIFN + Lac group received CIFN with lactoferrin and the CIFN group received CIFN alone. Nine patients in each group completed this trial; the other patients dropped out because of side effects. Three, two and four patients were categorized as complete responders, relapsers and non-responders, respectively, in the CIFN + Lac group, and four, one and four in the CIFN group, respectively. There was no statistically significant difference in virologic response between the two groups. During the follow up after CIFN therapy with continued lactoferrin, there were two relapsers in the CIFN + Lac group and their HCV-RNA titers before treatment were over 400KIU/ml. In conclusion, the combination therapy of CIFN and lactoferrin did not increase the response rate or prevent relapse after discontinuation of IFN.

PCR-probe capture hybridization assay and statistical model for SEN virus prevalence estimation

SEN viruses (SENV) are newly discovered blood-borne single-stranded circular DNA viruses that may play a role in liver disease. To date, no serologic assays are available for the detection of SENV antigens or antibodies. We report on a rapid and sensitive molecular assay for the detection of four SENV strains (SENV-A, -C, -D, -H). This method uses PCR with universal primers and microwell capture hybridization with type-specific probes. Cut-off points to define "infected" based on chemiluminescence readings were determined from a statistical mixture model applied to samples from 300 injection drug users (IDUs) in San Francisco. Based on the estimated cut-off points, we examined the prevalence of SENV infection among 232 healthy US blood donors and assessed sensitivity and specificity of the assay in a small validation sample of infected individuals with partial sequence information.

Role of hepatitis B virus genotypes Ba and C, core promoter and precore mutations on hepatocellular carcinoma: a case control study

The role of hepatitis B virus (HBV) genotypes, core promoter (CP) and precore mutants on hepatocellular carcinoma (HCC) is still controversial. We aimed to determine their role on the development and clinical features of HCC. HBV genotypes and CP/precore mutations were determined in 90 HCC patients and 180 matched control patients. In the 90 HCC patients, 22 (24.4%) and 68 (75.6%) had subtype Ba and genotype C, respectively. The prevalence of genotype C and CP mutations was significantly higher in HCC patients compared with controls (75.6 versus 57.8%, P = 0.004; 90.9 versus 74.8%, respectively, P = 0.007). Among carriers of genotype C, 91.8% of the HCC patients and 88.8% of controls had CP mutations. Among carriers of subtype Ba, HCC patients had a higher prevalence of CP mutations compared with controls (88.2 versus 54.5%, respectively, P = 0.02). By logistic regression analysis, the only factor associated with HCC was a mutation of the CP region (P = 0.032). There were no differences in the clinical features on presentation, the chance of receiving treatment and the cumulative survival rate for chemoembolization-treated patients between patients with subtype Ba and genotype C. There was too small a number of CP wild-type to do a similar comparison with CP mutants. In conclusion, there was a significantly higher prevalence of both genotype C and CP mutations in patients with HCC. The association between HBV genotype C and HCC was probably not genuine but was due to the high percentage of CP mutations in patients with genotype C.

Two subtypes of genotype B (Ba and Bj) of hepatitis B virus in Japan

We have previously reported 2 subtypes of hepatitis B virus (HBV) genotype B, one of which has the recombination with genotype C over the precore region plus core gene (Ba) and the other of which does not (Bj). A restriction fragment-length polymorphism method with 2 endonucleases was newly developed for distinguishing between subtypes Ba and Bj and was applied to 313 carriers of HBV genotype B in Japan. Subtype Ba was detected in 38 (12%) and subtype Bj in 275 (88%) of the carriers of HBV genotype B. Hepatitis B e antigen in serum was found more frequently in patients with chronic infection with subtype Ba than in those with chronic infection with subtype Bj (8 [32%] of 25 vs. 25 [9%] of 273; P<.01). The new method for distinguishing between Ba and Bj by restriction fragment-length polymorphism would be useful in examining the distribution of these 2 subtypes in situations in which HBV genotype B is prevalent.

