Classification of hepatitis B virus genotype B into 2 major types based on characterization of a novel subgenotype in Arctic indigenous populations

Rate and durability of the clearance of HBsAg in Alaska Native persons with long-term HBV infection: 1982-2019

BACKGROUND AND AIMS

A functional cure and therapeutic end point of chronic HBV infection is defined as the clearance of HBsAg from serum. Little is known about the long-term durability of HBsAg loss in the Alaskan Native population.

APPROACH AND RESULTS

We performed a retrospective cohort study of Alaska Native patients with chronic HBV-monoinfection from January 1982 through December 2019. The original group in this cohort was identified during a 1982 to 1987 population-based screening for 3 HBV serologic markers in 53,000 Alaska Native persons. With close to 32,000 years of follow-up, we assessed the frequency and duration of HBsAg seroclearance (HBsAg-negative for > 6 mo). We examined factors associated with HBsAg clearance and followed persons for a median of 13.1 years afterward to assess the durability of HBsAg clearance. Among 1079 persons with an average length of follow-up of 33 years, 260 (24%) cleared HBsAg at a constant rate of 0.82% per person/per year. Of the 260 persons who cleared, 249 (96%) remained HBsAg-negative, while 11 persons had ≥ 2 transient HBsAg-positive results in subsequent follow-up.

CONCLUSIONS

Of the patients with chronic HBV monoinfection, 0.82% of people per year achieved a functional cure. HBsAg seroclearance was durable for treated and nontreated patients and lasted, on average, over 13 years without seroreversion.

Origin and dispersal history of Hepatitis B virus in Eastern Eurasia

Hepatitis B virus is a globally distributed pathogen and the history of HBV infection in humans predates 10000 years. However, long-term evolutionary history of HBV in Eastern Eurasia remains elusive. We present 34 ancient HBV genomes dating between approximately 5000 to 400 years ago sourced from 17 sites across Eastern Eurasia. Ten sequences have full coverage, and only two sequences have less than 50% coverage. Our results suggest a potential origin of genotypes B and D in Eastern Asia. We observed a higher level of HBV diversity within Eastern Eurasia compared to Western Eurasia between 5000 and 3000 years ago, characterized by the presence of five different genotypes (A, B, C, D, WENBA), underscoring the significance of human migrations and interactions in the spread of HBV. Our results suggest the possibility of a transition from non-recombinant subgenotypes (B1, B5) to recombinant subgenotypes (B2 - B4). This suggests a shift in epidemiological dynamics within Eastern Eurasia over time. Here, our study elucidates the regional origins of prevalent genotypes and shifts in viral subgenotypes over centuries.

Characterization of Hepatitis B virus based complete genome analysis improves molecular surveillance and enables identification of a recombinant C/D strain in the Netherlands

Hepatitis B Virus (HBV) is classified into 10 HBV genotypes (A-J) based a >7.5 % divergence within the complete genome or a >4 % divergence in the S-gene. In addition, recombinant strains with common breakpoints at the gene boundaries of the preS1/preS2/S- and preC/C-gene are often identified. Analysis of HBV based on the complete genome is essential for public health surveillance as it provides higher genetic resolution to conduct accurate characterization and phylogenetic analysis of circulating strains and identify possible recombinants. Currently two separate assays are used for HBV-surveillance; the S-gene for typing, and due to the higher genetic variation, the C-gene to gain insight in transmission patterns. The aim of the study was to develop a complete genome PCR-assay and evaluate the characterization and circulation of HBV strains through the use of the S-gene, C-gene and complete genome. For this HBV positive samples collected in the period 2017 through 2019 were selected. Analysis of the complete genome showed that complete genome analysis portrays a high genetic resolution that provided accurate characterization and analysis of the different circulating types in the Netherlands and enabled identification and characterization of a recombinant CD strain.

Concealed for a Long Time on the Marches of Empires: Hepatitis B Virus Genotype I

Genotype I, the penultimate HBV genotype to date, was granted the status of a bona fide genotype only in the XXIst century after some hesitations. The reason for these hesitations was that genotype I is a complex recombinant virus formed with segments from three original genotypes, A, C, and G. It was estimated that genotype I is responsible for only an infinitesimal fraction (<1.0%) of the chronic HBV infection burden worldwide. Furthermore, most probably due to its recent discovery and rarity, the natural history of infection with genotype I is poorly known in comparison with those of genotypes B or C that predominate in their area of circulation. Overall, genotype I is a minor genotype infecting ethnic minorities. It is endemic to the Southeast Asian Massif or Eastern Zomia, a vast mountainous or hilly region of 2.5 million km2 spreading from Eastern India to China, inhabited by a little more than 100 million persons belonging primarily to ethnic minorities speaking various types of languages (Tibeto-Burman, Austroasiatic, and Tai-Kadai) who managed to escape the authority of central states during historical times. Genotype I consists of two subtypes: I1, present in China, Laos, Thailand, and Vietnam; and I2, encountered in India, Laos, and Vietnam.

A review of epidemiology and clinical relevance of Hepatitis B virus genotypes and subgenotypes

BACKGROUND

Hepatitis B virus (HBV) infection is a global public health burden, affecting nearly 300 million people around the world. Due to HBV population is considered to be represented as a viral quasispecies with genetic diversity, some reports showed that different genotypes of HBV have different viral effects, though the emergence of antiviral drugs that effectively inhibit viral replication, however, HBV infection has still not been eradicated and further research is needed.

SUMMARY

HBV has been classified into at least ten genotypes (A-J)  and more than 40 subgenotypes based on an intergroup or intragroup nucleotide difference across the whole genome, respectively. Inter genotypic recombinants were also observed during the HBV evolution. HBV genotypes and subgenotypes have distinct ethno-geographical distributions, as well as evident differences in their biological characteristics. HBV genotypes and subgenotypes also have close association with disease severity, long-term clinical outcomes, and response to antiviral therapy.

KEYMESSAGES

In this review, we up-dated the epidemiological characteristics, clinical features and prognosis of HBV infection with dissimilar genotype/subgenotypes, to better understanding and developing individualized prevention and treatment strategies.

HBV Genotype: A Significant Risk Factor in Determining Which Patients With Chronic HBV Infection Should Undergo Surveillance for HCC: The Hepatitis B Alaska Study

BACKGROUND AND AIMS

Information is limited regarding HBV genotype and the outcome of chronic HBV (CHB) infection. We examined the effect of HBV genotype on HCC occurrence in Alaska Native (AN) persons with CHB, where five HBV genotypes are found: A2, B6, C2, D, and F1.

APPROACH AND RESULTS

We calculated HCC incidence per 1,000 person-years of follow-up to determine which groups by age, sex, and genotype met current American Association for the Study of Liver Diseases (AASLD) HCC surveillance criteria. We used Poisson regression to compare HCC risk by genotype, age, sex, and Alaska region. Incidence of HCC was calculated using the sex-specific AASLD cutoff recommended for the Asian population of 50 years for women and 40 years for men. HCC screening was conducted semiannually using alpha-fetoprotein levels and abdominal ultrasound. Among 1,185 AN persons, median follow-up was 35.1 years; 667 (63%) were male. The HBV genotype distribution was 49% D, 18% F, 13% A, 6% C, 3% B, 0.1% H, and 12% undetermined. Sixty-three cases of HCC occurred. HCC incidence for genotype F was 5.73 per 1,000 person-years of follow-up, followed by 4.77 for C, 1.28 for A, 0.47 for D, and 0.00 for B. The HCC risk was higher for genotypes F (relative rate [RR], 12.7; 95% CI, 6.1-26.4), C (RR, 10.6; 95% CI, 4.3-26.0), and A (RR, 2.9; 95% CI, 1.0-8.0) compared to genotypes B and D. Among men < 40 years of age and women < 50 years of age, genotype F had the highest incidence (4.79/1,000 person-years).

CONCLUSIONS

HBV genotype was strongly associated with HCC. HBV genotype should be considered in risk factor stratification.

