Classifying hepatitis B virus genotypes

Co-Infection with Hepatitis B Virus Genotype D and Other Genotypes in Western Japan

OBJECTIVE

Genotypes B and C are the prevalent hepatitis B virus (HBV) genotypes in eastern Asia. Although very rare in this region of the world, genotype D was found to be prevalent in a small area of western Japan. In this study, we confirm the frequency and clinical significance of co-infection with different genotypes among patients from that area infected with genotype D.

METHODS

Twenty-three patients from the same area of western Japan infected with HBV genotype D, determined using a genotyping enzyme immunoassay, were studied. Cloning was done using DNA extracted from serum samples, and polymerase chain reaction assays with the restriction fragment length polymorphism for HBV genotyping were performed with 10 clones from each patient.

RESULTS

Four (17.4%) of the 23 patients were found to be co-infected with HBV genotype C, and the HB surface antigen subtype was ayw in both mono- and co-infected patients. No clinical differences were found between mono-infected and co-infected patients carrying genotype D.

CONCLUSION

A significant number of patients from the study area found to be infected with HBV genotype D were co-infected with genotype C. Additional study with a larger number of patients is needed to elucidate the possible clinical significance.

A new intertype recombinant between genotypes C and D of hepatitis B virus identified in China

Hepatitis B virus (HBV) genotypes have a characteristic geographical distribution. More than 90 % of chronic HBV patients in China are infected with genotypes B or C. Here, eight HBV isolates that were initially classified as genotype D by PCR-restriction fragment length polymorphism analysis were analysed in detail. The complete HBV genome was sequenced and compared with 32 sequences retrieved from GenBank, representing HBV genotypes A–G. Phylogenetic analysis of the S gene (nt 10–800) classified all eight isolates as genotype D. However, phylogenetic analyses of nt 800–10 and the open reading frames (ORFs) of the precore/core and X genes classified all eight isolates as genotype C. This discordance between phylogenetic trees reconstructed on different ORFs suggested that intertype recombination has occurred in all eight isolates. By using the simplot program, the site of recombination with genotype D was located in the preS2/S region, spanning nt 10–799 in seven of eight isolates and nt 10–1499 in the other isolate. These results demonstrate that intertype recombination should be considered as a type of variation that increases the genetic diversity of HBV. Hybrids of different HBV genotypes might exhibit specific virological properties and their significance in the diagnosis and management of chronic hepatitis B deserves further investigation.

The prevalence and evolution of sex in microorganisms

The origin of sex and how sex is maintained are among the biggest puzzles in biology. Most investigations into this problem have focused on complex eukaryotes like animals and plants. This mini-review summarizes recent progress in our understanding of the evolution of sex, highlighting results from studies of experimental and natural populations of microorganisms. Increasing evidence indicates that sexual reproduction in natural populations of viruses, bacteria, and eukaryotic microbes is much more prevalent than previously thought. In addition, investigations using experimental microbial populations are providing important parameters relevant to our understanding of the origin and maintenance of sex. It is argued that microbes are excellent model organisms to explore the mechanisms responsible for the evolution of sex.

Comparison of full length sequences of hepatitis B virus isolates in hepatocellular carcinoma patients and asymptomatic carriers of Korea

Relatively few genomic sequences of Korean hepatitis B virus (HBV) isolates are available. Moreover, no comparative study has been made between the full-length genomes of Korean HBV isolates and clinical status. To evaluate mutations in HBV isolates obtained from chronically infected HBV patients in terms of clinical significance, we determined the genomic sequences of HBV isolates obtained from three hepatocellular carcinoma (HCC) patients (He52, He53, and He82) and from three asymptomatic carriers (He74, He100, and He127). A comparison of sequence variations showed that the HBV isolates from the three HCC patients showed higher frequencies of mutation than the isolates from the three asymptomatic carriers. Three characteristic mutation patterns were identified in the HBV isolates from the HCC patients, which distinguished the HBV isolates from the asymptomatic carriers. First, HBV isolates from the three HCC patients both had double mutations in a core promoter (T1762/A1764) and a precore mutation (A1896). Second, although these isolates belonged to genotype C, 11 amino acids deletions in the preS1 region, specific for HBV genotype D, were detected in the isolates of two HCC patients (He52 and He82). Third, mutations (I127T/N, K130M, and V131I) at three codons in the carboxy functional region of X protein were observed in isolates from all three HCC patients. Additionally, phylogenetic analysis based on the entire HBV sequences showed that all six isolates belonged to genotype C2, as do other Korean strains.

