Genome-wide association of IL28B with response to pegylated interferon-alpha and ribavirin therapy for chronic hepatitis C

The recommended treatment for patients with chronic hepatitis C, pegylated interferon-alpha (PEG-IFN-alpha) plus ribavirin (RBV), does not provide sustained virologic response (SVR) in all patients. We report a genome-wide association study (GWAS) to null virological response (NVR) in the treatment of patients with hepatitis C virus (HCV) genotype 1 within a Japanese population. We found two SNPs near the gene IL28B on chromosome 19 to be strongly associated with NVR (rs12980275, P = 1.93 x 10(-13), and rs8099917, 3.11 x 10(-15)). We replicated these associations in an independent cohort (combined P values, 2.84 x 10(-27) (OR = 17.7; 95% CI = 10.0-31.3) and 2.68 x 10(-32) (OR = 27.1; 95% CI = 14.6-50.3), respectively). Compared to NVR, these SNPs were also associated with SVR (rs12980275, P = 3.99 x 10(-24), and rs8099917, P = 1.11 x 10(-27)). In further fine mapping of the region, seven SNPs (rs8105790, rs11881222, rs8103142, rs28416813, rs4803219, rs8099917 and rs7248668) located in the IL28B region showed the most significant associations (P = 5.52 x 10(-28)-2.68 x 10(-32); OR = 22.3-27.1). Real-time quantitative PCR assays in peripheral blood mononuclear cells showed lower IL28B expression levels in individuals carrying the minor alleles (P = 0.015).

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.

A case-control study for differences among hepatitis B virus infections of genotypes A (subtypes Aa and Ae) and D

There are two subtypes of hepatitis B virus genotype A (HBV/A) and they are provisionally designated Aa ("a" standing for Africa/Asia) and Ae ("e" for Europe). In a case-control study, 78 HBV/Aa, 78HBV/Ae, and 78HBV/D carriers from several countries were compared. The prevalence of HBe antigen (HBeAg) in serum was significantly lower in carriers of HBV/Aa than in carriers of HBV/Ae (31% vs. 49%; P = .033), with a difference more obvious in the carriers aged 30 years or younger (34% vs. 67%; P = .029). HBV DNA levels in the carriers of HBV/Aa (median, 3.46 log copies/mL; 95% CI, 2.93-3.95) were significantly lower than those of carriers of HBV/Ae (6.09 log copies/mL; 95% CI, 4.24-7.64) or of carriers of HBV/D (5.48 log copies/mL; 95% CI, 4.06-7.02), regardless of the HBeAg status (P < .001). The most specific and frequent substitutions in 54 HBV/Aa isolates were double substitutions for T1809 (100%) and T1812 (96%) immediately upstream of the precore initiation codon, which would interfere with the translation of HBeAg in HBV/Aa infections. They were not detected in 57 HBV/Ae or 61 HBV/D isolates examined. The double mutation in the core promoter (T1762/A1764) was more frequent in both HBV/Aa (50%) and HBV/Ae (44%) than in HBV/D isolates (25%; P < .01), whereas the precore mutation (A1896) occurred in HBV/D isolates only (48%; P < .0001). In conclusion, the clearance of HBeAg from serum may occur by different mechanisms in HBV/Aa, HBV/Ae, and HBV/D infections, which may influence clinical manifestations in the Western countries where both genotypes A and D are prevalent.

Specific mutations in enhancer II/core promoter of hepatitis B virus subgenotypes C1/C2 increase the risk of hepatocellular carcinoma

BACKGROUND/AIMS

Hepatitis B virus genotype C (HBV/C) has been classified into two geographically distinct subgenotypes; HBV/C1/Cs (Southeast Asia) and HBV/C2/Ce (East Asia).

METHODS

Viral differences in enhancer II/core promoter and precore regions between the subgenotypes and their association with hepatocellular carcinoma (HCC) were assessed in a matched cross-sectional control study of 118 carriers (from Hong Kong) with HBV/C1/Cs (48.0 years, 81% male, 40% HBeAg+, 44% HCC) and 210 HBV/C2/Ce (172 from Japan, 38 from Hong Kong) (50.2 years, 78% male, 30% HBeAg+, 46% HCC).