Cross-Protection of Hepatitis B Vaccination among Different Genotypes

Hepatitis B (HB) vaccination is the most effective method for preventing HB virus (HBV) infection. Universal HB vaccination containing recombinant HB surface antigens (HBsAg) is recommended. Our data revealed that human monoclonal HB surface antibody (anti-HBs) from individuals inoculated with genotype C-based HB vaccine induced cross-protection against HBV genotype A infection. An in vitro infection model demonstrated anti-HBs-positive sera from individuals inoculated with genotype A- or C-based HB vaccine harbored polyclonal anti-HBs that could bind to non-vaccinated genotype HBV. However, because there were low titers of anti-HBs specific for HBsAg of non-vaccinated genotype, high anti-HBs titers would be required to prevent non-vaccinated genotype HBV infection. Clinically, the 2015 Centers for Disease Control and Prevention guidelines state that periodic monitoring of anti-HBs levels after routine HB vaccination is not needed and that booster doses of HB vaccine are not recommended. However, the American Red Cross suggests that HB-vaccine-induced immune memory might be limited; although HB vaccination can prevent clinical liver injury (hepatitis), subclinical HBV infections of non-vaccinated genotypes resulting in detectable HB core antibody could not be completely prevented. Therefore, monitoring anti-HBs levels after routine vaccination might be necessary for certain subjects in high-risk groups.

Analysis of HBV Genomes Integrated into the Genomes of Human Hepatoma PLC/PRF/5 Cells by HBV Sequence Capture-Based Next-Generation Sequencing

Hepatitis B virus (HBV) infection is a leading cause of hepatocellular carcinoma (HCC) worldwide. The integration of HBV genomic DNA into the host genome occurs randomly, early after infection, and is associated with hepatocarcinogenesis in HBV-infected patients. Therefore, it is important to analyze HBV genome integration. We analyzed HBV genome integration in human hepatoma PLC/PRF/5 cells by HBV sequence capture-based next-generation sequencing (NGS) methods. We confirmed the results by using Sanger sequencing methods. We observed that HBV genotype A is integrated into the genome of PLC/PRF/5 cells. HBV sequence capture-based NGS is useful for the analysis of HBV genome integrants and their locations in the human genome. Among the HBV genome integrants, we performed functional analysis and demonstrated the automatic expression of some HBV proteins encoded by HBV integrants from chromosomes 3 and 11 in Huh7 cells transfected with these DNA sequences. HBV sequence capture-based NGS may be a useful tool for the assessment of HBV genome integration into the human genome in clinical samples and suggests new strategies for hepatocarcinogenesis in HBV infection.

Analysis of genomic-length HBV sequences to determine genotype and subgenotype reference sequences

Hepatitis B virus (HBV) is a diverse, partially double-stranded DNA virus, with 9 genotypes (A-I), and a putative 10th genotype (J), characterized thus far. Given the broadening interest in HBV sequencing, there is an increasing requirement for a consistent, unified approach to HBV genotype and subgenotype classification. We set out to generate an updated resource of reference sequences using the diversity of all genomic-length HBV sequences available in public databases. We collated and aligned genomic-length HBV sequences from public databases and used maximum-likelihood phylogenetic analysis to identify genotype clusters. Within each genotype, we examined the phylogenetic support for currently defined subgenotypes, as well as identifying well-supported clades and deriving reference sequences for them. Based on the phylogenies generated, we present a comprehensive set of HBV reference sequences at the genotype and subgenotype level. All of the generated data, including the alignments, phylogenies and chosen reference sequences, are available online (https://doi.org/10.6084/m9.figshare.8851946) as a simple open-access resource.

Towards Genotype-Specific Care for Chronic Hepatitis B: The First 6 Years Follow Up From the CHARM Cohort Study

Objective

There is increasing evidence to suggest that, among those with chronic hepatitis B virus infection, the natural history and rate of progression to cirrhosis and hepatocellular carcinoma is influenced by hepatitis B virus genotype. The unique hepatitis B virus genotype C4 circulates among Indigenous Australians. The aim of this work is to describe the process of establishing this cohort and review the first 6 years of available data in an effort to understand the real-world clinical care and natural history of this subgenotype.

Method

We followed a longitudinal cohort of Indigenous Australians from the Northern Territory of Australia with established subgenotype C4 infections. We assigned phases of disease according to Gastroenterological Society of Australia and Asian Pacific Association for the Study of the Liver criteria using clinical and laboratory information that had been collected for clinical management.

Results

Of 193 patients followed over a median of 38 months, 58 (30%) individuals transitioned from 1 disease phase to another, 10 (5%) cleared hepatitis B e antigen, and 6 cleared hepatitis B surface antigen (3%). In this relatively young cohort (median age 40.3 years), 26 (13%) had cirrhosis by the end of the follow up period, with the majority of these being in the immune control phase of disease.

Conclusions

In this cohort of hepatitis B subgenotype C4 patients, we report an aggressive and dynamic clinical phenotype. High rates of cirrhosis at a young age appear to occur in the early phases of disease.

A systematic genotype and subgenotype re-ranking of hepatitis B virus under a novel classification standard

Background and aim

It is commonly noticed that chaotic and inefficient subgenotyping are universally used academically and clinically, a standardized HBV genotype/subgenotype classification criterion is urgently acquired. Sequence similarity, which was commonly used for the last three decades, should be upgraded by phylogenetic analysis in genotyping of recombinant-free HBV strains.

Methods

In this study, 4,429 HBV whole-genome sequences were employed to reconstruct the phylogeny of HBV using Bayesian inference. After excluding recombinant sequences, calculating partitioned evolutionary models, excluding recombinant sequences, reconstructing phylogenetic trees, and performing a correlation analysis of genetic distances, geographical distribution and serotypes, we systematically redefined the genotypes and subgenotypes of HBV.

Results

Compared to previous taxonomy, fourteen subgenotypes (A5-A7; B5-B9; C2-C4, C7; and D6-D7) were revised in the new standard. Now the HBV is divided into ten genotypes (A-J) and 24 subgenotypes (A1-A3; B1-B5; C1-C6; D1-D6; and F1-F4).

Conclusion

Our robust genotype/subgenotype new taxonomy has objectively re-molded the current shape of HBV classification. We believe that all future hepatitis B related researches or diagnosis will be benefited under the new HBV genotyping/subgenotyping standards.

Molecular epidemiology, phylogenetic analysis and genotype distribution of hepatitis B virus in Saudi Arabia: Predominance of genotype D1

Despite the implementation of various vaccination programs, hepatitis B virus (HBV) poses a considerable health problem in Saudi Arabia. Insight on HBV evolutionary history in the region is limited. We performed a comprehensive epidemiological and phylogenetic reconstruction based on a large cohort of HBV infected patients. Three hundred and nineteen HBV-infected patients with different clinical manifestations, including inactive and active chronic carriers and patients with cirrhosis and hepatocellular carcinoma (HCC), were enrolled in this study. The full-length large S gene was amplified and sequenced. Phylogenetic analysis was performed to determine the genotype and subgenotypes of the isolates. Phylogenetic tree analysis revealed that genotype D is the most dominant genotype among patients. Moreover, this analysis identified two strains with genotype E isolated from active carriers. Detailed phylogenetic analyses confirmed the presence of four HBV D subgenotypes, D1 (93%, n = 296), D2 (0.02%, n = 5), D3 (0.003%, n = 1), and D4 (0.003%, n = 1). In addition, six genotype D strains were not assigned to any existing HBV D subgenotype. The large S gene of eight strains showed signatures of genotype recombination between the genotypes D and A and between D and E. Several strains harbored medically important point mutations at the protein level. Along with the dominance of the HBV genotype D, isolation of the E genotype and several recombinant strains from patients with Saudi Arabian origin is an essential result for decisions involving therapeutic measures for patients. Development of vaccines and detection of diagnostic escape mutations at antigenic epitopes on the HBsAg will be valuable to public health authorities. Furthermore, the diversity at the nucleotide and amino acid levels and different proportions of dN/dS at the PreS1, PreS2, and HBsAg reveal the selective pressure trend from inactive status towards advanced liver diseases.