Hepatitis B virus: significance of genotypes

Hepatitis B Virus (HBV) genotypes have come of age. The concept that HBV genotypes may influence the course of disease and relevant biological differences has now been recognised. However, there are still major gaps in our knowledge. Most clinical data come from Asia and describe findings in patients infected with genotypes B and C. Large scale studies with genotypes A and D as found in Europe or A, D and E from Africa are urgently needed to broaden our understanding. Experimental data which explain in vivo findings in terms of differences in molecular biology in vitro are still in the beginning. The succeeding years will see many interesting studies which will aid our understanding of how variants and genotypes of HBV influence the spectrum of disease in people infected with HBV.

Hepatitis B virus genotypes

Eight genotypes of hepatitis B virus (A-H) are currently recognized, and subgenotypes have recently been described in four of these genotypes (A, B, C and F). The genotypes show a distinct geographical distribution between and even within regions, and are proving to be an invaluable tool in tracing the molecular evolution and patterns and modes of spread of hepatitis B virus. Structural and functional differences between genotypes can influence the severity, course and likelihood of complications, and response to treatment of hepatitis B virus infection and possibly vaccination against the virus. Although the number of studies on these genotypes has increased dramatically during recent years, much remains to be learnt about their full implications.

Hepatitis B virus genotypes and precore mutations in Scottish blood donors

BACKGROUND AND OBJECTIVES

This study was carried out to determine the frequency of hepatitis B virus (HBV) core promoter variants (nucleotide positions 1762, 1764) and precore variants (nucleotide position 1896) in hepatitis B surface antigen (HBsAg)-positive Scottish blood donors. HBV genotypes present in this population were also identified.

MATERIALS AND METHODS

A total of 85 HBsAg-positive blood donor samples were included in the study. Of these, 79 were polymerase chain reaction (PCR) positive and had sequence and mutation information. They were divided into two groups: group 1 (23 individuals) were hepatitis B e antigen (HBeAg)-positive and negative for antibody to HBe (anti-HBe); and group 2 (56 individuals) were HBeAg negative and positive for anti-HBe. A line probe assay was used to detect mutations, and a comparison was made by using direct sequence analysis. A different line probe assay was used to identify HBV genotype.

RESULTS

The frequencies of mutations in group 1 were 22% each for mutations 1762, 1764 and 1896, increasing to 26%, 35% and 55% in group 2, respectively. By contrast, direct sequence analysis failed to identify 70% of wild-type/mutant mixes. The prevalence of viral genotypes was 41% for genotype A, 12% for genotype B, 5% for genotype C, 30% for genotype D and 12% for mixed-genotype infections. Precore mutations were seen in 10%, 88%, 25% and 74% of genotypes A, B, C and D, respectively.

CONCLUSIONS

The results indicate that core promoter and/or precore mutants may be under-reported. The combination of HBV PCR and line probe assays is useful for supplementing HBV serological tests. Non-Caucasian genotypes are present in the UK blood-donating population and will therefore affect the demographics of HBV infection.

Tracing the history of hepatitis B virus genotype D in western Japan

The major hepatitis B virus (HBV) genotypes in Japan are B and C. HBV genotype D (HBV/D), however, is widespread in a small area of Western Japan, where the Gianotti-Crosti syndrome caused by HBV subtype ayw, which is suspected to be HBV/D, was endemic in the 1970s. The aim of the study was to elucidate its origin, time of transmission, and spread in this area. Genotyping of HBV-DNA was done in 363 patients with HBV infection. The year of birth was checked in patients with HBV/D. The full genome sequences of 20 HBV/D strains, 2 of which were obtained from a single carrier with a 19-year-interval, were analyzed. An evolutionary rate, the date of the most recent common ancestor, and the effective number of HBV/D infections were calculated. Fifty-two of 363 patients were infected with HBV/D, and 39 were born in 1970s. In a phylogenetic tree, the 20 HBV/D strains produced a definite cluster, and the evolutionary rate was calculated to be 5.4 x 10(-5) nucleotide substitutions/site/year. The root of the tree was estimated to be in approximately 1,900 and began to spread from the 1940s, leading to a rapid increase of infected patients in the 1970s. From these results, it is suspected that HBV/D was likely transmitted to the area investigated approximately 100 years ago and then spread widely in the 1970s. From the history of the area and the genetic analysis, HBV/D in this area was speculated to be of Russian origin.