RESULTS

Univariate analyses showed that mutation V1753 was predictive for HCC among HBeAg-positive-C1/Cs-carriers (P=0.0055), and T1653 among HBeAg-positive-C2/Ce-carriers (P=0.018), and T1653 or V1753 or T1762/A1764 among HBeAg-negative-C2/Ce-carriers (P<0.05). In the multivariate analysis on all HBV/C subjects, independent predictive factors for HCC were subgenotype C2/Ce (odds ratio, 4.21; 95% confidence interval, 1.07-16.23), T1653 (3.64; 1.93-6.86), V1753 (3.07; 1.66-5.65) and T1762/A1764 (2.58; 1.21-5.49) mutations, age (50 years), gender (male) and HBeAg (positive).

CONCLUSIONS

Our data indicate that T1653 and/or V1753 mutations in addition to T1762/A1764 are differently associated with HCC in context of HBeAg status among HBV/C1/Cs and C2/Ce-carriers. HBV/C subgenotypes have specific mutation patterns, which is probably responsible for increased carcinogenesis of HBV/C2/Ce.

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.

Molecular tracing of the global hepatitis C virus epidemic predicts regional patterns of hepatocellular carcinoma mortality

BACKGROUND & AIMS

Molecular evolutionary analysis based on coalescent theory can provide important insights into epidemiologic processes worldwide. This approach was combined with analyses of the hepatitis C virus (HCV) epidemiologic-historical background and HCV-related hepatocellular carcinoma (HCC) in different countries.

METHODS

The HCV gene sequences of 131 genotype 1b (HCV-1b) strains from Japan, 38 HCV-1a strains from the United States, 33 HCV-1b strains from Spain, 27 HCV-3a strains from the former Soviet Union (FSU), 47 HCV-4a strains from Egypt, 25 HCV-5a strains from South Africa, and 24 HCV-6a strains from Hong Kong isolated in this study and previous studies were analyzed.

RESULTS

The coalescent analysis indicated that a transition from constant size to rapid exponential growth (spread time) occurred in Japan in the 1920s (HCV-1b), but not until the 1940s for the same genotype in Spain and other European countries. The spread time of HCV-1a in the United States was estimated to be in the 1960s; HCV-3a in the FSU, HCV-5a in South Africa, and HCV-6a in Hong Kong in the 1960s, mid-1950s, and late 1970s, respectively. Three different linear progression curves were determined by analysis of the relationship between HCV seroprevalence and HCC mortality in different geographic regions; a steep ascent indicated the greatest progression to HCC in Japan, a near horizontal line indicated the least progression in the United States and the FSU, and an intermediate slope was observed in Europe.

CONCLUSIONS

These findings strongly suggest that the initial spread time of HCV is associated with the progression dynamics of HCC in each area, irrespective of genotype.

New genotypes of TT virus (TTV) and a genotyping assay based on restriction fragment length polymorphism

A phylogenetic analysis, using the open reading frame I sequence of 93 TT viruses (TTV) obtained from various geographical areas, indicated that the virus could be classified into six different genotypes including three hitherto unreported genotypes. The high reliability of the six clusters was confirmed by bootstrap analysis. On the basis of these sequence data, a new simple genotyping assay based on a restriction fragment length polymorphism of TTV was developed. Using the enzymes NdeI and PstI, followed by cleavage with NlaIII or MseI, it was possible to distinguish between the six TTV genotypes. This system will provide the framework for future detailed epidemiological and clinical investigations.

Genome-wide association study identified ITPA/DDRGK1 variants reflecting thrombocytopenia in pegylated interferon and ribavirin therapy for chronic hepatitis C

Hematologic abnormalities during current therapy with pegylated interferon and ribavirin (PEG-IFN/RBV) for chronic hepatitis C (CHC) often necessitate dose reduction and premature withdrawal from therapy. The aim of this study was to identify host factors associated with IFN-induced thrombocytopenia by genome-wide association study (GWAS). In the GWAS stage using 900K single-nucleotide polymorphism (SNP) microarrays, 303 Japanese CHC patients treated with PEG-IFN/RBV therapy were genotyped. One SNP (rs11697186) located on DDRGK1 gene on chromosome 20 showed strong associations in the minor-allele-dominant model with the decrease of platelet counts in response to PEG-IFN/RBV therapy [P = 8.17 × 10(-9); odds ratio (OR) = 4.6]. These associations were replicated in another sample set (n = 391) and the combined P-values reached 5.29 × 10(-17) (OR = 4.5). Fine mapping with 22 SNPs around DDRGK1 and ITPA genes showed that rs11697186 at the GWAS stage had a strong linkage disequilibrium with rs1127354, known as a functional variant in the ITPA gene. The ITPA-AA/CA genotype was independently associated with a higher degree of reduction in platelet counts at week 4 (P < 0.0001), as well as protection against the reduction in hemoglobin, whereas the CC genotype had significantly less reduction in the mean platelet counts compared with the AA/CA genotype (P < 0.0001 for weeks 2, 4, 8, 12), due to a reactive increase of the platelet count through weeks 1-4. Our present results may provide a valuable pharmacogenetic diagnostic tool for tailoring PEG-IFN/RBV dosing to minimize drug-induced adverse events.