Characteristics and evolutionary history of hepatitis B virus quasi-subgenotype B3 in Southeast Asia

To analyze the hepatitis B virus (HBV) quasi-subgenotype B3 characters and molecular evolution in Southeast Asia, 411 serum samples with HBsAg positive were collected from Xishuangbanna, China. After DNA extraction, PCR amplification and sequencing, a total of 183 HBV full-length genomes were obtained. Phylogenetic analysis showed 139 stains (76.0%) were genotype B, 41 strains were genotype C (22.4%) and 3 strains were genotype I (1.6%). Among genotype B, 34 sequences were identified as quasi-subgenotype B3. Quasi-subgenotype B3 sequences from this study and quasi-subgenotype B3 sequences from the GenBank (total of 141 complete genome sequences) were grouped into quasi-subgenotype B3 (B3, formerly B5, Chinese B6 and B7-9). Sixteen peculiar nucleotides distributed in quasi-subgenotype B3 were identified, which were differ from B1, B2, B4 and B5(formerly B6) (nt93 T, nt100C, nt355 G, nt843 T, nt861C, nt912C, nt929 T, nt930 G, nt1023 T, nt1041 T, nt2651C, nt2693 T, nt2970C, nt3054A, nt3087A and nt3171 G). Then Evolutionary dynamics analysis of HBV quasi-subgenotype B3 was performed. The mean rate of nucleotide substitution for HBV quasi-subgenotype B3 was estimated to be around 5.556-5.660 × 10^-4 substitutions/site/year. Estimated time to most recent ancestor of quasi-subgenotype B3 was around the 1847-1945(95%HPD), and Yunnan strains might be the parental strains. The Bayesian sky plot showed a steady spreading of HBV quasi-genotype B3 from early of 1940s to 90 s. In summary, HBV quasi-subgenotype B3 infection is prevalent in Southeast Asia based on the current reports and still with a high prevalence rate based on the evolutionary dynamics analysis. Current vaccine and nucleotide analogues might have effective prevention and treatment for HBV quasi-subgenotype B3 based on the rare clinically relevant mutation sites included in quasi-subgenotype B3.

Molecular characterization of hepatitis B virus in Vietnam

Background

Hepatitis B virus (HBV) infection is a major public health problem globally. HBV genotypes and subgenotypes influence disease transmission, progression, and treatment outcome. A study was conducted among treatment naive chronic HBV patients in southern Vietnam to determine the genotypes and subgenotypes of HBV.

Methods

A prospective, exploratory study was conducted among treatment naïve chronic HBV patients attending at the Hospital for Tropical Diseases, in Ho Chi Minh City, Vietnam during 2012, 2014 and 2016. HBV DNA positive samples (systematically selected 2% of all treatment naïve chronic patients during 2012 and 2014, and 8% of all treatment naïve chronic patients during 2016) were subjected to whole genome sequencing (WGS) either by Sanger or Illumina sequencing. WGS was used to define genotype, sub-genotype, recombination, and the prevalence of drug resistance and virulence-associated mutations.

Results

One hundred thirty five treatment naïve chronic HBV patients including 18 from 2012, 24 from 2014, and 93 from 2016 were enrolled. Of 135 sequenced viruses, 72.6% and 27.4% were genotypes B and C respectively. Among genotype B isolates, 87.8% and 12.2% were subgenotypes B4 and B2 respectively. A G1896A mutation in the precore gene was present in 30.6% of genotype B isolates. The genotype C isolates were all subgenotype C1 and 78.4% (29/37) of them had at least one basal core promoter (BCP) mutation. A1762T and G1764 T mutations and a double mutation (A1762T and G1764 T) in the BCP region were significantly more frequent in genotype C1 isolates (p < 0.001).

Conclusion

HBV genotype B including subgenotype B4 is predominant in southern Vietnam. However, one fourth of the chronic HBV infections were caused by subgenotype C1.

Electronic supplementary material

The online version of this article (10.1186/s12879-017-2697-x) contains supplementary material, which is available to authorized users.

Tracing hepatitis B virus (HBV) genotype B5 (formerly B6) evolutionary history in the circumpolar Arctic through phylogeographic modelling

Background

Indigenous populations of the circumpolar Arctic are considered to be endemically infected (>2% prevalence) with hepatitis B virus (HBV), with subgenotype B5 (formerly B6) unique to these populations. The distinctive properties of HBV/B5, including high nucleotide diversity yet no significant liver disease, suggest virus adaptation through long-term host-pathogen association.

Methods

To investigate the origin and evolutionary spread of HBV/B5 into the circumpolar Arctic, fifty-seven partial and full genome sequences from Alaska, Canada and Greenland, having known location and sampling dates spanning 40 years, were phylogeographically investigated by Bayesian analysis (BEAST 2) using a reversible-jump-based substitution model and a clock rate estimated at 4.1 × 10⁻⁵ substitutions/site/year.

Results

Following an initial divergence from an Asian viral ancestor approximately 1954 years before present (YBP; 95% highest probability density interval [1188, 2901]), HBV/B5 coalescence occurred almost 1000 years later. Surprisingly, the HBV/B5 ancestor appears to locate first to Greenland in a rapid coastal route progression based on the landscape aware geographic model, with subsequent B5 evolution and spread westward. Bayesian skyline plot analysis demonstrated an HBV/B5 population expansion occurring approximately 400 YBP, coinciding with the disruption of the Neo-Eskimo Thule culture into more heterogeneous and regionally distinct Inuit populations throughout the North American Arctic.

Discussion

HBV/B5 origin and spread appears to occur coincident with the movement of Neo-Eskimo (Inuit) populations within the past 1000 years, further supporting the hypothesis of HBV/host co-expansion, and illustrating the concept of host-pathogen adaptation and balance.

Clustering infection of hepatitis B virus genotype B4 among residents in Vietnam, and its genomic characters both intra- and extra-family

Vietnam has a high rate of hepatitis B virus (HBV) infection and a high mortality rate from hepatocellular carcinoma. We performed a detailed genetic analysis of 48 residents and four families from Binh Thuan Province, a southern coastal area of Vietnam. The route of infection and genomic characteristics related to hepatocellular carcinoma (HCC) were studied in HBV spread among carriers that we detected in our previous hepatitis survey. The HBV genotype was B4 in 91.7% and C1 in 8.3% of the cases. The intra-family’s HBV sequence homology was high at 96.8–99.4%. However, it was also high at 99.4–99.8% among residents of the same age and sex as family members. In addition, full genome analysis was performed in 21 cases. The core region of all 20 isolates with genotype B4 was a recombinant of genotype C, and pre-S deletion was found in 20% of cases. The promoter mutation G1613A was found in 13.6% of cases, and a 24 bp insertion from nt1673 in the X region was found in 6.3% of cases. The phylogenetic tree and homology analysis of the HBV full genome suggested the probability and its possibility of horizontal transmission not only within families nor vertical transmission but within cohorts of the same generation in the population. Moreover, the HBV genotype B4 isolates were found not only to be recombinants of genotype C, which results in a high cancer risk, but also to have other risk of HCC, pre-S deletions, the G1613A mutation, and X region insertions corresponding to the promoter. These genomic characters were suggested to be one of the factors to explain the high HCC mortality rate in Vietnam.

15year fulminant hepatitis B follow-up in Belgium: Viral evolution and signature of demographic change

Fulminant hepatitis among different clinical outcomes of hepatitis B virus infection is very rare and manifests high mortality rate, however it has not been investigated in Belgian inhabitants yet. In the frame of a retrospective study between 1995 and 2010, 80 serum samples (in some cases serial samples) archived in Biobank, were collected from 24 patients who had clinically developed fulminant infection of hepatitis B virus. In total, 33 hepatitis B virus (HBV) strains (31 full-length genome and 2 partial viral genes) of different HBV genotypes and subgenotypes including A2, B2, D1, D2, D3 and E, were amplified, sequenced and phylogenetically analyzed. HBV isolated strains from native and exotic patients were characterized by genome variations associated with viral invasiveness. Although several mutations at nucleotide and protein levels were detected, evolutionary analyses revealed a negative selective pressure over the viral genomes. This study revealed influence of immigration through a steady change in the viral epidemiological profile of the Belgian population.

Incidence of hepatocellular carcinoma according to hepatitis B virus genotype in Alaska Native people

BACKGROUND & AIMS

Most regions of the world have ≤3 co-circulating hepatitis B virus (HBV) genotypes, which limits direct comparisons of hepatocellular carcinoma (HCC) risk among HBV-infected persons by genotype. We evaluated HCC incidence by HBV genotype in a cohort of Alaska Native (AN) persons where five HBV genotypes (A, B, C, D, F) have been identified.

METHODS

Our cohort comprised AN persons with chronic HBV infection identified during 1983-2012 who consented to participate in this study. Cohort persons were offered annual hepatitis B e antigen (HBeAg) testing and semi-annual HCC screening. We developed a logistic regression model to compare HCC risk by genotype, adjusting for age, sex, region and HBeAg status.

RESULTS

Among the 1235 consenting study participants, 711 (57.6%) were male, 510 (41.3%) were HBeAg positive at cohort entry and 43 (3.5%) developed HCC. The HBV genotype was known for 1142 (92.5%) persons (13.5% A, 3.9% B, 6.7% C, 56.9% D, 19.0% F). The HCC incidence/1000 person-years of follow-up for genotypes A, B, C, D and F was 1.3, 0, 5.5, 0.4 and 4.2 respectively. Compared with persons with HBV genotype B/D infection, the HCC risk was higher for persons with genotypes A [adjusted odds ratio (aOR): 3.9, 95% confidence interval (CI): 1.14-13.74], C (aOR: 16.3, 95% CI: 5.20-51.11) and F (aOR: 13.9, 95% CI: 5.30-36.69).

