Intergenotype recombinant analysis of full-length hepatitis B virus genomes from 516 Chinese patients with different illness categories

Genome analysis and recombination characterization of duck hepatitis B virus isolated from ducks and geese in central China, 2017 to 2019

Owing to its high similarity to human hepatitis B virus (HBV), duck HBV (DHBV) is often used as an essential model for HBV research. Although intergenotypic recombination of HBV is common, it remains unclear whether the intergenotypic recombination of human HBV is exactly the same as that of DHBV. In this study, 119 serum samples of duck and goose were collected from 51 farms (29 duck and 22 goose farms) in the central and eastern regions of China. A total of 22 strains isolated from the 22 DHBV positive flock were sequenced. Genome sequence alignment revealed that the duck- and goose-origin strains shared the highest and lowest similarities (99.7 and 90.52%, respectively). The complete genomes of these DHBV and 31 reference strains were analyzed using phylogenetic methods and classified into 3 clusters, which corresponded to the previously identified DHBV-I, DHBV-II, and DHBV-III branches. Recombination analyses of the 53 DHBV genomes indicated 2 major intergenotypic recombination events with high confidence values. These recombination events occurred between the genotypes of the Chinese isolates Y180813HB (Chinese branch [DHBV-Ⅰ]) and E170101AH (Chinese branch [DHBV-Ⅱ]) and the Western isolate DHBV-XY (Western branch [DHBV-Ⅲ]), resulting in the emergence of 2 Chinese recombinant isolates Y190303HN and Y170101HB. In addition, 40% (2/5) goose-origin and 58.8% (10/17) duck-origin DHBV in this study harbored the mutation site of G133E in preS, which promote the pathogenicity of DHBV. This is the first study to report on the genome analysis and recombination characterization of DHBV isolated from Chinese geese. Further, continuous investigation and molecular identification of DHBV should be conducted to attract researchers' attention.

Mutations and methods of analysis of mutations in Hepatitis B virus

Immunization programmes against hepatitis-B are being carried out since more than three decades but still HBV is a major public health problem. Hepatitis B virus (HBV) genome consists of circular and partial double stranded DNA. Due to partial double stranded DNA, it uses an RNA intermediate during replication. This replicative strategy of HBV and lack of polymerase proofreading activity give rise to error occurrences comparable to retroviruses. The low fidelity of polymerase, overlapping reading frames and high replication rate produces many non-identical variants at every cycle of replication. Therefore, HBV spreads with mutations and variations. The mutations have been reported both in non-structural as well as structural genes of HBV genome. Recent advances in molecular biology have made easier to analyse these mutations. Hepatitis B antiviral therapy and immunization are all influenced by genetic variability. The analysis and understanding of these mutations are important for therapy against hepatitis B and updating of diagnostic tools. The present review discusses about mutations occurring in whole HBV genome. The mutation occurring both in structural and non-structural genes and non-coding regions have been described in details. It is much more informative because most of literature available, covers only individual gene or DNA regions of HBV.

In silico Analysis of Genetic Diversity of Human Hepatitis B Virus in Southeast Asia, Australia and New Zealand

The extent of whole genome diversity amongst hepatitis B virus (HBV) genotypes is not well described. This study aimed to update the current distribution of HBV types and to investigate mutation rates and nucleotide diversity between genotypes in Southeast Asia, Australia and New Zealand. We retrieved 930 human HBV complete genomes from these regions from the NCBI nucleotide database for genotyping, detection of potential recombination, serotype prediction, mutation identification and comparative genome analyses. Overall, HBV genotypes B (44.1%) and C (46.2%) together with predicted serotypes adr (36%), adw2 (29%) and ayw1 (19.9%) were the most commonly circulating HBV types in the studied region. The three HBV variants identified most frequently were p.V5L, c.1896G>A and double mutation c.1762A>T/c.1764G>A, while genotypes B and C had the widest range of mutation types. The study also highlighted the distinct nucleotide diversity of HBV genotypes for whole genome and along the genome length. Therefore, this study provided a robust update to HBV currently circulating in Southeast Asia, Australia and New Zealand as well as an insight into the association of HBV genetic hypervariability and prevalence of well reported mutations.

Novel subgenotype D11 of hepatitis B virus in NaPo County, Guangxi, bordering Vietnam

Hepatitis B virus has been classified into 10 genotypes and 48 subgenotypes worldwide. We found previously, through polymerase chain reaction (PCR) amplification of a sample collected in 2011, that an HBsAg carrier was infected with two genotypes (B and D) of HBV. We carried out cloning, sequencing and phylogenetic analysis of the complete genomes and, for confirmation, analysed a sample collected from the same individual in 2018. Fifteen complete sequences were obtained from each sample. The carrier was infected in 2011 by genotypes B and D and by various recombinants, but only genotype D was present in 2018. The major and minor parents of the recombinants are genotypes B and D, respectively, although the recombination breakpoints vary among them. All 23 genotype D isolates form a cluster, branching out from other subgenotype D sequences and supported by a 100 % bootstrap value. Based on complete genome sequences, almost all of the estimated intragroup nucleotide divergence values between our isolates and HBV subgenotypes D1-D10 exceed 4 %. Compared to the other subgenotypes (D1-D10), 35 unique amino acids were present in our isolates. Our data provide evidence for a novel subgenotype, provisionally designated HBV subgenotype D11.