Exponential spread of hepatitis C virus genotype 4a in Egypt

Hepatitis C virus (HCV) infects >10% of the general population in Egypt, in which intravenous injection with an antimony compound for endemic schistosomiasis in the past has been implicated. To simulate the epidemic history of HCV in Egypt, sera were obtained from 3608 blood donors at 13 governorates in or surrounding the Nile valley during 1999. The prevalence of antibody to HCV (anti-HCV) and genotypes was determined in them, and the molecular evolutionary analysis based on the neutral theory was applied to HCV isolates of genotype 4a, which is outstandingly prevalent in Egypt and indigenous there. Of 3608 sera, 317 (8.8%) were positive for anti-HCV. The molecular evolutionary analysis on 47 HCV genotype 4a isolates of carriers from various districts in Egypt indicated that the spread of HCV-4a would have increased exponentially during the 1940s through 1980 when oral medications became available. In conclusion, the estimated spread time is consistent with the duration of intravenous antimony campaigns in Egypt.

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.

HCC risk post-SVR with DAAs in East Asians: findings from the REAL-C cohort

BACKGROUND

Despite HCV cure, patients remain at risk for HCC, but risk factor data for HCC following SVR are limited for Asian patients.

METHODS

To address this gap, we analyzed 5814 patients (5646 SVR, 168 non-SVR) from the Real-World Evidence from the Asia Liver Consortium for HCV (REAL-C) who did not have HCC or a history of HCC at baseline (pre-DAA treatment) and did not develop HCC within 6 months of baseline. To assess the effect of SVR on HCC incidence, we used 1:4 propensity score matching [(PSM), age, sex, baseline cirrhosis, and baseline AFP] to balance the SVR and non-SVR groups.

RESULTS

In the PSM cohort (160 non-SVR and 612 SVR), the HCC incidence rate per 100 person years was higher in the non-SVR compared to the SVR group (5.26 vs. 1.94, p < 0.001). Achieving SVR was independently associated with decreased HCC risk (adjusted HR [aHR]: 0.41, p = 0.002). Next, we stratified the SVR cohort of 5646 patients to cirrhotic and noncirrhotic subgroups. Among cirrhotic SVR patients, aged ≥ 60, having an albumin bilirubin grade (ALBI) of 2 or 3 (aHR: 2.5, p < 0.001), and baseline AFP ≥ 10 ng/mL (aHR: 1.6, p = 0.001) were associated with higher HCC risk, while among the non-cirrhotic SVR group, only baseline AFP ≥ 10 ng/mL was significant (aHR: 4.26, p = 0.005).

CONCLUSIONS

Achieving SVR decreases HCC risk; however, among East Asians, patients with elevated pretreatment AFP remained at risk. Pretreatment AFP, an easily obtained serum marker, may provide both prognostic and surveillance value for HCC in East Asian patients who obtained SVR.

Molecular tracing of Japan-indigenous hepatitis E viruses

The ancestor(s) of apparently Japan-indigenous strains of Hepatitis E virus (HEV) was probably of foreign origin, but it remains unclear when and from where it made inroads. In this study, 24 genotype 3 and 24 genotype 4 HEV strains recovered in Japan each showed a significant cluster, clearly distinct from those of foreign strains, in the phylogenetic tree constructed from an 821 nt RNA polymerase gene fragment. The evolutionary rate, approximately 0.8 x 10(-3) nucleotide substitutions per site per year, enabled tracing of the demographic history of HEV and suggested that the ancestors of Japan-indigenous HEV had made inroads around 1900, when several kinds of Yorkshire pig were imported from the UK to Japan. Interestingly, the evolutionary growth of genotype 3 in Japan has been slow since the 1920s, whereas genotype 4 has spread rapidly since the 1980s. In conclusion, these data suggest that the indigenization and spread of HEV in Japan were associated with the popularization of eating pork.