CONCLUSION

HBV genotype is independently associated with HCC risk. AN persons with genotypes A, C and F are at higher risk compared with genotypes B or D.

Surveillance of infectious diseases in the Arctic

OBJECTIVES

This study reviews how social and environmental issues affect health in Arctic populations and describes infectious disease surveillance in Arctic Nations with a special focus on the activities of the International Circumpolar Surveillance (ICS) project.

METHODS

We reviewed the literature over the past 2 decades looking at Arctic living conditions and their effects on health and Arctic surveillance for infectious diseases.

RESULTS

In regards to other regions worldwide, the Arctic climate and environment are extreme. Arctic and sub-Arctic populations live in markedly different social and physical environments compared to those of their more southern dwelling counterparts. A cold northern climate means people spending more time indoors, amplifying the effects of household crowding, smoking and inadequate ventilation on the person-to-person spread of infectious diseases. The spread of zoonotic infections north as the climate warms, emergence of antibiotic resistance among bacterial pathogens, the re-emergence of tuberculosis, the entrance of HIV into Arctic communities, the specter of pandemic influenza or the sudden emergence and introduction of new viral pathogens pose new challenges to residents, governments and public health authorities of all Arctic countries. ICS is a network of hospitals, public health agencies, and reference laboratories throughout the Arctic working together for the purposes of collecting, comparing and sharing of uniform laboratory and epidemiological data on infectious diseases of concern and assisting in the formulation of prevention and control strategies (Fig. 1). In addition, circumpolar infectious disease research workgroups and sentinel surveillance systems for bacterial and viral pathogens exist.

CONCLUSIONS

The ICS system is a successful example of collaborative surveillance and research in an extreme environment.

Virological characteristics of hepatitis B genotype G/A2 recombination virus in Japan

AIM

We identified four cases of infection with hepatitis B virus genotype G and A2 recombinant (HBV/G/A2) strains, which were initially overlooked by enzyme immunoassay-based genotyping. The patients were all men who have sex with men (MSM) and inhabited several metropolitan areas of Japan, suggesting that the recombinant strains may be circulating among high-risk groups such as MSM. Here, we investigated the genomic structure and virological properties of the HBV/G/A2 strains.

METHODS

Complete genome sequences of the isolates were determined and phylogenetically analyzed. Replication efficiency of HBV/G/A2 was investigated by transfecting plasmids containing 1.24-fold viral genome. The in vivo viral kinetics of HBV/G/A2 were investigated using chimeric mice with humanized livers.

RESULTS

Phylogenetic analysis revealed that the four strains were almost identical (>99.7% homologous). The preS2/S region of these strains was highly homologous to that of genotype A2 and the remaining region was almost identical to that of genotype G, reflecting inter-genotypic recombination. Interestingly, in all four cases, genotype A was co-infected as a minor population. In vitro analysis revealed that HBV/G/A2 had a low replication rate. Although detectable viremia was not measurable following the inoculation of HBV/G/A2 into chimeric mice, subsequent superinfection of HBV genotype A greatly enhanced HBV/G/A2 replication and viral spread.

CONCLUSION

We found that four cases of HBV/G/A2 recombinant among MSM patients in the metropolitan areas of Japan, and HBV/A co-infections are required for its efficient replication. High-risk groups such as MSM should be carefully tested for infection of genotype G-derived variants.

Hepatitis B virus intergenotypic recombinants worldwide: An overview

Novel variants generated by recombination events between different hepatitis B virus (HBV) genotypes have been increasingly documented worldwide, and the role of recombination in the evolutionary history of HBV is of significant research interest. In the present study, large-scale data retrieval and analysis on HBV intergenotypic recombinant genomes were performed. The geographical distribution of HBV recombinants as well as the molecular processes involved in recombination were examined. After review of published data, a total of 436 complete HBV sequences, previously identified as recombinants, were included in the recombination detection analysis. About 60% of HBV recombinants were B/C (n=179) and C/D (n=83) hybrids. A/B/C, A/C, A/C/G, A/D, A/E, A/G, B/C/U (U=unknown genotype), C/F, C/G, C/J, D/E, D/F, and F/G hybrids were additionally identified. HBV intergenotypic sequences were reported in almost all geographical regions with similar circulation patterns as their original genotypes, indicating the potential for spreading in a wide range of human populations and developing their own epidemiology. Recombination breakpoints were non-randomly distributed in the genome, and specific favored sites detected, such as within nt 1700-2000 and 2100-2300 regions, which displayed a statistically significant difference in comparison with the remaining genome. Elucidation of the effects of recombination events on the evolutionary history of HBV is critical to understand current and future evolution trends.

Hepatitis B virus genotypes and genome characteristics in China

AIM: To analyze the hepatitis B virus (HBV) characters in China, as well as the correlation between several HBV mutation and hepatitis symptoms.

METHODS: A total of 1148 HBV genome sequences from patients throughout China were collected via the National Center For Biotechnology Information database (information including: genotype, territory and clinical status). HBV genotypes were classified by a direct reference from the Genbank sequence annotation, phylogenetic tree and online software analysis (http://www.ncbi.nlm.nih.gov/projects/genotyping/formpage.cgi). The phylogenetic tree was constructed based on the neighbor-joining method by MEGA5.0 software. HBV sequences were grouped based on phylogenetic tree and the distance between the groups was calculated by using the computer between group mean distance methods. Seven hundred and twelve HBV sequences with clear annotation of clinical symptoms were selected to analyses the correlation of mutation and clinical symptoms. Characteristics of sequences were analyzed by using DNAStar and BioEdit software packages. The codon usage bias and RNA secondary structures analysis were performed by RNAdraw software. Recombination analysis was performed by using Simplot software.

RESULTS: In China, HBV genotype C was the predominant in Northeastern, genotype B was predominant in Central Southern areas, genotype B and C were both dominant in Southwestern areas, and the recombinant genotype C/D was predominant in Northwestern areas. C2 and B2 were identified as the two major sub-genotypes, FJ386674 might be a putative sub-genotype as B10. The basal core promoter double mutation and pre-C mutation showed various significant differences between hepatitis symptoms. In addition to ATG, many other HBV initiation codons also exist. HBV has codon usage bias; the termination codon of X, C and P open reading frames (ORF) were TAA, TAG, and TGA, respectively. The major stop codons of S-ORF were TAA (96.45%) and TGA (83.60%) in B2 and C2 subtype, respectively.

CONCLUSION: This study recapitulated the epidemiology of HBV in China, and the information might be meaningful critical for the future prevention and therapy of HBV infections.

Distribution and epidemiologic trends of HBV genotypes and subtypes in 14 countries neighboring china

BACKGROUND

The number of cases of HBV infection reported by the WHO for each district and country is positively correlated with the number of HBV sequences in the database isolated from the corresponding district and country.

OBJECTIVES

This study determined distribution characteristics of HBV genotypes and subtypes in 14 countries neighboring China. The progress made in genomic research involving HBV was also reviewed.

MATERIALS AND METHODS

Nine hundred fifty-one complete genome sequences of HBV from 14 countries neighboring China were selected from NCBI. The sequence-related information was analyzed and recorded. One hundred seventy-two sequences of HBV genotype B were screened for alignment using DNA star and MEGA 5.1.

RESULTS

Dominant HBV genotypes in the countries neighboring China were genotypes B, C and D and dominant subtypes were adw2 and adrq+. The association between genotype and serotype of HBV in these countries was shown to differ from previous research results. As shown by sequence alignment, the sequence divergence between five subgenotypes (B3, B5, B7, B8 and B9) was below 4%. The B subgenotypes shared six common specific amino acid sites in the S region.

CONCLUSIONS

The B3, B5, B7, B8 and B9 subgenotypes can be clustered into quasi-sub-genotype B3 and the open reading frame of HBV has a start codon preference; however, whether a mutation in the start codon in the pre-S2 region has an impact on survival and replication of HBV remains to be determined.

