Complete genome sequence and phylogenetic analysis of hepatitis B virus (HBV) isolates from patients with chronic HBV infection in Korea

Although there is a report of high rate of hepatitis B virus (HBV) infection in South Korea, only a few entire genome sequences of HBV isolates from Korea have been reported. To obtain the complete nucleotide sequence of the Korean HBV, viral DNA was extracted from sera of Korean patients with chronic HBV infection who have not been exposed to any antiviral treatment. Complete genomic sequences were determined on three Korean HBV isolates. The entire genomic length of Korean HBV isolates, designated as KUHB84, KUHB81, and KUHB95, was 3,215 base pairs. No deletions and insertions were observed. Core promoter mutations (T1762/A1764) were detected in two isolates, KUHB84 and KUHB95. Phylogenetic analysis based on the entire genomic sequences showed that the Korean HBV isolates were genotype C and related closely to the Japanese HBV.     

Distribution of hepatitis B virus (HBV) genotypes among HBV carriers in the Cote d'Ivoire: complete genome sequence and phylogenetic relatedness of HBV genotype E

The characteristics of hepatitis B virus (HBV) genotype E are not well known because only a few studies have been carried out by complete genome analysis. The aim of this study was to elucidate the distribution of HBV genotypes in Cote d'Ivoire, and to clarify the genotype-related characteristics of genotype E. The distribution of HBV genotypes among 48 HBV carriers in Cote d'Ivoire was determined using serological and genetic methods. The characteristics of genotype E were evaluated by complete genome sequences, and further investigations of small S gene, basic core promoter (BCP) mutation, and precore mutation were undertaken. HBV genotype distribution among the 48 carriers was 6.3% for genotype A, 6.3% for genotype D, and 87.4% for genotype E. Complete genomes of two genotype E strains were sequenced, and found to have 98.2% to 99.2% homology at the nucleotide level when compared with genotype E strains reported previously. In 24 genotype E carriers, the precore mutation was detected in 75% of the patients without HBeAg, in contrast to only 25% of the patients with HBeAg (P < 0.05). All 24 strains have T at nucleotide 1858 in the precore region. In contrast, BCP double mutation was detected in 17% of the patients with HBeAg, and 33% of the patients without HBeAg. These results indicated as the following: (1) genotypes A, D, and E of HBV exist in Cote d'Ivoire and genotype E is the most prevalent; (2) genotype E spread with low genetic diversity over the complete genome in West Africa; (3) HBV precore and/or BCP double variants were common among the patients with genotype E infections.     

Genotype characterization and phylogenetic analysis of hepatitis B virus isolates from Iranian patients

Hepatitis B virus (HBV) is one of the major causative agents of acute and chronic liver disease worldwide and is believed to be responsible for a million deaths annually. Eight genotypes of HBV, A to H, have been described on the basis of similarity of the complete genomes sequence. Although, it is reported that the predominant HBV genotype in the Mediterranean area and the middle east is genotype D, there are no reports on HBV genotypes prevalent in Iran. In this study, the C and S regions of HBV from 26 chronic hepatitis B Iranian patients were amplified and sequenced. Phylogenetic analysis revealed that all Iranian HBV isolates sequences were classified into genotype D with bootstrap values of 100%, 73%, and 100% (1,000 replicates each) for S, C, and preS2 regions, respectively. The mean percent intra-distance of S and C regions were 0.8% and 2.3%, respectively. The mean percent inter-distance of S and C regions between Iranians and genotype D isolates were 1.7% and 3.0%, respectively, and the range of mean percent nucleotide distance of S and C regions between Iranians and the other reference isolates were 7.9%-17.5% and 4.8%-14.7%, respectively. Thirteen out of 23 HBV C region sequences showed nucleotide "A" at position 1896 (precore mutant) in C region. Nucleotide 1858 showed presence of "T" in all isolates. No insertion or deletion was found in both regions. SimPlot and BootScanning analyses did not show any recombination between Iranian isolates and other genotypes in both regions.     