Molecular evolutionary analyses implicate injection treatment for schistosomiasis in the initial hepatitis C epidemics in Japan

BACKGROUND/AIMS

The mortality due to hepatocellular carcinoma (HCC) has ranged widely in various areas of Japan since 30 years ago and the incidence was particularly high in once Schistosoma japonicum (Sj)-endemic areas. Our aim was to estimate the spread time of hepatitis C virus (HCV) infection in the past with possible relevance to a higher incidence of HCC in once Sj-endemic than Sj-nonendemic areas.

METHODS

During 2001, 131 strains of HCV-1b were obtained from patients in three previously Sj-endemic areas, as well as Sj-nonendemic areas in Japan and a cross-sectional study was conducted on them with molecular evolutionary analyses.

RESULTS

A phylogenetic tree reconstructed on HCV-1b sequences in the NS5B region disclosed 2 independent clusters for Sj-positive and -negative groups with a high bootstrap value. The estimated effective number of HCV-infections indicated a transition from quiescence to rapid exponential growth in the 1920s among patients with schistosomiasis, which is 20 years earlier than that among patients without schistosomiasis.

CONCLUSIONS

The estimated spread time in previously Sj-endemic areas in Japan coincides with injection treatment for Sj since 1921. A high incidence of HCC there would be attributed to a long duration of HCV infection since 1920s.

lambda-Interferons and the single nucleotide polymorphisms: A milestone to tailor-made therapy for chronic hepatitis C

Type III interferons (IFN) (IFN-lambda1, -lambda2, -lambda3/interleukin [IL]-29, -28A, -28B) are cytokines with type I IFN-like antiviral activities. Most cells have expressed both type I and III IFN following Toll-like receptor (TLR) stimulation or viral infection, whereas the ability of cells to respond to IFN-lambda was restricted to a specific subset of cells. It was reported that signal transduction pathway of IFN-lambda was similar to that of IFN-alpha/beta although a receptor adapted by IFN-lambda were distinct from that of IFN-alpha/beta. However, the clinical significance and the role of each IFN-lambda were unclear. Recent genome-wide association studies (GWAS) of the human whole genome revealed several single nucleotide polymorphism sites (SNP) strongly associated with the response to pegylated IFN-alpha (PEG-IFN) plus ribavirin (RBV) treatment in chronic hepatitis C patients. The SNP, which are located near the IL-28B gene of chromosome 19, were discovered simultaneously by three independent studies opening a new prospective in hepatitis C research. The present review highlights significant insights that can be derived from the GWAS approach, and summarizes current knowledge of in vitro and in vivo study on the role of IFN-lambda in antiviral effect.

Characteristics of hepatitis B virus genotype G coinfected with genotype H in chimeric mice carrying human hepatocytes

Accumulated evidence indicated that hepatitis B virus genotype G (HBV/G) is present exclusively in coinfection with other HBV genotypes. In Mexico, HBV/G from 6 men who had sex with men were coinfected with HBV/H. Phylogenetically complete genomes of the 6 Mexican HBV/G strains were closely related to previous ones from the US/Europe. Using uPA/SCID mice with human hepatocytes, monoinfection with HBV/G did not result in detectable HBV DNA in serum, whereas superinfection with HBV/G at week 10 inoculated HBV/H when HBV/H DNA was elevated to >10(7) copies/mL has enhanced the replication of HBV/G. The HBV/G was enhanced in another 3 inoculated with a serum passage containing HBV/G with a trace of HBV/H. Coinfection of mice with HBV/G and H induced fibrosis in the liver. In conclusion, the replication of HBV/G can be enhanced remarkably when it is coinfected with HBV/H. Coinfection with HBV/G may be directly cytopathic in immunosuppressive conditions.