Genotypes and genetic variability of hepatitis B virus

Sequence heterogeneity is a feature of hepatitis B virus (HBV), the prototype member of the family Hepadnaviridae. Based on an intergroup divergence of greater than 7.5% across the complete genome, HBV has been classified phylogenetically into 9 genotypes, A-I, with a putative 10th genotype 'J', isolated from a single individual. With between approximately 4 and 8% intergroup nucleotide divergence across the complete genome and good bootstrap support, genotypes A-D, F, H, and I are classified further into subgenotypes. There is a broad and highly statistically significant correlation between serological subtypes and genotypes, and in some cases, serological subtypes can be used to differentiate subgenotypes. The genotypes, and certain subgenotypes, have distinct geographical distributions and are important in both the clinical manifestation of infection and response to antiviral therapy. HBV genotypes/subgenotypes and genetic variability of HBV are useful in epidemiological and transmission studies, tracing human migrations, and in predicting the risk for the development of severe liver disease and response to antiviral therapy. Moreover, knowledge of the genotype/subgenotype is important in implementing preventative strategies. Thus, it is crucial that new strains are correctly assigned to their respective genotype/subgenotype and consistent, unambiguous, and generally accepted nomenclature is utilized.

Molecular identification of hepatitis B virus genotypes/subgenotypes: revised classification hurdles and updated resolutions

The clinical course of infections with the hepatitis B virus (HBV) substantially varies between individuals, as a consequence of a complex interplay between viral, host, environmental and other factors. Due to the high genetic variability of HBV, the virus can be categorized into different HBV genotypes and subgenotypes, which considerably differ with respect to geographical distribution, transmission routes, disease progression, responses to antiviral therapy or vaccination, and clinical outcome measures such as cirrhosis or hepatocellular carcinoma. However, HBV (sub)genotyping has caused some controversies in the past due to misclassifications and incorrect interpretations of different genotyping methods. Thus, an accurate, holistic and dynamic classification system is essential. In this review article, we aimed at highlighting potential pitfalls in genetic and phylogenetic analyses of HBV and suggest novel terms for HBV classification. Analyzing full-length genome sequences when classifying genotypes and subgenotypes is the foremost prerequisite of this classification system. Careful attention must be paid to all aspects of phylogenetic analysis, such as bootstrapping values and meeting the necessary thresholds for (sub)genotyping. Quasi-subgenotype refers to subgenotypes that were incorrectly suggested to be novel. As many of these strains were misclassified due to genetic differences resulting from recombination, we propose the term "recombino-subgenotype". Moreover, immigration is an important confounding facet of global HBV distribution and substantially changes the geographic pattern of HBV (sub)genotypes. We therefore suggest the term "immigro-subgenotype" to distinguish exotic (sub)genotypes from native ones. We are strongly convinced that applying these two proposed terms in HBV classification will help harmonize this rapidly progressing field and allow for improved prophylaxis, diagnosis and treatment.

Novel point mutations and mutational complexes in the enhancer II, core promoter and precore regions of hepatitis B virus genotype D1 associated with hepatocellular carcinoma in Saudi Arabia

In this study, a cohort of 182 patients [55 hepatocellular carcinoma (HCC) and 127 non-HCC] infected with hepatitis B virus (HBV) in Saudi Arabia was investigated to study the relationship between sequence variation in the enhancer II (EnhII), basal core promoter (BCP) and precore regions of HBV genotype D (HBV/D) and the risk of HCC. HBV genotypes were determined by sequencing analysis and/or enzyme-linked immunosorbent assay. Variations in the EnhII, BCP and precore regions were compared between 107 non-HCC and 45 HCC patients infected with HBV/D, followed by age-matched analysis of 40 cases versus equal number of controls. Age and male gender were significantly associated with HCC (p = 0.0001 and p = 0.03, respectively). Serological markers such as aspartate aminotransferase, albumin and anti-HBe were significantly associated with HCC (p = 0.0001 for all), whereas HBeAg positivity was associated with non-HCC (p = 0.0001). The most prevalent HBV genotype was HBV/D (94%), followed by HBV/E (4%), HBV/A (1.6%) and HBV/C (0.5%). For HBV/D1, genomic mutations associated with HCC were T1673/G1679, G1727, C1741, C1761, A1757/T1764/G1766, T1773, T1773/G1775 and C1909. Age- and gender-adjusted stepwise logistic regression analysis indicated that mutations G1727 [odds ratio (OR) = 18.3; 95% confidence interval (CI) = 2.8-118.4; p = 0.002], A1757/T1764/G1766 (OR = 4.7; 95% CI = 1.3-17.2; p = 0.01) and T1773 (OR = 14.06; 95% CI = 2.3-84.8; p = 0.004) are independent predictors of HCC development. These results implicate novel individual and combination patterns of mutations in the X/precore region of HBV/D1 as predictors of HCC. Risk stratification based on these mutation complexes would be useful in determining high-risk patients and improving diagnostic and treatment strategies for HBV/D1.

A paucity of liver disease in Canadian Inuit with chronic hepatitis B virus, subgenotype B6 infection

Clinical observations suggest that chronic hepatitis B virus (HBV) infections in the Canadian Inuit are less often associated with serious adverse outcomes than has been described in other HBV-infected patient populations. The aim of this study was to document the clinical and biochemical features, liver-related morbidity and all-cause mortality in Canadian Inuit with chronic HBV infections. Administrative databases were reviewed for individuals identified as hepatitis B surface antigen (HBsAg) positive during a 1983-85 seroepidemiological survey of viral hepatitis in Baffin Island, Canada. An equal number of age- and gender-matched HBsAg-negative individuals from the same communities served as controls. Baseline HBV viral loads, genotypes and specific mutations were compared in HBsAg-positive survivors and nonsurvivors. A subset of surviving HBsAg-positive carriers were reassessed 25-30 years following their initial diagnosis for evidence of advanced liver disease and changes to their serological/virological findings. One hundred and forty four HBsAg-positive individuals were identified. All were Canadian Inuit. The mean age at diagnosis was 38 ± 17 years and 69 (61%) were male. Median follow-up was 23 years (range: 2-28 years). Viral quantitation from stored sera could be performed in 70 infected individuals. The median viral load was 4.3 log 10 IU/ml (range: 2.3-8.8 log 10 IU/ml), and all were genotype B, subgenotype B6. Liver biochemistry, morbidity and all-cause mortality rates were similar in HBsAg-positive carriers and controls. Following multivariate analyses, only age at diagnosis predicted mortality in HBsAg carriers. In a subset of 30 HBsAg-positive survivors who underwent follow-up assessments, clinical, biochemical and radiological examinations of the liver were essentially normal. 23/30 (77%) remained HBsAg positive and 17/19 (90%) HBV-DNA positive. The genotype and prevalence of genomic mutations in this cohort remained largely unchanged, but quantifiable viral loads were significantly lower (P < 0.003). The results of this study suggest that chronic HBV infections in the Canadian Inuit are infrequently associated with serious adverse outcomes. Whether this finding reflects unique features of the host, presence or absence of external factors that influence the course of HBV and/or intrinsic properties of the HBV B6 subgenotype remains to be determined.

The Arctic Human Health Initiative: a legacy of the International Polar Year 2007-2009

BACKGROUND

The International Polar Year (IPY) 2007-2008 represented a unique opportunity to further stimulate cooperation and coordination on Arctic health research and increase the awareness and visibility of Arctic regions. The Arctic Human Health Initiative (AHHI) was a US-led Arctic Council IPY coordinating project that aimed to build and expand on existing International Union for Circumpolar Health (IUCH) and Arctic Council human health interests. The project aimed to link researchers with potential international collaborators and to serve as a focal point for human health research, education, outreach and communication activities during the IPY. The progress of projects conducted as part of this initiative up until the end of the Arctic Council Swedish chairmanship in May 2013 is summarized in this report.

DESIGN

The overall goals of the AHHI was to increase awareness and visibility of human health concerns of Arctic peoples, foster human health research, and promote health strategies that will improve health and well-being of all Arctic residents. Proposed activities to be recognized through the initiative included: expanding research networks that will enhance surveillance and monitoring of health issues of concern to Arctic peoples, and increase collaboration and coordination of human health research; fostering research that will examine the health impact of anthropogenic pollution, rapid modernization and economic development, climate variability, infectious and chronic diseases, intentional and unintentional injuries, promoting education, outreach and communication that will focus public and political attention on Arctic health issues, using a variety of publications, printed and electronic reports from scientific conferences, symposia and workshops targeting researchers, students, communities and policy makers; promoting the translation of research into health policy and community action including implementation of prevention strategies and health promotion; and promoting synergy and strategic direction of Arctic human health research and health promotion.