Insights From Deep Sequencing of the HBV Genome-Unique, Tiny, and Misunderstood

Hepatitis B virus (HBV) is a unique, tiny, partially double-stranded, reverse-transcribing DNA virus with proteins encoded by multiple overlapping reading frames. The substitution rate is surprisingly high for a DNA virus, but lower than that of other reverse transcribing organisms. More than 260 million people worldwide have chronic HBV infection, which causes 0.8 million deaths a year. Because of the high burden of disease, international health agencies have set the goal of eliminating HBV infection by 2030. Nonetheless, the intriguing HBV genome has not been well characterized. We summarize data on the HBV genome structure and replication cycle, explain and quantify diversity within and among infected individuals, and discuss advances that can be offered by application of next-generation sequencing technology. In-depth HBV genome analyses could increase our understanding of disease pathogenesis and allow us to better predict patient outcomes, optimize treatment, and develop new therapeutics.

Clinical implication and viral mutation in basal core promoter/pre-core of hepatitis B virus C/D recombinant

BACKGROUND AND AIM

Hepatitis B virus (HBV) C/D recombinant is predominant in Tibet in Western China. Although the geographical and ethnic distributions of the C/D recombinant have been described, the clinical implication and the characteristics of viral mutation in the basal core promoter (BCP)/pre-core (PC) region remain unclear.

METHODS

A total of 174 chronic HBV carriers, including 115 with chronic hepatitis B, 45 with liver cirrhosis, and 14 with hepatocellular carcinoma, were enrolled. Using next-generation sequencing, the S and BCP/PC genes were determined and analyzed.

RESULTS

Genotypes B, C2, D, and C/D recombinant were detected in 1.1% (2/174), 19.5% (34/174), 0.6% (1/174) and 78.7% (137/174) of the patients, respectively. The clinical parameters and viral mutation frequency in the BCP/PC region were compared between C2- and C/D recombinant-infected patients. The distribution of C2 and C/D did not differ by disease status or liver function. Significantly higher levels of HBV DNA (6.7 ± 1.6 vs. 5.9 ± 1.5, p = 0.014), HBeAg (263.5 vs. 20.0, p = 0.013) and A1762T/G1764A double-mutations (81.0 vs. 61.8%, p = 0.018), but a lower frequency of G1896A stop mutation (33.6 vs. 76.5%, p < 0.001) was observed in patients with the C/D recombinant than in patients with genotype C2. The clonal frequencies of A1762T, G1764A, G1896A and A1846T were lower in patients with C/D than C2.

CONCLUSION

The C/D recombinant has different mutation pattern in the BCP/PC region compared with genotype C2. The lower clonal frequencies of BCP/PC mutations may explain the higher levels of HBV DNA and HBeAg in C/D-infected patients.

Acute-on-chronic liver failure in chronic hepatitis B: an update

Acute-on-chronic liver failure is a common pattern of end-stage liver disease in clinical practice and occurs frequently in patients with chronic hepatitis B or HBV-related cirrhosis. New progress in recent years leads to a better understanding of this disease. Areas covered: This review updates the current comprehensive knowledge about HBV-ACLF from epidemiological studies, experimental studies, and clinical studies and provide new insights into the definition, diagnostic criteria, epidemiology, nature history, pathogenesis, treatment and prognostication of HBV-ACLF. Expert commentary: Patients with chronic hepatitis B or HBV-related cirrhosis are at risk of developing acute-on-chronic liver failure, with multi-organ failure and high short-term mortality. The precipitating events can be intra-hepatic or extra-hepatic and the underlying chronic liver injury can be cirrhotic or non-cirrhotic. Host and viral factors contribute to the susceptibility of developing HBV-ACLF. Systemic inflammation is the driver of HBV-ACLF, which can be attributed to non-sterile and sterile factors. Liver transplantation is the definitive treatment for HBV-ACLF. Cell therapy is a promising alternative to LT, but requires validation and still has concern of long-term safety. Other medical therapies, such as nucleoside analogue, artificial liver supporting and glucocorticoid may improve survival in a specific subgroup. New scoring systems improve the accuracy of prognostication in HBV-ACLF, which is critical for early identification of candidates for LT.