African origin of GB virus C/hepatitis G virus

Ninety-four GB virus C/hepatitis G virus (GBV-C/ HGV) RNA-positive serum samples were obtained from all over the world. We found that all 15 GBV-C/HGV isolates from the Pygmies and the Bantu in the Central African region had a 12-amino acid indel (i.e. insertion or deletion) in the non-structural protein (NS) 5A region. Phylogenetic analyses of the NS5A region, using GBV-A as an outgroup, showed that these 15 isolates had diverged from the common ancestor much earlier than the remaining isolates, indicating an African origin of GBV-C/HGV.

A new genotype of TT virus (TTV) infection among Colombian native Indians

Serum TTV DNA was assayed in 140 native Indians and 40 members of the general population in Colombia to determine the prevalence of TT virus (TTV) infection among Colombian native Indians. Of the 140 native Indians, 23 (16.4%) were positive for TTV DNA, compared to 4 (10.0%) of 40 from the general population (P = not significant). The prevalence of TTV DNA among native Indians was much higher than that of HBsAg and anti-HCV. Comparison of subjects with and without TTV DNA revealed no significant differences in all characteristics between the two groups. A phylogenetic tree, using the open reading frame 1 sequence (222 bp), indicated that the virus could be classified into four different genotypes, including three previously reported ones. The results show that TTV infection is common in Colombian native Indians without liver disease and also indicate the existence of a novel genotype of TTV.

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.

GB virus C/hepatitis G virus infection among Colombian native Indians

To elucidate the prevalence of GB virus C/hepatitis G virus (GBV-C/HGV) infection in Colombian native Indians, serum GBV-C/HGV RNA was assayed in 163 native Indians and 67 members of the general population in Colombia. The native Indians (males:females = 40:123) and the members of the general population (males:females = 20:47) were tested by reverse transcription-semi-nested polymerase chain reaction. Of the 163 native Indians, 10 (6.1%) were positive for GBV-C/HGV RNA, compared with one (1.5%) of 67 from the general population. All Indians were negative for hepatitis B surface antigen and antibody to hepatitis C virus. Of 10 Indians with GBV-C/HGV RNA, the genotype of nine subjects was the Asian type. These data indicated that 1) the prevalence of GBV-C/HGV RNA in Colombian native Indians is high, and 2) GBV-C/HGV was probably brought from Asia and inherited for generations in some native Indian groups.

Two subtypes (subgenotypes) of hepatitis B virus genotype C: A novel subtyping assay based on restriction fragment length polymorphism

Recently hepatitis B virus genotype C (HBV/C) has been classified into geographically typical two subtypes (subgenotypes); HBV/C1 in Southeast Asia (Cs) and HBV/C2 in East Asia (Ce). Our aim is to develop a rapid subtyping assay and to examine the virological features of these two subtypes. Based on 171 HBV/C strains retrieved from the database, 17 single nucleotides polymorphisms (SNPs) were found between two subtypes. Taking advantage of five SNPs in non-overlapping polymerase region, a restriction fragment length polymporphism method with three endonucleases was newly developed for distinguishing between HBV/Cs and HBV/Ce. The method was applied to 49 HBV/C carriers from Japan and Hong Kong. The 24 in Hong Kong were classified into HBV/Cs, and the 25 in Japan were HBV/Ce, confirmed by sequencing. Some specific mutations were detected in the encapsidation signal; precore stop mutation (A1896), accompanied by a C-to-T substitution at nt 1858, was found in HBV/Ce strains, and another precore mutation (A1898), accompanied by a C-to-T mutation at nt 1856, was found in HBV/Cs. Especially, two closely linked mutations (A1896 and A1899) in HBV/Ce could stabilize the epsilon loop structure more efficiently and influece viral replication. Hence, these virological differences between the two subtypes might influence clinical features.

Increasing genetic diversity of hepatitis C virus in haemophiliacs with human immunodeficiency virus coinfection

Patients with inherited bleeding disorders who received clotting factor concentrates before 1987 have high rates of hepatitis C virus (HCV) or HCV/human immunodeficiency virus (HIV) infection. To determine whether the persistent nature of HIV affects the genetic diversity of HCV by less selective pressure through the immunosuppression of HIV/HCV-coinfected patients, both the change of genetic diversity and selective pressure were examined in the HCV envelope genes (E1 and E2) of 325 genotype 1a subclones from eight HIV-positive and five HIV-negative patients with two time points (more than 6 years apart). To infer the genetic diversity of HCV in each patient, we used two approaches. One method was to estimate the difference of total evolutionary distances in the phylogenetic tree between the two time points, and another was to estimate the changes of genetic diversity along the time based on the coalescence theory. The two results indicate that the HIV-positive group has significantly more diverse population structure than the HIV-negative group. A comparative analysis of the synonymous and non-synonymous substitutions found that the HIV-positive group was subject to less selective pressure than the HIV-negative group. In conclusion, HIV-positive patients would have a more diversified HCV population than HIV-negative patients due to less selective pressure from the immune system.