RESULTS

As of 31 March, 2009, the official end of the IPY, AHHI represented a total of 38 proposals, including 21 individual Expressions of Intent (EoI), and 9 full proposals (FP), submitted to the IPY Joint Committee for review and approval from lead investigators from the US, Canada, Greenland, Norway, Finland, Sweden and the Russian Federation. In addition, there were 10 National Initiatives (NI-projects undertaken during IPY beyond the IPY Joint Committee review process). Individual project details can be viewed at www.arctichealth.org. The AHHI currently monitors the progress of 28 individual active human health projects in the following thematic areas: health network expansion (5 projects), infectious disease research (7 projects), environmental health research (7 projects), behavioral and mental health research (4 projects), and outreach education and communication (5 projects).

CONCLUSIONS

While some projects have been completed, others will continue well beyond the IPY. The IPY 2007-2008 represented a unique opportunity to further stimulate cooperation and coordination on Arctic health research and increase the awareness and visibility of Arctic regions.

Hepatitis B virus subgenotyping: history, effects of recombination, misclassifications, and corrections

Hepatitis B virus (HBV) has evolved into phylogenetically separable genotypes and subgenotypes. Accurately assigning the subgenotype for an HBV strain is of clinical and epidemiological significance. In this paper, we review the recommendations currently employed for HBV subgenotyping, the history of HBV subgenotyping, the effects of recombination on HBV subgenotyping, misclassifications in HBV subgenotyping, and suggestions are made to correct the misclassifications. Finally, proposals are made to guide future HBV subgenotyping.

Dating the origin and dispersal of hepatitis B virus infection in humans and primates

The origin of hepatitis B virus (HBV) infection in humans and other primates remains largely unresolved. Understanding the origin of HBV is crucial because it provides a framework for studying the burden, and subsequently the evolution, of HBV pathogenicity with respect to changes in human population size and life expectancy. To investigate this controversy we examined the relationship between HBV phylogeny and genetic diversity of modern humans, investigated the timescale of global HBV dispersal, and tested the hypothesis of HBV-human co-divergence. We find that the global distribution of HBV genotypes and subgenotypes are consistent with the major prehistoric modern human migrations. We calibrate the HBV molecular clock using the divergence times of different indigenous human populations based on archaeological and genetic evidence and show that HBV jumped into humans around 33,600 years ago; 95% higher posterior density (HPD): 22,000-47,100 years ago (estimated substitution rate: 2.2 × 10(-6) ; 95% HPD: 1.5-3.0 × 10(-6) substitutions/site/year). This coincides with the origin of modern non-African humans. Crucially, the most pronounced increase in the HBV pandemic correlates with the global population increase over the last 5,000 years. We also show that the non-human HBV clades in orangutans and gibbons resulted from cross-species transmission events from humans that occurred no earlier than 6,100 years ago.

CONCLUSION

Our study provides, for the first time, an estimated timescale for the HBV epidemic that closely coincides with dates of human dispersals, supporting the hypothesis that HBV has been co-expanding and co-migrating with human populations for the last 40,000 years. (HEPATOLOGY 2013).

New HBV subgenotype D9, a novel D/C recombinant, identified in patients with chronic HBeAg-negative infection in Eastern India

Genome diversity is a hallmark of hepatitis B virus (HBV), which allowed its classification into 10 genotypes (A-J) and numerous subgenotypes. Among them, Genotype D is currently segregated into eight subgenotypes (D1-D8). Here, we report the identification and characterization of a novel subgenotype within genotype D of HBV from chronic hepatitis B e antigen (HBeAg)-negative patients of Eastern India. Phylogenetic tree analysis based on complete genome sequences revealed that six of 39 HBV/D isolates formed a distinct cluster supported by high bootstrap value and had nucleotide divergence >4% relative to the known D subgenotypes (D1-D8), justifying their assignment into a new subgenotype (D9). By comparing the amino acid sequences of the four ORFs of HBV/D9 with D1-D8, 36 specific residues, including a unique one (E(112) in the core region), were identified that could be considered as a signature of D9. Further analysis by Simplot, BootScan and jpHMM demonstrated that D9 resulted from a discrete recombination with genotype C over the precore-core region. This type of recombination has not been described previously as all C/D recombinants reported so far possessed genotype C backbones with mosaic fragments derived from HBV/D. Interestingly, compared to other subgenotypes of HBV/D, D9 isolates had a higher frequency of mutations (A1762T and G1764A) in the basal core promoter region that had been implicated in the development of hepatocellular carcinoma. Further investigations are needed to determine the overall prevalence and clinical significance of these newly characterized D9 strains and to assess the impact of inter-genotypic recombination on viral properties.

Genetic diversity of hepatitis B virus genotypes B6, D and F among circumpolar indigenous individuals

Hepatitis B virus (HBV) infection is highly prevalent in circumpolar indigenous peoples. However, the clinical outcome is extremely variable, such that while hepatocellular carcinoma (HCC) is uncommon in Canadian Inuit, the incidence of HCC is slightly higher in Greenlanders than in Danes, and it is especially high in Alaskan Native people infected with HBV genotypes F (HBV/F) and C (HBV/C). These differences may be associated with the genomic variability of the predominant HBV genotype in each group. The purpose of this study was to determine the rate, nature and regional susceptibility of HBV genomic mutations among circumpolar indigenous individuals. Paired serum samples, separated by 5-6 years, were analysed from Canadian and Greenlandic Inuit infected with HBV genotype B6 (HBV/B6) and HBV/D, respectively, and from Alaskan Native people infected with HBV/F, each having subsequently developed HCC. Phylogenetic and mutational analyses were performed on full-genome sequences, and the dynamic evolution within the quasispecies population of each patient group was determined by clonal analysis of the non-overlapping core coding region. Mutations associated with severe outcomes predominated in HBV/F, mostly within the precore/core and PreS1 region. HBV/B6 genomes exhibited higher diversity compared to HBV/D and HBV/F, particularly within the core coding region. Thus, differing mutational profiles and genetic variability were observed among different HBV genotypes predominating in circumpolar indigenous patients. The unusual observation of persistently high genetic variability with HBV/B6 despite clinical inactivity could be due to the evolution of a host-pathogen balance, but other possible factors also need to be explored.

The prevalence and long term outcome of occult hepatitis B virus infections in community based populations

Features of occult hepatitis B infection in community-based populations have yet to be described. In this study we documented: (1) the prevalence and demographics, (2) associated serology and viral loads, and (3) clinical outcomes of occult hepatitis B infection in community-based populations. Hepatitis B surface antigen (HBsAg)-negative sera collected from three Northern Canadian communities (HBsAg prevalences: 11-12%) in 1983-1985 were tested for HBV-DNA by nested stage polymerase chain reaction. Of 706 HBsAg negative sera, 9 (1.3%) were HBV-DNA positive. The median age of occult hepatitis B infected patients at the time of sampling was 9.8 years (range 3.1-50.4 years) and six (67%) were female. Two (22%) individuals were anti-HBs positive (in the absence of prior vaccination). Viral loads were undetectable in all but two samples (2.40 and 2.86  log₁₀ IU/ml). Only one of the five (20%) patients who were assessed clinically, remained HBV-DNA positive at 25-30 year follow-up. There was no clinical, biochemical or radiologic evidence of chronic hepatitis, cirrhosis or hepatocellular carcinoma in these individuals or on review of the charts from the remaining four infected patients. The results of this study suggest that in community-based populations: (1) occult hepatitis B infection is not as common as HBsAg positive infection, (2) the majority of infected subjects are young females, (3) a minority are anti-HBs positive, (4) viral loads are either undetectable or low, and (5) in the absence of concurrent liver disease, occult hepatitis B infection does not appear to be associated with long term adverse clinical outcomes.

Subgenotyping of genotype C hepatitis B virus: correcting misclassifications and identifying a novel subgenotype

Background

More than ten subgenotypes of genotype C Hepatitis B virus (HBV) have been reported, including C1 to C16 and two C/D recombinant subgenotypes (CD1 and CD2), however, inconsistent designations of these subgenotypes still exist.

Methodology/Principal Findings

We performed a phylogenetic analysis of all full-length genotype C HBV genome sequences to correct the misclassifications of HBV subgenotypes and to study the influence of recombination on HBV subgenotyping. Our results showed that although inclusion of the recombinant sequences changed the topology of the phylogenetic tree, it did not affect the subgenotyping of the non-recombinant sequences, except subgenotype C2. In addition, most of the subgenotypes have been properly designated. However, several misclassifications of HBV subgenotypes have been identified and corrected. For example, C11 proposed by Utsumi and colleagues in 2011 was found to be grouped with C12 proposed by Mulyanto and colleagues. Two sequences, GQ358157 and GU721029, previously designated as C6 have been re-designated as C12 and C7, respectively. Moreover, a quasi-subgenotype C2 was proposed, which included the old C2, several previously unclassified sequences and previously designated C14. In particular, we identified a novel subgenotype, tentative C14, which was well supported by phylogenetic analysis and sequence divergence of >4%.

