HBV Genotype Research Articles

Performances of NeuMoDx™, a random-access system for hepatitis B virus DNA and hepatitis C virus RNA quantification

ObjectiveMonitoring of viral loads (VL) for hepatitis B and C viruses (HBV; HCV) is essential to evaluate disease progression and treatment response. Automated, random-access rapid systems are becoming standard to provide clinicians with reliable VL. The aim of this study was to evaluate the analytical performances of the recently launched NeuMoDx™ for HBV-DNA and HCV-RNA quantification. MethodsClinical samples routinely quantified on the Beckman–Veris system were either retrospectively (frozen samples; HBV n = 178, HCV n = 249), or in parallel (fresh primary tubes; HBV n = 103, HCV n = 117) tested using NeuMoDx™. Linearity range was assessed on serial dilutions of high-titre plasmas containing different genotypes for HBV (A–E, n = 9) and HCV (1a,1b,2–5, n = 12). ResultsOverall test failure, mostly internal control amplification failure, was 2.3% and was not influenced by matrix types (fresh or frozen). For HBV VL, κ agreement was 74%, with 27 (12.6%) discrepancies. Correlation between HBV assays on 72 quantified samples by both methods was excellent (r = 0.963) with a mean bias (NeuMoDx™–Veris) of 0.21 log IU/mL. For HCV VL, κ agreement reached 94%, with 9 (2.8%) discrepancies. The r correlation factor between assays on 104 samples was 0.960 with a mean bias of –0.14 log IU/mL (NeuMoDx™–Veris). Serial dilutions confirmed the claimed linear ranges for all analysed HBV and HCV genotypes. The mean turnaround time was 72 minutes (range 55–101 minutes) for HBV and 96 minutes (range 78–133 minutes) for HCV. ConclusionResults obtained on the NeuMoDx™ confirmed the overall good functionality of the system with a short turn-around-time, full traceability and easy handling. These results on HBV and HCV VL look promising and should be challenged with further comparisons.

Importance of HBsAg recognition by HLA molecules as revealed by responsiveness to different hepatitis B vaccines

Hepatitis B (HB) vaccines (Heptavax-II and Bimmugen) designed based on HBV genotypes A and C are mainly used for vaccination against HB in Japan. To determine whether there are differences in the genetic background associated with vaccine responsiveness, genome-wide association studies were performed on 555 Heptavax-II and 1193 Bimmugen recipients. Further HLA imputation and detailed analysis of the association with HLA genes showed that two haplotypes, DRB1*13:02-DQB1*06:04 and DRB1*04:05-DQB1*04:01, were significantly associated in comparison with high-responders (HBsAb > 100 mIU/mL) for the two HB vaccines. In particular, HLA-DRB1*13:02-DQB1*06:04 haplotype is of great interest in the sense that it could only be detected by direct analysis of the high-responders in vaccination with Heptavax-II or Bimmugen. Compared with healthy controls, DRB1*13:02-DQB1*06:04 was significantly less frequent in high-responders when vaccinated with Heptavax-II, indicating that high antibody titers were less likely to be obtained with Heptavax-II. As Bimmugen and Heptavax-II tended to have high and low vaccine responses to DRB1*13:02, 15 residues were found in the Heptavax-II-derived antigenic peptide predicted to have the most unstable HLA-peptide binding. Further functional analysis of selected hepatitis B patients with HLA haplotypes identified in this study is expected to lead to an understanding of the mechanisms underlying liver disease.

Analytical validation of hepatitis B core-related antigen (HBcrAg) using dried blood spots (DBS).

Limited access to nucleic acid testing (NAT) to quantify HBV DNA levels, an essential tool to determine anti‐HBV treatment eligibility, represents a significant barrier to scale up HBV diagnostic services in resource‐limited countries. Hepatitis B core‐related antigen (HBcrAg) has the potential to become an affordable alternative because of its low cost (US$ <15/assay) and strong correlation with HBV DNA levels in treatment‐naïve patients. However, the current assay requires plasma or serum. To further facilitate its application to decentralized settings, we developed and evaluated a standardized procedure to quantify HBcrAg using dried blood spots as a tool to diagnose HBV‐infected people with high viraemia. We evaluated the following elution method optimized to quantify HBcrAg: suspension of a punched blood‐soaked disc (11 mm) of Whatman 903 Protein Saver Card in 450 µL of PBS 0.05% Tween 20, followed by an incubation for 4 h at room temperature and a centrifugation at 10,000 g for 10 minutes. 150 µL of DBS eluate was used to quantify HBcrAg using chemiluminescent enzyme immunoassay (LUMIPULSE® G600II, Fujirebio). The limit of detection of dried blood spot HBcrAg in relation with HBV DNA levels was 19,115 IU/mL across the five major HBV genotypes (A/B/C/D/E). A strong linear correlation was confirmed between dried blood spot HBcrAg and HBV DNA levels (r = 0.94, p < 0.0001) in samples with high viral loads (range: 3.7–7.0 log IU/mL). The coefficient of variation ranged between 4.0–11.2% for repeatability and 3.9–12.2% for reproducibility. Analytical specificity was 100% (95% CI: 83.9–100%) in HBV‐negative samples. Using our elution method, it may be possible to identify HBV‐infected patients with high viraemia who need antiviral therapy using dried blood spot and HBcrAg. A large‐scale clinical validation is warranted in resource‐limited countries.