Complete genomic sequence and phylogenetic relatedness of hepatitis B virus isolates from Iran

Hepatitis B virus (HBV) is one of the main etiological agents of acute and chronic liver disease that is still a major public health problem in the world. Numerous HBV isolates have grouped into eight genotypes, A to H, based on the complete genome sequence. To date, no study has been carried out on the complete HBV genome sequence in Iran. The objective of this study was to investigate the complete genome sequence organization and phylogenetic analysis of the five HBV strains, which obtained from Iranian chronic infected patients. Results showed that Iranian strains were closely related to each other, with 97-100% nucleotide similarity. Phylogenetic analysis based on the complete genome sequences and the precore/core gene sequences revealed that all strains were of genotype D, sub-genotype D1 with bootstrap value 100 and 99%, respectively. The S gene encoded Arg122, Pro127, and Lys160 corresponding to subtype ayw2. Iranian HBV isolates had closely related with Turkish HBV strains. All strains had a nucleotide length of 3,182 base pair (bp) except IR-P4 strain, with a 3,185 bp in length and with a unique Phe89 insertion in the X gene. The intragenotypic divergence of the complete genome sequence of Iranian strains was 1.8% and the intergenotypic in genotype D was 3.8% and with the other genotypes was 7.9-15.4%. In conclusion, this study revealed that the HBV genotype D, sub-genotype D1, subtype ayw2 dominates in the Iranian infected patients. A single Phe89 insertion in the X gene of the one Iranian strain with an unforeseen length of 3185 bp was identified.     

Hepatitis B virus infection of peripheral blood mononuclear cells is common in acute and chronic hepatitis

Hepatitis B virus (HBV) infection of peripheral blood mononuclear cells (PBMCs) has been observed in all stages of liver disease. Thus far all information about the physical state of HBV in mononuclear blood cells comes from Southern blot analysis and in situ hybridization. In this study we focused our attention on the presence of HBV DNA sequences in PBMCs of 30 patients with acute type B hepatitis and 6 patients with chronic active hepatitis by utilizing both Southern blot analysis and the polymerase chain reaction (PCR). Southern blot analysis showed no HBV DNA sequences in PBMCs of the acute hepatitis patients, although the sensitivity of our method enabled us to detect as little as 1 pg of cloned HBV insert. As far as the chronic hepatitis patients are concerned Southern blot analysis revealed the presence of HBV DNA sequences in 5 out of 6 patients but intermittently at successive follow-up times. On the other hand we were able to demonstrate the presence of HBV related sequences in 14 out of 30 acute hepatitis patients (5 HBeAg positive, 9 antiHBe positive) and in all 6 chronic hepatitis patients by PCR. Our results indicate that the involvement of PBMCs with HBV during acute HBV infection occurs at a very low level, often below the detection limit of the Southern blot technique.     

Hepatitis B virus DNA in sera of virus carriers positive exclusively for antibodies to the hepatitis B core antigen

The prevalence of serum HBV DNA in individuals positive for anti-HBc alone was determined by the polymerase chain reaction in two groups with endemic HBV infection from Canton (group A) and Hainan (group B), provinces of China. Twenty-one out of 294 individuals in group A (7.2%) and 193 out of 1995 in group B (9.7%) were positive for anti-HBc but negative for other markers of ongoing or past HBV infection (HBsAg and anti-HBs). HBV DNA was detected in 6/21 sera in group A (28.6%) and 68/193 in group B (35.2%) in their initial serum specimen. One of the six HBV-DNA-positive individuals in group A became negative after 6 months and four of the 58 positive in group B became negative at 4 years of follow-up. All of the individuals remained positive for anti-HBc and negative for anti-HBs, but one of them became positive for HBsAg on follow-up. None of the anti-HBc- and HBV-DNA-positive subjects had symptoms of liver diseases. They were, therefore, defined as chronic asymptomatic HBV carriers with undetectable HBsAg. This type of carrier should be added to the typical HBsAg-positive carrier, who constitutes about 10-15% of the general Chinese population, to give a more complete estimate of asymptomatic HBV carriers in China.     