Conclusions/Significance

A number of misclassifications in the subgenotyping of genotype C HBV have been identified in this study. After correcting the misclassifications, we proposed a better classification for the subgenotyping of genotype C HBV, in which a novel quasi-subgenotype C2 and a novel subgenotype, tentative C14, were described. Based on this large-scale analysis, we propose that a novel subgenotype should only be reported after a complete comparison of all relevant sequences rather than a few representative sequences only.

Subgenotype reclassification of genotype B hepatitis B virus

Background

Nine subgenotypes from genotype B have been identified for hepatitis B virus (HBV). However, these subgenotypes were less conclusive as they were often designated based on a few representative strains. In addition, subgenotype B6 was designated twice for viruses of different origin.

Methods

All complete genome sequences of genotype B HBV were phylogenetically analyzed. Sequence divergences between different potential subgenotypes were also assessed.

Results

Both phylogenetic and sequence divergence analyses supported the designation of subgenotypes B1, B2, B4, and B6 (from Arctic). However, sequence divergences between previously designated B3, B5, B7, B8, B9 and another B6 (from China) were mostly less than 4%. In addition, subgenotype B3 did not form a monophyly.

Conclusion

Current evidence failed to classify original B5, B7, B8, B9, and B6 (from China) as subgenotypes. Instead, they could be considered as a quasi-subgenotype B3 of Southeast Asian and Chinese origin. In addition, previously designated B6 (from Arctic) should be renamed as B5 for continuous numbering. This novel classification is well supported by both the phylogeny and sequence divergence of > 4%.

HBV genotypes: relevance to natural history, pathogenesis and treatment of chronic hepatitis B

Although chronic HBV infection is the leading cause of chronic liver disease and death worldwide, there are substantial differences in its clinical courses regarding prevalence, mode of transmission, characteristics of each phase, responses to antiviral therapy, and development of cirrhosis and hepatocellular carcinoma, according to geographical areas (Asia versus Western Europe and North America versus Africa). Furthermore, the clinical course in infected individuals depends on a complex interplay among various factors including viral, host, environmental and other factors. Recently, understanding of molecular characteristics of the prevailing HBV genotypes, frequently accompanied mutations and their clinical implications might explain these geographical differences more pertinently. Hence, in this article, we review the global epidemiology and the natural history of HBV infection, with emphasis on summarizing the different HBV genotypes according to regions.

Identification of novel inter-genotypic recombinants of human hepatitis B viruses by large-scale phylogenetic analysis

Recombination plays an important role in the evolutionary history of Hepatitis B virus (HBV). We performed a phylogenetic analysis of 3403 full-length HBV genome sequences isolated from humans to define the genotype. The genome sequences were divided into 13 sub-datasets, each approximately 250 bp in length. Genotype designations obtained from the sub-datasets that differed from the genotype defined by the whole genome were assigned as putative recombinants. Our results showed that 3379 out of 3403 sequences belonged to the previously described and putative genotypes A to J respectively, with 315 sequences defined in this analysis. The remaining 24 viruses had sequence divergence of less than 8% with both genotypes B and C and were provisionally assigned genotype "BC". 1047 out of 3403 sequences were identified to be putative recombinants, of which 72 were identified to be novel recombinants. Notably, all viruses of the herein described genotype "BC" were identified to be B/C recombinants.

HBeAg and not genotypes predicts viral load in patients with hepatitis B in Denmark: a nationwide cohort study

OBJECTIVE

To explore the influence of HBV genotype on viral load in patients with HBV infection, and to investigate the relation to gender, age and country of origin or antibodies against hepatitis Be antigen (anti-HBe).

MATERIALS

We investigated 1025 patients with hepatitis B virus infection in a nationwide study in Denmark.

RESULTS

Prevalence of genotypes were: 10.5% A, 17.3% B, 20.5% C, 45.7% D, 3.2% E, 0.6% F, 1.1% G and 1% had more than one genotype. Nearly 60% of patients with genotype A were from Africa, 82% and 93% with genotypes B or C were from East Asia, 62% with genotype D came from the Middle East and 91% with genotype E came from Africa. More women had genotypes B (p = 0.006) or C (p < 0.001) while more men had genotypes A (p = 0.015) or D (p < 0.001). Women with genotypes B and D were younger than men (p < 0.001, p = 0.026). Viral load differed in genotype A and D compared with B and C (p < 0.001), and between anti-HBe and hepatitis B e antigen (HBeAg) positive patients (median values 5.4 × 10(3) IU/ml and 7.4 × 10(7) IU/ml, respectively, p < 0.001). Viral load depended on the presence of HBeAg (p < 0.001; OR, 95% CI: 0.05, 0.03-0.07) in the adjusted analysis and was not affected by origin (p = 0.65), age (p = 0.12), gender (p = 0.06) or genotype (p = 0.10).

CONCLUSION

HBeAg status and not HBV genotype influenced viral load in this nationwide study. HBeAg positive patients had median HBV-DNA levels 10,000 times higher than those anti-HBe positive across genotypes.

Effectiveness of the targeted hepatitis B vaccination program in Greenland

OBJECTIVES

To evaluate the effectiveness of the hepatitis B virus (HBV) vaccination program in Greenland, which targets children born to mothers who are positive for HBV surface antigen (HBsAg), we determined vaccination coverage, levels of postvaccination antibodies, and frequency of breakthrough infections in at-risk children.

METHODS

We conducted a population-based retrospective cohort study with data from nationwide registries. We identified all children born to HBsAg-positive mothers from 1992 to 2007 and collected data on their HBV vaccination status. In 2008 to 2010, we tested the children for HBV core antibody, HBsAg, and anti-HBsAg antibody (HBsAb).

RESULTS

Of 4050 pregnant women, 3.2% were HBsAg positive. Of 207 children born to these women, 20% received no vaccinations, and only 58% received at least 3 vaccinations. At follow-up, HBsAb levels in vaccinated children were much lower than expected, and 8 (6%) of 140 at-risk children had breakthrough infections, with 4 chronically infected (persistently HBsAg positive).

CONCLUSIONS

The prevention program targeting children at risk for HBV in Greenland is ineffective. HBV vaccination should be included in the universal childhood vaccination program, and postvaccination HBsAb levels should be monitored.

Hepatocellular carcinoma and other liver disease among Greenlanders chronically infected with hepatitis B virus: a population-based study

BACKGROUND

In Greenland, the prevalence of hepatitis B surface antigen carriers, reflecting chronic hepatitis B virus (HBV) infection, is 5%-10%. However, the incidence of cirrhosis and hepatocellular carcinoma in this population has been reported to be low. We investigated this discrepancy in a large population-based cohort study.

METHODS

In total, 8879 Greenlanders (16% of the population) were recruited for population-based surveys performed from May 5 to July 7, 1987, and from November 1 to November 21, 1998, with follow-up until March 31, 2010. HBV status was based on serological testing, supplemented by data from all available HBV registries in Greenland to determine changes in HBV status over time. Information on morbidity and mortality was obtained from the Patient Discharge Registry, the Cancer Registry, and the Central Registration System. Sex, age, ethnicity, and period-adjusted incidence rate ratios (IRRs) were estimated using Poisson regression. World standardized rates were derived from these and World Health Organization data.

RESULTS

The 650 chronically HBV-infected persons had higher rates of hepatocellular carcinoma (adjusted IRR = 8.70; 95% CI = 2.06 to 36.7), liver disease (adjusted IRR = 5.73, 95% CI = 3.52 to 9.34), and all-cause mortality (adjusted IRR = 1.47; 95% CI = 1.21 to 1.79) than the 5160 HBV-negative persons. However, the world standardized incidence rates of hepatocellular carcinoma (38.5 cancers per 100 000 person-years) and cirrhosis (24 cases per 100 000 person-years) among chronically HBV-infected persons were low compared with results from population-based studies from countries with low, intermediate, and high rates of endemic HBV infection.

CONCLUSION

The relatively low incidence of hepatocellular carcinoma and other HBV-related morbidity among chronic HBV-infected persons in Greenland suggest a more benign course of HBV among the Greenlandic Inuit than in populations in other parts of the world.