Virological outcomes in patients infected chronically with hepatitis B virus genotype A in comparison with genotypes B and C

In a single hospital in Tokyo, the 87 patients infected persistently with hepatitis B virus (HBV) genotype A, the 413 with B, and the 3,389 with C were compared for virological outcome. Hepatitis B surface antigen (HBsAg) was cleared from the serum in 12% (3/26), 2% (2/112), and 3% (23/826) of patients with genotypes A, B, and C, respectively, at 5 years of follow-up (P = 0.0395). Hepatitis B e antigen (HBeAg) was cleared from serum more frequently in patients with genotype B than those with A or C (78% [32/41] vs. 58% [11/19] or 45% [251/562], P = 0.00001) at 5 years. Of the 45 individuals infected with genotype A and followed for 3 years or longer, HBeAg was more frequent (16% [3/19] vs. 73% [19/26], P = 0.0002) and levels of HBV DNA higher (median <2.6 [range: <2.6-5.6] vs. >7.6 [<2.6->7.6] log copies/ml, P = 0.001) in the 26 patients with biopsy-proven chronic hepatitis than the 19 asymptomatic carriers. Among the 26 hepatitis patients infected with HBV genotype A, decreases in HBV DNA were less frequent (20% [1/5] vs. 93% [13/14] or 86% [6/7], P = 0.0095) and increases in serum levels of hyaluronic acid > or =10 ng/ml commoner (80% [4/5] vs. 14% [2/14] or 14% [1/7], P = 0.017) in the patients who kept HBeAg than in those who seroconverted or who remained HBeAg-negative. In conclusion, patients persistently infected with HBV genotype A fare better than those with genotype B or C. However, high levels of HBV DNA continue in those in whom HBeAg persists along with fibrosis in the liver.

Influence of hepatitis B virus genotypes on the response to antiviral therapies

Hepatitis B virus (HBV) has been classified into eight genotypes (A-H) based on genome sequence divergence. Genotypes of HBV have distinct geographical distributions, and two genotypes account for most HBV worldwide. Hepatitis B e antigen expression lasts longer and liver disease is more severe with graver outcomes in carriers of genotype C than B in Asia. Accumulating lines of evidence indicate a better response to interferon and lamivudine in patients with chronic hepatitis B who are infected with genotype B rather than C. The therapeutic response may differ, however, in patients infected with HBV of the same genotype. For example, the response to lamivudine is poorer in patients infected with subtype Ba, which contains a recombination with genotype C, than in those with subtype Bj without such a recombination. Influence of genotypes on therapeutic response needs to be examined in patients infected with the other genotypes, particularly in those with genotype A or D infection.

YMDD mutants in patients with chronic hepatitis B before treatment are not selected by lamivudine

Hepatitis B virus (HBV) mutants with mutations in the YMDD motif of viral DNA polymerase/reverse transcriptase are described in patients infected with HBV who have not received lamivudine therapy, but their pathogenetic potential is not clear. These mutants were detected by the polymerase chain reaction with peptide nucleic acid clamping in pretreatment sera from two patients who later received lamivudine. One patient developed acute exacerbation with hepatic encephalopathy and received lamivudine along with plasma exchange, which were effective on his illness. YIDD mutants were detected in all three pretreatment sera and both posttreatment sera from him. HBV DNA clones from pretreatment and posttreatment sera, however, did not have the same amino acid sequence. In the other patient who developed severe breakthrough hepatitis after receiving lamivudine, YIDD mutants were detected in two pretreatment and two posttreatment sera. When amino acid sequences of HBV DNA clones with the YIDD mutation were compared before and after he received lamivudine, however, they were not in accord. Hence, YIDD mutants in both patients with chronic hepatitis B before treatment were not selected by lamivudine after they had been placed on it. Numerous amino acid conversions were detected in HBV DNA clones with YIDD mutations, and some of them created stop codons in the overlapping S gene sequence. In Conclusion, HBV mutants with mutations in the YMDD motif in patients before treatment would not be selected by lamivudine or induce breakthrough hepatitis, and some of these would not be replication-competent due to stop codons in the S gene.

Highly reproducible transient transfections for the study of hepatitis B virus replication based on an internal GFP reporter system

High throughput studies of hepatitis B virus (HBV) replication are limited by the absence of convenient and reliable in vitro systems that can be utilised to examine mutations emerging as a consequence of selective pressures such as drug therapy, immune response and genotypic evolution. We have developed an efficient and reproducible method of transfecting a human hepatoma cell line (Huh7) with a replication competent clone of HBV, which utilises an internal reporter of transfection efficiency. Wild type (WT) and a common lamivudine (LMV) resistant mutant virus characterised by a methionine to isoleucine mutation in the highly conserved YMDD motif of the polymerase gene were used to highlight the utility of this in vitro transfection procedure in studying common HBV mutations. The presence of an internal GFP reporter increased the efficiency of generating highly reproducible results and facilitated multiple forms of analysis from a single transfection accurately.

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.