Lack of integrated TT virus (TTV) genomes in cellular DNA in infected human hematopoietic cells

TT virus (TTV) isolated from the serum of a patient with posttransfusion hepatitis has been characterized as a member of the Circoviridae, a family of small DNA viruses with single-stranded circular genomes. TTV appeared to infect not only the serum and liver, but also the peripheral blood mononuclear cells (PBMC). We investigated the prevalence of TTV DNA in human hematopoietic cells, based on 84 mononuclear cell samples obtained from the bone marrow or lymph nodes of patients with hematopoietic malignancies including leukemia, malignant lymphoma and aplastic anemia. Forty-nine (58.3%) out of the 84 samples were positive for TTV DNA with polymerase chain reaction analysis, which was almost similar to the frequency found in the patients' serum. Southern blot analyses using a 3.2-kb fragment derived from the TTV DNA, however, showed no evidence supporting the fact that the TTV genomes are integrated into the human hematopoietic cell genomes, thus suggesting their existence as episomal forms.

Prognostic indicators of breakthrough hepatitis during lamivudine monotherapy for chronic hepatitis B virus infection

BACKGROUND

Breakthrough hepatitis (BTH), defined as a flare of transaminases alanine aminotransferase [ALT]) can occur during lamivudine monotherapy for hepatitis B virus (HBV) infection. There have been many reports of lamivudine-resistant mutations within the C domain of the viral reverse transcriptase; however, the appearance of these mutants is not necessarily correlated with BTH during lamivudine therapy.

METHODS AND RESULTS

Entire serial HBV genomic sequences before and during lamivudine therapy for 4 patients with BTH and 1 patient without BTH were analyzed and showed changes in the pre-S region. These changes may be associated with ALT flares. Further investigation in a cohort of 36 patients with a median treatment period of 25 months showed that 21 patients had a rise in HBV-DNA titer, of whom 18 had BTH. Univariate statistical analyses showed that possible prognostic indicators for the occurrence of BTH were pre-S deletions ( P = 0.03) and L180M/M204L mutations ( P = 0.04). By multivariate Cox regression analyses, significant variables were pre-S deletions (hazard ratio, 0.17; 95% confidence internal (CI), 0.044-0.66) and precore mutations (hazard ratio, 5.70; 95% CI, 1.74-18.71) prior to the commencement of lamivudine monotherapy. Interestingly, BTH occurred after the selection of the wild-type species in the pre-S region during lamivudine monotherapy.

CONCLUSIONS

These results suggest that patients with HBV pre-S deletion mutants should be monitored carefully during lamivudine therapy.

Identification of a novel 23kDa protein encoded by putative open reading frame 2 of TT virus (TTV) genotype 1 different from the other genotypes

We report the entire open reading frames (ORFs) sequences of four TT virus (TTV) isolates, one genotype 2 (G2) and three G4 isolates. Despite a DNA virus, TTV possesses high rate of amino acid (aa) substitution: the aa sequence homology of ORF1 and 2 is lower than the nucleotide homology. The partial 'N22' region of ORF1 is suitable for genotyping of 'prototype TTV' isolates, because the phylogenetic tree from partial 'N22' sequence is consistent with that from the entire ORF1. Based on our sequence data, ORF2 from most isolates excluding G1 encode truncated 49 aa (pORF2a) because of an in-frame stop codon, although ORF2s from most G1 isolates encode 202 aa (pORF2ab). Just downstream the stop codon, another ORF encoding a protein of approximately 150 aa (pORF2b) is found, whose homology is quite low among these genotypes. Our in vitro transcription/translation study supports that all G1a and a part of G b without an in-frame stop codon dominantly encode pORF2ab, a novel 23 kDa protein, whereas the other genotypes with an in-frame stop codon encode pORF2b (17 kDa). Our data indicate TTV G1a and a part of G1b should have different characteristics from the other genotypes.