Dominant replication of either virus in dual infection with hepatitis viruses B and C

To characterize the state of dual infection with hepatitis B virus (HBV) and hepatitis C virus (HCV), HBV-DNA and HCV-RNA levels were determined by spot hybridization or polymerase chain reaction in the sera of patients who were positive for both hepatitis B surface antigen and HCV antibody. Among 27 patients who showed evidence of double infection, 21 (77.8%) had detectable levels of only either HBV or HCV genome in their sera, 2 (7.4%) showed none of the viral genomes, and 4 (14.8%) had both HBV-DNA and HCV-RNA. In the 4 patients with both HBV-DNA and HCV-RNA, the titers of HCV-RNA or HBV-DNA were lower than those in the patients with HCV-RNA or HBV-DNA alone. In some patients with chronic hepatitis, the viruses appeared to replicate in turn in the course of the disease. These results indicate that the viruses show alternating dominance in replication in most of the patients who have dual infection with HBV and HCV, probably due to interference of the viruses. © 1995 Wiley-Liss, Inc.     

慢性乙型肝炎与HLA-DRB1等位基因相关性的研究

目的探讨慢性乙型肝炎与HLA-DRB1等位基因多态性之间的 关系。方法采用聚合酶链反应/序列特异性引物（PCR/SSP）技术对52例 慢性乙型肝炎和106例正常人的HLA-DRB1等位基因多态性进行了分析。结果HLA-DRB1*0301在慢性乙型肝炎组的等位基因频率明显高于对照组（17.13% vs 5.67%, χ2=12.306 8, Pc=0.007 4, RR=4.15）。HLA-D RB1*1101/1104在慢性乙型肝炎组的等位基因频率明显低于对照组（0.96% vs 6.13%, χ2=4.619 6, RR=0.14），但经较正后，Pc＞0.05。其他等位基因频率在实验组 和对照组间差异无显著性。结论H LA-DRB1*0301与慢性乙型肝炎的易感性呈正相关，可能是慢性乙型肝炎的易感基因。     

Complete genome sequence and phylogenetic analysis of hepatitis B virus (HBV) isolated from Mongolian patients with chronic HBV infection

Although there is a report of a high rate of hepatitis B virus (HBV) infection in Mongolia, the entire nucleotide sequence of HBV circulating among Mongolian patients has not been reported. To obtain the complete nucleotide sequence of the Mongolian HBV, viral DNA was extracted from sera of patients with HBV infection. Six Mongolian HBV strains were amplified by PCR. Complete genomic sequences were determined for two Mongolian HBV isolates, MBT181 and MMU36. The entire genome of Mongolian HBV isolates was 3,182 bp long and genetic distance between Mongolian HBV isolates was 3.2%. Precore stop codon resulting from a guanine to adenine mutation at nucleotide 1,896 was detected in MBT181 strain. Based on phylogenetic analysis, the six Mongolian isolates were classified as genotype D.     

Prevalence of hepatitis-C virus RNA in serum and throat washings of children with chronic hepatitis

Serum samples from 46 children with chronic and probably transfusion acquired hepatitis were tested for the presence of hepatitis C virus (HCV) RNA by a “nested” polymerase chain reaction (PCR) assay, to judge a possible risk of HCV transmission from these patients. In 73% of the samples, viral RNA was detected, indicating a high virus prevalence in this patient group. High titers of HCV-RNA were observed in some sera as shown by the detection of virus in some samples even at dilutions of 10^?3. Comparison of simultaneously obtained PCR results and ALT values revealed no significant correlation between virus presence in serum and higher ALT levels. It was, however, shown that unusually high ALT values may reflect a high titer of viral RNA in serum. To investigate the prevalence of viral RNA in saliva, which could be a vehicle of virus transmission, 35 throat washing samples from the HCV-infected children were screened by PCR. Using three different sample preparation procedures, 20% of the throat washings were found to be positive for HCV-RNA. This indicates a prevalence of virus in this fluid lower than that reported previously. © 1994 Wiley-Liss, Inc.     