Eight genotypes (A-H) of hepatitis B virus infecting patients from San Francisco and their demographic, clinical, and virological characteristics

Clinical lines of evidence have been accumulated that hepatitis B virus (HBV) genotypes have characteristic geographical distributions and distinct clinical impact on liver diseases. The distribution of HBV genotypes was determined with reference to hepatitis B e antigen (HBeAg) and alanine aminotransferase (ALT) levels in 165 patients with hepatitis B in San Francisco. HBV genotypes were determined by enzyme-linked immunosorbent assay (ELISA) and the unclassified samples were sequenced within the S region for phylogenetic analysis. Genotype A occurred in 60 (36%) patients, B in 16 (10%), C in 56 (34%), D in 19 (12%), E in 1 (1%), F in 1 (1%), G in 8 (5%), and H in 4 (2%). Caucasians were infected predominantly with HBV genotype A (HBV/A) (38 of 57 [67%]), Asians with HBV/C (45 of 63 [71%]), and Hispanics with HBV/F and HBV/H (4 of 9 [44%]). Serum ALT levels were higher in the patients infected with HBV/A (P = 0.03) or HBV/G (P = 0.02) than HBV/C. HBeAg was more frequent in patients infected with HBV/G than HBV/C or HBV/D (7 of 8 [88%] vs. 25 of 56 [45%] or 6 of 19 [32%], P = 0.03 or 0.01). In conclusion, eight genotypes (A-H) were identified in San Francisco in association with various ethnicities and then influenced ALT levels as well as the prevalence of serum HBeAg. HBV genotype H might be identified by combination of preS2 serotpe bksf and HBsAg serotype adw.

Epidemiology of HBV genotypes by nested PCR with multi-paired primers

AIM: To investigate the epidemiology of HBV genotypes among HBV-infected persons in northern China.

METHODS: The HBV DNA in 801 sera samples collected from hepatitis patients (594), healthy controls (154), and HCV-infected patients (53) were tested by nested PCR, the positive sera were then genotyped by nested PCR with six pairs of HBV genotype-specific primers (A to F).

RESULTS: 464 samples (57.9%) were HBV DNA positive among the 801 samples. Among 594 cases with various hepatitis B clinical manifestations, 74.4% (442/594) were HBV-DNA positive, while 8.4% (13/154) of healthy controls were HBV-DNA positive. There was significant difference between the hepatitis patients and healthy controls (P < 0.01). 17% (9/53) of HCV-infected patients were HBV-DNA positive, too. Among the 464 HBV-DNA positive samples, the persentage of genotype A was 5.2% (24/464), genotype B 7.1% (33/464), and type C 77.2% (358/464), type D 2.4% (11/464), while none of type E and F had been found in those samples. 14 samples (3%) were both type B and C positive. The 24 samples could not be genotyped in this study.

CONCLUSION: The HBV genotypes prevailed among HBV-infected persons in northern China are types A, B, C, and D, and the major genotype is type C (77.2%). Type C is also the major genotype among the clinical groups. There is no statistical difference between the groups.

Functional implications of the spectrum of mutations found in 234 cases with X-linked juvenile retinoschisis. The Retinoschisis Consortium

X-linked retinoschisis (XLRS) is the most common cause of juvenile macular degeneration in males, resulting in vision loss early in life. The gene involved in XLRS was identified recently. It encodes a protein with a disoidin domain, suggested to be involved in cell-cell interactions. We have screened the gene for mutations in 234 familial and sporadic retinoschisis cases and identified 82 different mutations in 214 (91%). Thirty one mutations were found more than once, i.e. 2-10 times, with the exception of the 214G-->A mutation which was found in 34 apparently unrelated cases. The origin of the patients, the linkage data and the site of the mutations (mainly CG dinucleotides) indicate that most recurrent mutations had independent origins and thus suggest the existence of a significant new mutation rate in XLRS1. The mutations identified cover the entire spectrum, from small intra-genic deletions (7%), to nonsense (6%), missense (75%), small frameshifting insertions/deletions (6%) and splice site mutations (6%). Since, regardless of the mutation type, no females with a typical RS phenotype were identified, RS seems to be caused by loss-of-function mutations only. Mutations occurred non-randomly, with hotspots at several CG dinucleotides and a C6stretch. Exons 1-3 contained few, mainly translation-truncating mutations, arguing against an important functional role for this segment of the protein. Exons 4-6, encoding the discoidin domain, contained most, mainly missense mutations. An alignment of 32 discoidin domain proteins was constructed to reveal the consensus sequence and to deduce the functional importance of the missense mutations identified. The mutation analysis revealed a high preponderance of mutations involving or creating cysteine residues, pointing to sites important for the tertiary folding and/or protein function, and highlights several amino acids which may be involved in XLRS1-specific protein-protein interactions. Despite the enormous mutation heterogeneity, patients have relatively uniform clinical manifestations although with great intra-familial variation in age at onset and progression.