Hepatitis B genotypes in chronic hepatitis B and lamivudine therapy

The influence of hepatitis B virus (HBV) genotypes on the natural history and the response to treatment of patients with chronic hepatitis B are of potential interest. Compared to the patients with HBV genotype C, those with genotype B were of a younger age and had a higher cumulative rate of hepatitis B e antigen (HBeAg) seroconversion during the initial 6 years of follow-up. The earlier HBeAg seroconversion in the patients with genotype B, however, did not provide them with a benefit in terms of a reduced risk of developing long-term complications. The response to lamivudine therapy was evaluated in 21 patients infected with HBV genotype B (all of subtype Ba) and 61 with genotype C. There were no differences in the virological response to lamivudine therapy, based on the reduction in median logarithmic HBV DNA titer as well as alanine aminotransferase (ALT) levels, normalization of ALT and the rate of HBeAg seroconversion between the patients with genotypes B and C. No differences were noted either, in the frequency of YMDD mutants at week 52 or the cumulative risk of HBV DNA breakthroughs with YMDD mutations during long-term lamivudine therapy (median 37.5 months). In conclusion, there is no influence of HBV genotypes on the development of long-term complications and lamivudine therapy in Hong Kong.

Comparison of genotypes C and D of the hepatitis B virus in Japan: A clinical and molecular biological study

The genotype-related differences between genotype C and genotype D of the hepatitis B virus (HBV) remain unknown. The relationship was studied between the HBV genotypes and their clinical features, paying special attention to genotypes C and D. Serum samples from 413 HBV carriers were genotyped using an enzyme immunoassay (EIA) and by restriction fragment length polymorphism. The nucleotide sequences at the basic core promoter (BCP) and precore (PreC) regions were analysed by direct sequencing. The full genome sequences of three HBV genotype D cases were also examined. Almost all carriers with HBV genotype D were asymptomatic carriers (84.2%). Genotype D was not found in patients with liver cirrhosis and hepatocellular carcinoma. In contrast, carriers with genotype C had mainly chronic liver disease (63.2%; P<0.001). The ratio of hepatitis B e antigen (HBeAg)/anti-HBe was significantly higher in genotype C than in genotype D in the young age-matched group (P<0.01). The mutation at BCP (T1762, A1764) was significantly lower in genotype D than in genotype C among HBeAg-negative patients (P<0.05). The HBV full-genome sequences are very similar to certain HBV genotype D sequences from Europe. In conclusion, genotype C was associated with chronic liver disease, whereas genotype D was related to asymptomatic carriers with earlier HBeAg seroconversion. Thus, the outcome of chronic HBV infection may be different in persons infected with HBV genotypes C and D.

Predicting relapse after cessation of Lamivudine monotherapy for chronic hepatitis B virus infection

There have been reports of relapse after cessation of lamivudine monotherapy for hepatitis B virus (HBV) infection. The aim of this study was to examine factors that predict posttreatment relapse. Comparison 22 patients who experienced relapse with 11 who did not after cessation of therapy showed that predictive factors for nonrelapse were hepatitis B e antigen seroconversion and duration of undetectable HBV DNA load (<0.7 log IU/mL), as determined by HBV real-time detection direct testing. However, 7 of 12 patients with seroconversion experienced relapse after cessation of therapy. Multivariate analysis revealed that the duration of an undetectable HBV DNA load was the only independent predictive factor for nonrelapse (odds ratio, 0.50; 95% confidence interval, 0.27-0.9). More-prolonged lamivudine therapy is required after seroconversion, and persistent duration of an HBV DNA level of <0.7 log IU/mL for >6 months can more accurately aid in the decision of when to stop lamivudine therapy.

Reliability of hepatitis C virus core antigen assay for detection of viremia in HCV genotypes 1, 2, 3, and 4 infected blood donors: A collaborative study between Japan, Egypt, and Uzbekistan