Incremental value of HBcrAg to classify 1582 HBeAg-negative individuals in chronic infection without liver disease or hepatitis.

An accurate, single-point differential diagnosis between HBeAg-negative infection (ENI) and chronic hepatitis B (CHB) is an unmet need. To assess the diagnostic value of the new hepatitis B core-related antigen (HBcrAg) assay. A retrospective anonymised data analysis was performed in a multicentre European (nine centres and six countries) cohort of 1582 consecutive HBsAg-positive/HBeAg-negative subjects classified according to EASL guidelines as: 550-CHB, 710-ENI and 322-GZ (grey-zone, HBV-DNA <20000IU/mL). Mean age was 44 (±13.2y), 59% were men; HBV genotypes were 15% A, 2% B, 2% C, 45% D, 9% E, 1% F and 26% unknown. Median HBV-DNA serum levels were 2.2 (1.5-2.7), 3.5 (3.2-3.8) and 5.6 (4.8-6.6) logIU/mL in ENI, GZ and CHB, P<0.0001. HBsAg serum levels (HBsAgsl) were comparable in CHB and GZ, but lower in ENI (2.9 [2.1-3.6] logIU/mL), P<0.0001. HBcrAg serum levels (HBcrAgsl) were <3 logU/mL in 90.7% (644/710) ENI, 75.2% (242/322) GZ and 4.7% (26/550) CHB (P<0.0001). Median HBcrAgsl were 4.8 (3.9-5.7), 2.5 (2.0-2.9) and 2.0 (2.0-2.5) logU/mL in CHB, GZ and ENI, (P<0.0001). ROC-AUCs for HBcrAg and HBsAg were 0.968 (95% CI, 0.958-0.977) and 0.732 (95% CI, 0.704-0.760) respectively. The optimal HBcrAgsl cut-off to distinguish CHB from ENI was 3.14 logU/mL (95% CI, 3.02-3.25, 91% SE, 93% SP and 92.4% DA). HBcrAgsl were associated with HBV genotypes (P<0.001, one-way ANOVA) but using genotype-specific cut-offs, HBcrAg DA remained unchanged with overlapping 95% CI. The HBcrAg assay showed high diagnostic performance in the accurate single-point identification of patients with HBeAg-negative CHB, independently of HBV genotype. This should prompt future prospective studies to confirm its diagnostic role in clinical practice.

Prevalence and characteristics of hepatitis B and D virus infections among HIV-positive individuals in Southwestern Nigeria

BackgroundCoinfections of HIV-positive individuals with Hepatitis B and D virus (HBV and HDV) are common and can be associated with rapid liver damage. Several antiretroviral drugs for HIV exhibit anti-HBV effect; however, the selection of HBV drug resistance mutations (DRMs) in individuals under HIV antiretroviral therapy (ART) has been reported but rarely in Nigeria. In this study the HBV/HDV prevalence and HBV DRMs in HIV-positive individuals in Southwestern Nigeria were assessed.MethodsPlasma samples collected from 310 HIV-positive individuals including 295 ART-experienced and 15 ART-naïve persons attending the HIV clinic in three south-western states of Nigeria between June 2017 and August 2017 were analysed by ELISA for HBsAg and anti-HDV. The presence of HDV RNA and HBV DNA was analysed by (RT)-PCR followed by sequencing and phylogenetic analyses for genotyping. The HBV reverse transcription (RT) region was amplified and sequenced for the analysis of drug resistance mutations.ResultsOverall, 16.1% (n = 50/310) of the HIV-positive individuals were positive for HBsAg, most of which were ART-experienced (94.0%; n = 47/50). From the 50 HBsAg-positive samples, 72.0% (n = 36/50) were positive for HBV DNA and 16.0% (n = 8/50) had detectable HDV RNA while 5.6% (n = 2/36) of the HBV-DNA positive samples had anti-HDV total antibodies. Sequences were available for 31/36 of the HBV DNA-positive and 3/8 HDV RNA-positive samples. HBV DNA-positive samples were characterised as HBV genotype E infections exclusively, while HDV genotype 1 was detected in the HDV RNA-positive samples. HBV DRMs V173L, L180M, S202I and M204V/I, which are associated with lamivudine resistance, were detected in 32.2% (n = 10/31) of the HBV DNA-positive samples. Most of these mutations (90.0%; n = 9/10) were present in the ART-experienced cohort.ConclusionsThis study indicates that HBV/HDV coinfections are common in HIV-positive individuals under ART in Nigeria. Furthermore, a high proportion of HBV DRMs which potentially compromise future treatment options were detected, underscoring the need for HBV screening prior to starting ART. Further studies should be performed to monitor a possible increase in the spread of HDV among populations at risk of HIV and HBV infections.