Novel HBV recombinants between genotypes B and C in 3'-terminal reverse transcriptase (RT) sequences are associated with enhanced viral DNA load, higher RT point mutation rates and place of birth among Chinese patients

As one of the major global public health concerns, hepatitis B virus (HBV) can be divided into at least eight genotypes, which may be related to disease severity and treatment response. We previously demonstrated that genotypes B and C HBV, with distinct geographical distribution in China, had divergent genotype-dependent amino acid polymorphisms and variations in reverse transcriptase (RT) gene region, a target of antiviral therapy using nucleos(t)ide analogues. Recently recombination between HBV genotypes B and C was reported to occur in the RT region. However, their frequency and clinical significance is poorly understood. Here full-length HBV RT sequences from 201 Chinese chronic hepatitis B (CHB) patients were amplified and sequenced, among which 31.34% (63/201) were genotype B whereas 68.66% (138/201) genotype C. Although no intergenotypic recombination was detected among C-genotype HBV, 38.10% (24/63) of B-genotype HBV had recombination with genotype C in the 3'-terminal RT sequences. The patients with B/C intergenotypic recombinants had significantly (P<0.05) higher serum HBV DNA level than the "pure" B-genotype cohort did. Moreover, the B/C intergenotypic recombinants were prone to more substitutions at several specific residues in the RT region than genotype B or C. Besides, unlike their parental genotypes, the recombinant HBV appeared to display an altered geographic distribution feature in China. Our findings provide novel insight into the virological, clinical and epidemiological features of new HBV B/C intergenotypic recombinants at the 3' end of RT sequences among Chinese CHB patients. The highly complex genetic background of the novel recombinant HBV carrying new mutations affecting RT protein may contribute to an enhanced heterogeneity in treatment response or prognosis among CHB patients.

HIV-hepatitis B virus coinfection: epidemiology, pathogenesis, and treatment

: HIV infection has a significant impact on the natural history of chronic hepatitis B virus (HBV) infection, with increased levels of HBV DNA, accelerated progression of liver disease and increased liver-associated mortality compared with HBV monoinfection. Widespread uptake and early initiation of HBV-active antiretroviral therapy has substantially improved the natural history of HIV-HBV coinfection but the prevalence of liver disease remains elevated in this population. In this paper, we review recent studies examining the natural history and pathogenesis of liver disease and seroconversion in HIV-HBV coinfection in the era of HBV-active antiretroviral therapy and the effects of HIV directly on liver disease. We also review novel therapeutics for the management of HBV with a particular emphasis on clinical strategies being developed for an HBV cure and an HIV cure and their impact on HIV-HBV coinfected individuals.

Natural history of acute and chronic hepatitis B: The role of HBV genotypes and mutants

Molecular epidemiologic studies reveal remarkable differences in the geographical distribution of hepatitis B virus (HBV) genotypes. The frequency of mutants among HBV genotypes also varies. The role of HBV genotypes/mutants in the pathogenesis of HBV infection and natural history of HBV infection has been extensively investigated. The distribution of HBV genotypes in acute hepatitis B patients reflects the predominant genotypes in a given geographic area. In chronic hepatitis B patients, genotype C and D have a higher frequency of basal core promoter A1762T/G1764A mutations than genotype A and B. HBV genotypes C, D and F carry a higher lifetime risk of cirrhosis and HCC development than genotype A and B. HBV pre-S/S gene mutations were associated with immune escape of hepatitis B immunoglobulin or vaccine-induced immunity. Mutations in the pre-S, core promoter and X regions correlate with an increased risk of cirrhosis and HCC. In summary, HBV genotypes and mutants are associated with the disease progression and long-term outcome of HBV infection. They may serve as viral genetic markers for risk stratification of chronic hepatitis B patients in clinical practice.

Distribution of hepatitis B virus C/D recombinant genotypes in Qinghai Province

AIM

To distinguish two forms of hepatitis B virus (HBV) C/D recombinant and investigate the distribution of HBV C/D recombinant genotypes in Qinghai Province.

METHODS

A total of 217 chronic HBV infected serum samples were collected from Qinghai Province. Two fragments of HBV, 535-1460 nt and 1779-2400 nt, were amplified and sequenced. The two forms of C/D recombinant were confirmed by the phylogenetic tree constructed based on 593-799 nt, 799-1450 nt and 1799-2400 nt. The samples of C/D recombinant were determined by INNO-LiPA HBV genotyping assay.

RESULTS

The distribution of HBV genotypes in Qinghai Province detected by the phylogenetic tree based on different fragments was as follows: CD1 (61.9%); CD2 (8.4%); C (27.0%) and B (2.8%). Ethnically, the C/D recombinant had a higher prevalence in Tibetan patients (91.5%) than in Han populations (62.6%). The distribution of HBV genotypes in Tibetan patients was significantly different from that in Han populations (χ² = 17.9, P < 0.01). Clinically, there was no significant difference in viral load between Tibetan and Han populations (F = 0.68, P > 0.05), and between males and females. There was no significant difference in HBeAg positive/negative ratios or HBV viral load between the C/D recombinant genotype and genotype C (χ² = 0.28, P > 0.05; t = 1.125, P > 0.05). The majority (87.8%) of samples of C/D recombinant were reported to be genotype D by INNO-LiPA HBV genotyping assay.

CONCLUSION

The CD1 (10-799 nt) recombinant of HBV is the dominant genotype in Qinghai Province. The clinical outcomes of different C/D recombinant genotypes should be further studied, and the results of INNO-LiPA HBV genotyping assay should be reinterpreted in Qinghai Province.