Nucleic acid amplification-based methods are used for confirmation of viremia in antibody to hepatitis C virus (anti-HCV)-positive patients. However, this technology is labor intensive, time consuming, requires complex laboratory conditions, and expensive. The aim of this study was to evaluate the sensitivity and specificity of the HCV core antigen (HCVcAg) assay as an alternative approach for confirmation of viremia in HCV-infected subjects with HCV genotype 1-4. Two hundred forty-six asymptomatic HCV RNA- positive donors were enrolled in this study, consisting of 122 blood donors from Egypt (116 with genotype 4, 4 with genotype 1, and 2 with 1 + 4 genotypes), 109 from Japan (85 with genotype 1, and 24 with genotype 2), and 15 from Uzbekistan (all with genotype 3). A total of 234 (95.1%) of 246 RNA-positive specimens were detected by the HCVcAg assay; the sensitivity of HCVcAg assay consisted 93.4, 100, 100, and 94.8% for genotypes 1, 2, 3, and 4, respectively in comparison with RT-PCR assay. The specificity of the assay was confirmed in the absence of the false-positive results among 53 anti-HCV-negative, but anti-Schistosoma mansoni (anti-Sm) positive donors from Egypt. A positive correlation between HCVcAg and HCV RNA concentration levels (r = 0.671, P < 0.05) was observed among specimens with HCV genotype 4. The mean HCVcAg level was significantly lower in specimens with genotype 4 (2,935 fmol/L) comparing to genotypes 1, 2, and 3 (5,034, 4,962, and 4,740 fmol/L, respectively). No specific mutation was found in the core-encoding region of the studied specimens. In conclusion, HCVcAg is shown to be specific, sensitive, and informative qualitative index for HCV viremia in asymptomatic carriers.

Evaluation of loss of heterozygosity before and after interferon therapy in patients with hepatitis C virus infection who developed hepatocellular carcinoma during follow up

BACKGROUND AND AIM

The aim of the present study was to determine whether evaluating the status of loss of heterozygosity (LOH) before interferon (IFN) therapy is predictive for development of hepatocellular carcinoma (HCC) in chronic hepatitis and liver cirrhosis patients.

METHODS

Eighteen patients with hepatitis C virus were studied, nine of whom developed HCC (HCC group) after IFN therapy and nine whom did not (non-HCC group). Samples before IFN therapy from both groups (pre-IFN-N and pre-IFN-H samples from the non-HCC and HCC groups, respectively) were analyzed for LOH using 12 microsatellite markers. To evaluate the LOH incidence in different steps in HCC patients, paired samples of cancerous tissue (CT) and adjacent non-CT (ANCT) obtained from the HCC group were also analyzed.

RESULTS

Frequency of LOH in the pre-IFN-H samples was significantly higher than that in the pre-IFN-N samples regardless of the response to IFN therapy. Interestingly, in the HCC group, there is no significant difference in the frequency of LOH among the pre-IFN-H, ANCT and CT samples.

CONCLUSIONS

The present results suggest the theory that genetic instability, such as LOH, had already accumulated at stages before the development of HCC. The authors propose that the status of LOH in chronic hepatitis and liver cirrhosis patients before IFN therapy could be a potential predictor for the development of HCC.

Development of real-time detection direct test for hepatitis B virus and comparison with two commercial tests using the WHO international standard

AIMS

A highly reproducible and sensitive hepatitis B virus real-time detection direct (HBV RTD-direct) test using DNA extraction by magnetic beads coated with polyclonal anti-HBsAg, followed by the real-time detection polymerase chain reaction (PCR) method, was developed for the detection of HBV DNA.

METHODS

The HBV DNA could be extracted from the HBsAg positive viral particles without resulting in viral DNA fragmentation. The HBV RTD-direct test was validated using a serial dilution panel of the WHO standard HBV DNA 97/746 I.

RESULTS

The test had a dynamic range of 0.7-8.0 log10 international units (IU) per mL and the results were shown to be comparable to those obtained with two commercially available tests: the HBV DNA transcription-mediated amplification-hybridization protection assay and the Amplicor HBV Monitor test. In addition, the HBV RTD-direct test, based on magnetic extraction, successfully eliminated PCR inhibitors in clinical specimens.

CONCLUSION

We conclude that the HBV RTD-direct test is an excellent alternative for monitoring patients undergoing antiviral treatment or for screening various clinical specimens.

Transforming growth factor-beta-1 genetic polymorphism in Japanese patients with chronic hepatitis C virus infection

BACKGROUND AND AIM

Transforming growth factor beta-1 (TGF-beta1) is one of the most dominant fibrogenic cytokines in hepatic fibrosis. The aim of the present study was to examine the effects of TGF-beta1 polymorphisms in Japanese patients with chronic hepatitis C virus (HCV) infection and in healthy control subjects.