Analysis of Hepatitis B Virus Genotype D in Greenland Suggests the Presence of a Novel Quasi-Subgenotype.

A disproportionate number of Greenland's Inuit population are chronically infected with Hepatitis B virus (HBV; 5–10%). HBV genotypes B and D are most prevalent in the circumpolar Arctic. Here, we report 39 novel HBV/D sequences from individuals residing in southwestern Greenland. We performed phylodynamic analyses with ancient HBV DNA calibrators to investigate the origin and relationship of these taxa to other HBV sequences. We inferred a substitution rate of 1.4 × 10−5 [95% HPD 8.8 × 10−6, 2.0 × 10−5] and a time to the most recent common ancestor of 629 CE [95% HPD 37–1138 CE]. The Greenland taxa form a sister clade to HBV/D2 sequences, specifically New Caledonian and Indigenous Taiwanese sequences. The Greenland sequences share amino acid signatures with subgenotypes D1 and D2 and ~97% sequence identity. Our results suggest the classification of these novel sequences does not fit within the current nomenclature. Thus, we propose these taxa be considered a novel quasi-subgenotype.

Hepatitis B-related hepatocellular carcinoma: surveillance strategy directed by immune-epidemiology.

Hepatitis B infection (HBV) is one of the most common causes of hepatocellular carcinoma (HCC) worldwide. The age of occurrence, prognosis and incidence vary dramatically depending on the region of the world. This geographic variation is largely dependent on the contrasting incidence of HBV, age of transmission of the virus, the timing of integration into the human genome, and different HBV genotypes, as well as environmental factors. It results in a wide difference in viral interaction with the immune system, genomic modulation and the consequent development of HCC in an individual. In this review, we describe many factors implicated in HCC development, provide insight regarding at-risk populations and explain societal recommendations for HCC surveillance in persons living with HBV in different continents of the world.

Specific determination of hepatitis B e antigen by antibodies targeting precore unique epitope facilitates clinical diagnosis and drug evaluation against hepatitis B virus infection

ABSTRACT Hepatitis B e antigen (HBeAg) is a widely used marker both for chronic hepatitis B (CHB) clinical management and HBV-related basic research. However, due to its high amino acid sequence homology to hepatitis B core antigen (HBcAg), most of available anti-HBe antibodies are cross-reactive with HBcAg resulting in high interference against accurate measurement of the status and level of HBeAg. In the study, we generated several monoclonal antibodies (mAbs) targeting various epitopes on HBeAg and HBcAg. Among these mAbs, a novel mAb 16D9, which recognizes the SKLCLG (aa −10 to −5) motif on the N-terminal residues of HBeAg that is absent on HBcAg, exhibited excellent detection sensitivity and specificity in pairing with another 14A7 mAb targeting the HBeAg C-terminus (STLPETTVVRRRGR, aa141 to 154). Based on these two mAbs, we developed a novel chemiluminescent HBeAg immunoassay (NTR-HBeAg) which could detect HBeAg derived from various HBV genotypes. In contrast to widely used commercial assays, the NTR-HBeAg completely eliminated the cross-reactivity with secreted HBcAg from precore mutant (G1896A) virus in either cell culture or patient sera. The improved specificity of the NTR-HBeAg assay enables its applicability in cccDNA-targeting drug screening in cell culture systems and also provides an accurate tool for clinical HBeAg detection.

Prevalence of Hepatitis B Virus Infection Among Voluntary Blood Donors from the Northeastern Region of Iran: Genotyping, Viral Load Characterization and Drug Resistance Prediction.