Analysis of the complete hepatitis B virus genome in patients with genotype C chronic hepatitis in relation to HBeAg and anti-HBe

To investigate the relationship between viral factors and the development of chronic hepatitis B, the entire hepatitis B virus (HBV) genome of chronic carriers at different disease stages were analyzed. Eighty genotype C HBV carriers including 12 hepatitis B e antigen (HBeAg) positive asymptomatic carriers (Group A), 49 HBeAg positive patients with chronic liver diseases (Group B) and 19 anti-HBe positive patients with chronic liver diseases (Group C) were studied. HBV nucleic acid from serum samples was sequenced directly and compared with GenBank reference sequences HBV X01587 and M12906. On phylogenetic analysis, 76 cases were genotype C2. Of the 76 genotype C2 cases, the nucleotide and amino acid substitution rates in the precore/core region were significantly higher in Groups B and C than in Group A, also in Group C than in Group B. The nucleotide substitution rates in the full genome and the core promoter region were significantly higher in Group C than in Group A, also in group C than in Group B. The nucleotide and amino acid substitution rates in the X region were significantly higher in Group C than in Group A. The amino acid substitution rate in the pre-S2 region was significantly higher in Group C than in Group B. Deletion mutations were found mainly in Groups B and C. This whole genome analysis of HBV chronic carriers suggested that the nucleotide substitutions and deletions in HBV were closely associated with the pathogenesis of chronic HBV infection.     

Specific deletions in the hepatitis B virus core open reading frame in patients with chronic active hepatitis B

The polymerase chain reaction (PCR) and DNA sequencing were used to examine genomic variation in the pre-core/core open reading frame of the hepatitis B virus (HBV) in chronically infected patients. Gel electrophoresis of amplification products showed the presence of shortened forms of the core gene in addition to the full length product. These shortened forms were seen only in patients with chronic active hepatitis (CAH) seropositive for HBeAg and not in patients with chronic persistent hepatitis (CPH) or HBeAg minus CAH. Cloning and DNA sequencing revealed the presence of a number of overlapping deletions within the core gene, the majority being in-frame, which were clustered within aa 81-114 of the core gene product. These deletions were found in patients with CAH from different racial and geographical backgrounds, whereas PCR analysis of the surface and ×open reading frames showed no shortened forms suggesting deletions to be specific to the core gene in these patients. Because the product of the core gene-the HBV core antigen–is believed to be the major target for T-cell-mediated liver damage, it seems likely that the products of core genes carrying deletions will alter immune recognition and may be of importance in the progression of inflammatory liver damage.     

Age-specific prevalence and significance of hepatitis B e antigen and antibody in chronic hepatitis B virus infection in Taiwan: a comparison among asymptomatic carriers, chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma

The age-specific prevalence of hepatitis B e antigen (HBeAg) and its antibody (anti-HBe) were studied by radioimmunoassay, and compared in a large series of patients with chronic hepatitis B virus (HBV) infection, including 268 asymptomatic carriers, 389 chronic hepatitis, 114 liver cirrhosis, and 278 hepatocellular carcinoma (HCC). The prevalence of HBeAg/anti-HBe in asymptomatic carriers and patients with chronic hepatitis correlated closely with age as HBeAg prevalence decreased and anti-HBe prevalence increased with increasing age (P less than 0.0005), and is probably due to high infection rate at young age in Taiwan. The prevalence of HBeAg in patients with both cirrhosis and HCC are much significantly lower and had no correlation with age. Two peaks of age-specific prevalence of HBeAg and anti-HBe were observed in patients with HCC, implicating two patterns of HBV infection in these patients. The difference in the prevalence of HBeAg and anti-HBe might indicate that asymptomatic carriers, chronic hepatitis, liver cirrhosis, and HCC are sequential sequelae of HBV infection.     