METHODS

The TGF-beta1 genotypes at codon 10 and codon 25 were determined in 206 Japanese patients with chronic HCV infection and in 101 Japanese healthy control subjects. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used for the detection of these polymorphisms. The degree of hepatic fibrosis was assessed by liver biopsy and graded according to the New Inuyama Classification for chronic hepatitis graded F0-4.

RESULTS

The authors found no significant differences in genotype distributions and allele frequency between the HCV patients and the healthy control subjects. The frequencies of the TT, TC, and CC genotypes of codon 10 were 24%, 42% and 35%, respectively, among the patients of the F0-2 group, and 31%, 40% and 29%, respectively, among those of the F3-4 group. No significant differences were shown between the TGF-beta1 polymorphism at codon 10 and the stage of hepatic fibrosis. In contrast, no genetic alteration of codon 25 was found in healthy controls and patients with chronic HCV infection.

CONCLUSION

These results suggest that there may not be a significant relationship between polymorphism at codon 10 and the development of progressive hepatic fibrosis in the Japanese population.

Human immunodeficiency virus in Uzbekistan: epidemiological and genetic analyses

This study investigates the molecular epidemiology of HIV in Uzbekistan--a former Soviet Union (FSU) country located in central Asia. A total of 18,910,370 subjects were involved in an HIV serological examination through a population survey conducted in 1987-2002. Rapid changes in epidemiological dynamics and transmission modes have been observed since 1999: incidence rose from 25 newly HIV-infected subjects per year to more than 100 new cases per month within the first half of 2002, and the rate of intravenous drug use (IVDU)-associated HIV infection increased to 75% per year during the same period. Thirty HIV-1 strains, isolated from specimens obtained in 1999-2000, were directly sequenced in the env region. Phylogenetic analysis revealed a relationship to genotype A in 56.7%, and to 03_CRFAB in 13.3%; both variants have been previously reported in the FSU. The majority (85.7%) of these strains were isolated from IVDUs. The demographic history of the most prevalent HIV strain in Uzbekistan was inferred from reconstructed molecular phylogenies; exponential growth of the viral population size was thus observed to occur after the mid-1990s. In summary, detectable HIV seroprevalence remains low in the general population of Uzbekistan. However, the current study demonstrates a substantially increasing number of new infections, in association with IVDU, and an exponentially growing effective population size of the IVDU-associated HIV strain.

Genotypes and phylogenetic characterization of hepatitis B and delta viruses in Egypt

Hepatitis B virus (HBV) and hepatitis D virus (HDV) sequences among HBV carriers from Egypt have not been evaluated sufficiently. The genotypes of HBV isolated from 105 serum samples from Egyptian carriers were determined. Four complete genomes and 11 entire preS1/S2/S genes were sequenced and evaluated. All serum samples were classified into HBV genotype D using serologic and genetic methods. The length of four complete nucleotide sequences was 3,182 bp. In all 15 samples, the common 33 nucleotides (11 amino acids) deletions in the preS1 region specific for HBV genotype D were observed. In the phylogenetic analysis based on the complete nucleotide sequences, all samples were clustered with the HBV isolates reported from previously Western and Mediterranean countries with nucleotide homology ranging from 96.0-98.0%. Of 75 HBsAg positive samples, anti-HDV was found in 15 (20%), and HDV RNA was detected in 9 of 15 (60%). The proportion of the patients with liver disease was higher in HBV carriers of anti-HDV positive with HDV RNA than in HBV carriers of anti-HDV positive without HDV RNA (P < 0.05). In the phylogenetic analysis based on the sequences in nucleotide position 853-1267 of HDV, nine samples were classified into HDV genotype I with the nucleotide homology ranging from 88.3-92.1% (mean; 90.5%) and clustered with HDV strains reported previously from Ethiopia, Somalia, Egypt, and Lebanon. These results indicate that HBV genotype D and HDV genotype I are most prevalent in Egypt, and HDV co-infection in HBV carriers is related to severity of liver disease.