Virologic and clinical characteristics of HBV genotypes/subgenotypes in 487 Chinese pediatric patients with CHB

Background

The association of hepatitis B virus (HBV) genotypes/subgenotypes with clinical characteristics is increasingly recognized. However, the virologic and clinical features of HBV genotypes/subgenotypes in pediatric patients remain largely unknown.

Methods

Four hundred and eighty-seven pediatric inpatients with CHB were investigated, including 217 nucleos(t)ide analog-experienced patients. HBV genotypes/subgenotypes and reverse transcriptase (RT) mutations were determined by direct sequencing. The stage of fibrosis and degree of inflammatory activity were evaluated by the Metavir score system.

Results

Among 487 enrolled pediatric patients, HBV genotype C2 and B2 were the most two prevalent (73.7% and 21.1%). Comparing with HBV/B2 infected patients, no significant difference was observed in the incidence rate and mutant patterns of lamivudine- or adefovir-resistant mutations in HBV/C2 infected patients (P > 0.05). Importantly, we found that the degree of hepatic inflammation degree, fibrosis stage and ALT level were significantly higher in HBV/C2-infected HBeAg positive patients than it was in HBV/B2-infected ones.

Conclusions

The pediatric patients with HBV/C2 infection might be more susceptible to develop severe liver pathogenesis.

Ethnogeographical structure of hepatitis B virus genotype distribution in Indonesia and discovery of a new subgenotype, B9

The distribution of hepatitis B virus (HBV) in the populations of island Southeast Asia is of medical and anthropological interest and is associated with an unusually high genetic diversity. This study examined the association of this HBV genetic diversity with the ethnogeography of the populations of the Indonesian archipelago. Whole genome analysis of 21 HBV isolates from East Nusa Tenggara and Papua revealed two recently reported HBV/B subgenotypes unique to the former, B7 (7 isolates) and B8 (5 isolates), and uncovered a further novel subgenotype designated B9 (4 isolates). Further isolates were collected from 419 individuals with defined ethnic backgrounds representing 40 populations. HBV/B was predominant in Austronesian-language-speaking populations, whereas HBV/C was the major genotype in Papua and Papua-influenced populations of Moluccas; HBV/B3 was the predominant subgenotype in the western half of the archipelago (speakers of the Western Malayo-Polynesian [WMP] branch of Austronesian languages), whereas B7, B8 and B9 were specific to Nusa Tenggara (Central Malayo-Polynesian (CMP)). The result provides the first direct evidence that the distribution of HBV genotypes/subgenotypes in the Indonesian archipelago is related to the ethnic origin of its populations and suggests that the HBV distribution is associated with the ancient migratory events in the peopling of the archipelago.

Distinct geographical and demographic distribution of hepatitis B virus genotypes in the Canadian Arctic as revealed through an extensive molecular epidemiological survey

Very little is known of hepatitis B virus (HBV) in Canadian Arctic indigenous populations, where HBV was considered endemic prior to the introduction of HBV vaccine. This study expands upon an HBV seroepidemiological survey conducted between 1983 and 1985 throughout the Canadian Arctic, to characterize HBV in this population. Archived hepatitis B surface antigen (HBsAg)-positive sera (n = 401) were processed for HBV DNA, followed by sequencing and phylogenetic analysis of the HBsAg- and HBcAg-coding regions. Sixty-nine per cent of samples (277/401) were DNA positive, with most having low viral load (median 3.4 log 10 IU/mL). The predominant HBV genotype observed was genotype B (HBV/B, 75%), followed by HBV/D (24%) and HBV/A (1%). All HBV/B strains clustered within subgenotype B6, a newly recognized HBV genotype among western circumpolar Inuit and Alaska Native people. HBV/D strains included both D3 (88%) and D4 (12%) subgenotypes, while all HBV/A strains were subgenotype A2. An association of HBV genotype B with Inuit living in the eastern Arctic and an association of genotype D with First Nation (Dene) living in the western Arctic was observed. This study establishes the high prevalence of HBV/B6 and HBV/D genotypes in Arctic populations and reveals their marked distribution within the Canadian Arctic based on geographical and demographic attributes.

Data mining on DNA sequences of hepatitis B virus

Extraction of meaningful information from large experimental data sets is a key element in bioinformatics research. One of the challenges is to identify genomic markers in Hepatitis B Virus (HBV) that are associated with HCC (liver cancer) development by comparing the complete genomic sequences of HBV among patients with HCC and those without HCC. In this study, a data mining framework, which includes molecular evolution analysis, clustering, feature selection, classifier learning, and classification, is introduced. Our research group has collected HBV DNA sequences, either genotype B or C, from over 200 patients specifically for this project. In the molecular evolution analysis and clustering, three subgroups have been identified in genotype C and a clustering method has been developed to separate the subgroups. In the feature selection process, potential markers are selected based on Information Gain for further classifier learning. Then, meaningful rules are learned by our algorithm called the Rule Learning, which is based on Evolutionary Algorithm. Also, a new classification method by Nonlinear Integral has been developed. Good performance of this method comes from the use of the fuzzy measure and the relevant nonlinear integral. The nonadditivity of the fuzzy measure reflects the importance of the feature attributes as well as their interactions. These two classifiers give explicit information on the importance of the individual mutated sites and their interactions toward the classification (potential causes of liver cancer in our case). A thorough comparison study of these two methods with existing methods is detailed. For genotype B, genotype C subgroups C1, C2, and C3, important mutation markers (sites) have been found, respectively. These two classification methods have been applied to classify never-seen-before examples for validation. The results show that the classification methods have more than 70 percent accuracy and 80 percent sensitivity for most data sets, which are considered high as an initial scanning method for liver cancer diagnosis.

Genotype X/C recombinant (putative genotype I) of hepatitis B virus is rare in Hanoi, Vietnam--genotypes B4 and C1 predominate

There are eight known genotypes of hepatitis B virus, A-H, and several subgenotypes, with rather well-defined geographic distributions. HBV genotypes were evaluated in 153 serum samples from Hanoi, Vietnam. Of the 87 samples that could be genotyped, genotype B was found in 67 (77%) and genotype C in 19 (22%). All genotype C strains were of subgenotype C1, and the majority of genotype B strains were B4, while a few were B2. The genotype X/C recombinant strain, identified previously in Swedish patients of indigenous Vietnamese origin, was found in one sample. This variant, proposed to be classified as genotype I, has been found recently also by others in Vietnam and Laos. The current study indicates that the genotype X/C recombinant may represent approximately 1% of the HBV strains circulating in Vietnam.

Natural history of chronic hepatitis B

In this article, the 4 phases of chronic HBV infection are reviewed and the factors that are associated with disease progression and the development of hepatocellular carcinoma (HCC) and cirrhosis are discussed. Also discussed is what is known to date about how to identify persons at the highest risk of developing HCC and/or cirrhosis. Finally, ways in which the natural history can be altered by hepatitis B vaccination and identification, close monitoring, and appropriate treatment of chronically infected individuals are reviewed.

Clearance of hepatitis B surface antigen and risk of hepatocellular carcinoma in a cohort chronically infected with hepatitis B virus

Some individuals who are chronically infected with hepatitis B virus (HBV) eventually lose hepatitis B surface antigen (HBsAg). Hepatocellular carcinoma (HCC) has been demonstrated to occur in a few patients after loss of HBsAg. Neither factors associated with loss of HBsAg nor the incidence of HCC thereafter have been clearly elucidated. We performed a prospective population-based cohort study in 1,271 Alaska Native persons with chronic HBV infection followed for an average of 19.6 years to determine factors associated with loss of HBsAg and risk of developing HCC thereafter. HBsAg loss occurred in 158 persons for a rate of HBsAg clearance of 0.7%/year. Older age, but not sex, was associated with clearance of HBsAg, and loss of HBsAg was not associated with any particular HBV genotypes (A, B, C, D, and F) found in this population. Participants were followed for an average of 108.9 months after HBsAg loss. Six patients, two with cirrhosis and four without, developed HCC a mean of 7.3 years after HBsAg clearance (range, 2.0-15.5 years). The incidence of HCC after clearance of HBsAg was 36.8 per 100,000 per year (95% CI 13.5-80.0) which was significantly lower than the rate in those who remained HBsAg-positive (195.7 cases per 100,000 person-years of follow-up [95% CI 141.1-264.5; P < 0.001]). After loss of HBsAg, HBV DNA was detected in the sera of 28 (18%) of those who cleared a median of 3.6 years after clearance.

CONCLUSION

HCC can occur in persons with chronic hepatitis B who have lost HBsAg, even in the absence of cirrhosis. These persons should still be followed with periodic liver ultrasound to detect HCC early.