Hepatitis B virus C gene heterogeneity in a familial cluster of anti-HBc negative chronic carriers

We studied a familial cluster of adult HBV chronic carriers characterized by serological markers of active viral replication, normal or slightly elevated ALT levels and, in four out of five cases, absence of anti-HBc reactivity. The nucleotide sequence of the pre-C/C region of HBV was analyzed in three patients, showing the presence of wild-type HBV sequences accompanied by different deleted molecules. Some of the variant genomes were able to encode proteins retaining HBcAg and/or HBeAg reactivity, whereas others contained deletions leading to the synthesis of truncated proteins that could not be immunoprecipitated by anti-HBc or anti-HBe mono- and polyclonal antibodies. Defective molecules encoded by the variant C gene sequences might play a role in the determination of the clinical profile observed in the analyzed patients. © 1994 Wiley-Liss, Inc.     

The absence of hepatitis B virus DNA in hepatitis B e antigen positive sera from chronic hepatitis B surface antigen carriers in China

Sera from 20 Chinese patients with chronic hepatitis B were examined for hepatitis B e antigen and hepatitis B virus (HBV) DNA. There was considerable discordance with HBV DNA not being detectable in 10 out of 13 (77%) patients who were hepatitis B e antigen positive. Further testing for anti-HBe and HBV-DNA polymerase activity confirmed the results. Possible reasons for this discordance are discussed but neither hepatitis D (delta) infection nor the acquired immunodeficiency syndrome (AIDS) could be implicated.     

II. Existing variations on the gene structure of hepatitis E virus strains from some regions of China

The isolation and identification of the 87A strain of hepatitis E virus (HEV) by means of cell culture have been described previously. This paper reports the nucleotide sequence of a portion of this HEV strain. The RNA extracted from the supernatants of the different passages of the 87A strain cultured in the A549 cell line was reverse-transcribed (RT) to cDNA, and then the polymerase chain reaction (PCR) amplification was carried out using the primers of HEV ET1.l region. The PCR products from 1) the supernatant of the infected cells at the fourth passage, 2) the virus concentrated by polyethylene glycol (PEG) precipitation at the tenth passage, and 3) the virus purified by a sucrose gradient at the tenth pas sage were sequenced. In addition, three other PCR products obtained from sera of acute hepa titis E patients in Beijing (B-9) and Guangzhou (G-9 and G-20) were also sequenced. The nucle otide sequences of the above four strains of HEV (located in the genome from positions 4545–4754) were compared to those of some reported HEV strains. The nucleotide sequences of the B-9 strain and the 87A strain were similar to the Burmese strain and may belong to the same branch of HEV. The nucleotide sequences of the G-9 strain and the G-20 strain were a novel and unique branch. The Chinese HEV strains are multiplex and variable in gene structure. © Wiley-Liss, Inc.     

Distribution of hepatitis B virus in the liver of chronic hepatitis C patients with occult hepatitis B virus infection

Although occult hepatitis B virus (HBV) infection (HBV-DNA in serum in the absence of hepatitis B surface antigen [HBsAg]) is common in chronic hepatitis C, its characteristics are not well known. In this work, the presence of HBV-DNA (by polymerase chain reaction; PCR) and its distribution (by in situ hybridization) in liver biopsies and peripheral blood mononuclear cells (PBMCs) from 32 patients with chronic hepatitis C and occult HBV infection and in 20 HBsAg chronic carriers were determined. The results showed that serum HBV-DNA levels were statistically lower (P = 0.001) in patients with occult HBV infection than in HBsAg chronic carriers. The HBV infection pattern in liver cells was identical between patients with occult HBV infection and those with chronic hepatitis B. However, the mean percentage of HBV-infected hepatocytes was significantly lower (P = 0.001) in patients with occult HBV infection (5 +/- 4.44%) than in HBsAg chronic carriers (17.99 +/- 11.58%). All patients with chronic hepatitis B have HBV-DNA in their PBMCs while this occurred in 50% of the cases with occult HBV infection. In conclusion, patients with occult HBV infection have a low number of HBV-infected hepatocytes and this fact could explain the lack of HBsAg detection and low viremia levels found in these cases.