High stability of enzyme immunoassay for hepatitis C virus core antigen-evaluation before and after incubation at room temperature

Hepatitis C virus (HCV) RNA is thought to be less stable than HCV core antigen (HCV-Ag), however there have been few studies on comparing the stability of HCV-Ag with that of HCV-RNA in vitro. The aim of this study is to evaluate serial levels of HCV-Ag and HCV-RNA in serum before and after incubation at 4 or 25 degrees C for 7 days to estimate an assay suitable for general laboratory use. In this study, we demonstrate that HCV-Ag levels are highly reproducible (coefficients of variation (CVs); 0.89-6.92%) and stable (84.8% of the initial level) with incubation of even 25 degrees C for 7 days, whereas HCV-RNA levels are much less reproducible (CVs; 9.13-29.66%) and decrease dramatically (15.1% of the initial level) after incubation, particularly at 25 degrees C. The measurement of the HCV-Ag level was found to be suitable for HCV quantification with serum samples stored either at 4 degrees C or under unknown conditions. Additionally, it successfully eliminated inhibitors such as heparin from plasma and could be applied to a variety of clinical specimens. Our data suggest the significance of measuring the HCV-Ag level during clinical management independently of the HCV-RNA level, particularly because of its high stability.

Prevalence of SEN viruses among injection drug users in the San Francisco Bay area

SEN viruses (SENVs) are newly discovered bloodborne viruses that may play a role in liver disease. SENV strain prevalence was examined in a race/ethnicity-stratified sample of 531 injection drug users (IDUs) from the San Francisco Bay area. Weighted prevalences were as follows: SENV-A, 45.7%; SENV-C/H, 35.6%; and SENV-D, 10.3%. Infection was associated with a longer duration of injection drug use. SENV-A was more common in black subjects (adjusted odds ratio [OR(a)], 4.37; 95% confidence interval [CI], 2.65-7.21) and Hispanic subjects (OR(a), 2.30; 95% CI, 1.38-3.85) than in white and non-Hispanic subjects, and the pattern was similar for SENV-C/H. For SENV-D, prevalence was similar in black and white subjects, but lower in Hispanic subjects; infection was less common among women than men (OR(a), 0.32; 95% CI, 0.15-0.71) and more common among men with at least 1 recent male sex partner than among heterosexual men (OR(a), 7.05; 95% CI, 2.62-18.95). SENV strains are common among San Francisco Bay area IDUs, and prevalence varies demographically within this group.

Impact of interleukin-1beta genetic polymorphisms on the development of hepatitis C virus-related hepatocellular carcinoma in Japan

To examine the effects of polymorphisms in the gene encoding proinflammatory interleukin (IL)-1beta in patients infected with hepatitis C virus (HCV) in Japan, we studied 364 patients with chronic HCV infection (146 of whom had hepatocellular carcinoma [HCC] and 218 of whom did not) and 230 healthy control subjects. IL-1B-511 and IL-1RN genotypes were ascertained, and IL-1B-511 genotype T/T was found to be significant risk factors for the development of HCC, indicating that polymorphism in the IL-1B-511 genetic locus is one of the possible determinants of progression of hepatitis C to HCC.

Hepatitis C virus molecular epidemiology in Uzbekistan

The aim of this study was to identify hepatitis C virus (HCV) genotypes and to estimate their prevalence in various risk groups and the regional distribution in Uzbekistan. Preliminary serological screening of 1,269 subjects revealed 6.5% anti-HCV-positive in a general population, 27.1% in patient groups, and 51.7% among intravenous drug users. HCV genotypes of 104 anti-HCV-positive subjects were determined using a PCR-genotyping system in core region, and the results were supported by nucleotide sequencing of the NS5B region. Genotype 1b identified in total 64.2%, was the most prevalent. The genotype 3a identified in 25.0% was the second one distributed. HCV genotypes 2a, 1a, 2b, and 3b were identified in 3.8%, 2.9%, 2.9%, and 1.0% of cases, respectively. The intravenous drug users were distinguished from other groups by having the highest prevalence of genotype 3a, i.e., 50.0%, higher than the 33.3% for genotype 1b in this group. Geographically, genotype 1b was common; genotype 3a was also found frequently in all three regions. Uncommon HCV genotypes (1a, 2a, 2b, and 3b) were found in comparatively greater variability in the western region. Molecular evolutionary analysis based on the NS5B region did not reveal specific clustering or indigenous strains among Uzbekistan HCV isolates. In summary, two main mechanisms of HCV infection distribution were observed in Uzbekistan: HCV 1b genotype infection is widespread through blood products, and HCV 3a genotype infection is spreading through the growing number of intravenous drug users.

A comparison of the molecular clock of hepatitis C virus in the United States and Japan predicts that hepatocellular carcinoma incidence in the United States will increase over the next two decades

The prevalence of hepatitis C virus (HCV)-related hepatocellular carcinoma (HCC) is considerably lower in the U.S. than in Japan. To elucidate this difference, we determined the time origin of the HCV epidemic in each country by using molecularly clocked long-term serial samples obtained from HCV carriers of genotypes 1a and 1b. The molecular clock estimated that HCV genotype 1 first appeared in Japan in around 1882, whereas emergence in the U.S. was delayed until around 1910. In addition, by statistical analysis using coalescent theory, the major spread time for HCV infection in Japan occurred in the 1930s, whereas widespread dissemination of HCV in the U.S. occurred in the 1960s. These estimates of viral spread time are consistent with epidemiologic observations and predict that the burden of HCC in the U.S. will increase in the next two to three decades, possibly to equal that currently experienced in Japan.

Observation of positive selection within hypervariable regions of a newly identified DNA virus (SEN virus)(1)

To elucidate the evolution of SEN virus (SEN-V), serial sequences of chronically SEN-V-infected patients were analyzed. In the hypervariable regions, non-synonymous substitutions significantly predominated. This could be attributed to positive selection in evading immune surveillance of the hosts and to establish a persistent infection. On the basis of the sequences in the two open reading frames of SEN-V DNA, the rate of synonymous substitutions was 7.32 x 10(-4) per site per year. Since this rate is close to RNA viruses and higher than other DNA viruses, the SEN-V might be replicated by machinery with poor or no proofreading function.

SEN virus infection and its relationship to transfusion-associated hepatitis

SEN virus (SEN-V) is a recently identified single-stranded, circular DNA virus. Two SEN-V variants (SENV-D and SENV-H) were assayed by polymerase chain reaction (PCR) to investigate their role in the causation of transfusion-associated non-A to E hepatitis. The incidence of SEN-V infection after transfusion was 30% (86 of 286) compared with 3% (3 of 97) among nontransfused controls (P < .001). Transfusion risk increased with the number of units transfused (P < .0001) and donor-recipient linkage for SEN-V was shown by sequence homology. The prevalence of SEN-V in 436 volunteer donors was 1.8%. Among patients with transfusion-associated non-A to E hepatitis, 11 of 12 (92%) were infected with SEN-V at the time of transfusion compared with 55 of 225 (24%) identically followed recipients who did not develop hepatitis (P < .001). No effect of SEN-V on the severity or persistence of coexistent hepatitis C virus (HCV) infection was observed. In 31 infected recipients, SEN-V persisted for greater than 1 year in 45% and for up to 12 years in 13%. SEN-V-specific RNA (a possible replicative intermediate) was recovered from liver tissue. In summary, SENV-D and -H were present in nearly 2% of US donors, and were unequivocally transmitted by transfusion and frequently persisted. The strong association of SEN-V with transfusion-associated non-A to E hepatitis compared with controls raises the possibility, but does not establish that SEN-V might be a causative agent of posttransfusion hepatitis. The vast majority of SEN-V-infected recipients did not develop hepatitis.

Genomic and molecular evolutionary analysis of a newly identified infectious agent (SEN virus) and its relationship to the TT virus family

A new group of transmissible single-stranded (ss) DNA viruses (SENV) distantly related to the large TT virus (TTV) family was recently identified. Eight different SENV isolates have been found, some with an association with posttransfusion hepatitis. A phylogenetic analysis of near-complete open-reading frame 1, including conserved motifs and excluding recombinant regions, was performed. The analysis used TTV-like minivirus as an outgroup, to determine a root of the phylogenetic tree, and compared 8 SENV isolates, 6 prototype TTV isolates, and 7 TTV variants (including SANBAN, TUS01, PMV, and YONBAN). Four distinct clusters separated by a bootstrap value of 100% were observed. YONBAN isolates formed a distinct outer group, representing the earliest recognized phylogenetic divergence (group 1). Prototype TTV formed group 2, PMV formed group 3, and SENV, SANBAN, and TUS01 isolates formed group 4, the most recently evolved group. This taxonomic classification suggests that these circular ssDNA viruses probably evolved from a common ancestor virus.