Blood donor selection, along with laboratory screening of the HBV, plays a pivotal role in providing safe blood products. This study was aimed to evaluate the prevalence, genotype, and drug resistance prediction of HBV among Iranian blood donors. This cross-sectional study was conducted on 47,506 blood donors referring to Golestan Blood Center from March 21, 2018, to March 20, 2019. Siemens Enzyngnost HBsAg6, INNO-LiPA Genotyping kits, and Nest-PCR were used for HBV screening, genotyping, and amplification of the polymerase gene, respectively. An online tool at hbv.geno2pheno.org and real-time PCR method were also utilized for drug resistance prediction and viral load measurement respectively. It was found that from among 47,506 donors, 47 (0.09%) were confirmed to be HBV positive subjects. About 0.94% of first-time blood donors (46 out of 4, 872) and 0.008% of repeated blood donors (1 out of 12,125) were found to be positive for HBV. First-time blood donors were also 8.6 times more likely to have a hepatitis B virus infection (odds ratio: 9.6; 95% confidence interval, 6.2 - 14.7). Seven donors had genotype D as predominant and one case had a mixed infection with genotypes A and D. Furthermore, the most predicted mutation in the polymerase gene was m204V, causing resistance to telbivudine and lamivudine. The results showed that the risk of HBV transmission is higher among first-time blood donors. Therefore, it is recommended that predonation laboratory screening in first-time blood donors be conducted to improve the safety of the donated blood in the studied region.

Molecular epidemiology of Hepatitis B virus, Hepatitis C virus, and Hepatitis D virus in general population of Afghanistan

This study gives a clue about genotypes, subgenotypes and subtypes of HBV, HCV and HDV viruses in general population of Afghanistan. A total of 234 HBsAg, 44 anti-HCV and 5 Anti-Delta positive patients belong to 25-70 age group were obtained through a rapid screening test among 5898 residents of Afghanistan. After quantifying viral load, genotyping of 61 HBV, 29 HCV and 1 HDV samples were accomplished by sequencing of a segment of the HBV Pre S, HCV NS5B, and HDV Delta antigen regions respectively. Clinically important variants of the HBV polymerase gene, the "a" determinant of HBsAg, HCV NS5B and NS3 regions were assessed. All HBV isolates were dispersed throughout the genotype D branch and ayw2 was the only subtypes found. The anti-HDV prevalence among HBsAg positive individuals was 2.2% and the single HDV sample, belonged to HDV genotype I. Analysis of HCV isolates revealed subtype HCV-1b in 75.86%, HCV-3a in 20.69% and HCV-3b in 3.44% patients. The observed mutant variants in the MHR of HBsAg were Y100 15%, Q101 5%, G102 15%, T115 45%, P120 5%, T131 5%. Likewise, S213T 10%, Q215P 5% and N248H 100% mutations were detected in the HBV polymerase region. C316N mutation was prevalent in 72.7% of HCV 1b participants. Genotypic variation in Afghan patients is in line with the ones existing in neighboring countries and regions. HBV genotypes D1, subtype ayw2, HDV RNA type I, and HCV RNA genotype 1b are likely to be dominant in Afghan patients.

Epidemiological serosurvey and molecular characterization of sexually transmitted infections among 1890 sheltered homeless people in Marseille: Cross-sectional one day-surveys (2000–2015)

ObjectivesWe observed the prevalence and distribution of potential risk factors for sexually transmitted infections (STIs) among Marseille homeless population. MethodsOver the 2000-2015 period, we enrolled 1890 sheltered homeless adults and collected serum samples. Markers of hepatitis B and C viruses (HBV, HCV) and Treponema pallidum were searched using the CMIA testing. Positive HBsAg or anti-HCV samples underwent sequencing; positive anti-T. pallidum sera were subjected to the RPR test. ResultsThe overall prevalence of HBsAg, anti-HBs, anti-HBc, anti-HCV and anti-T. pallidum (by CMIA and RPR) was 4.1%, 22.9%, 35.5%, 5.3% and (6.8%, 1.0%), respectively. We found a significantly higher prevalence of HBsAg and anti-T. pallidum among individuals born in sub-Saharan Africa (or Asia) compared to those born in Europe. Being older (>42 years), toxicomania status, cannabis use and underweight status (compared to normal status) were independent factors associated with HCV seropositivity. Using sequencing, we obtained a substantial diversity of HBV and HCV genotypes. One HCV sequence harbouring a L31M substitution in the NS5a protein may be associated with reduced drug sensitivity. ConclusionsThe positive relationship between toxicomania and HCV suggests the need for effective prevention programmes including health education activities and addiction treatment.

Epidemiological aspects and molecular characterization of the hepatitis B virus among blood donors in Lubumbashi, Democratic Republic of Congo.

The strains of HBV circulating among blood donors in Lubumbashi, Democratic Republic of Congo (DRC), are not yet characterized. The purpose of this study was to determine seroprevalence, changes in biochemical parameters during HBV infection and molecular characterization of HBV in blood donors in Lubumbashi. The detection of HBsAg was carried out by rapid diagnostic test then confirmed by the Liaison XL® Quant HBsAg technique. PCR targeting the P gene was carried out on LightCycler® 96 and genotyping by the sequencing technique on ABI 3500. The seroprevalence was 7.9%. The genotypes E (53.1%), A (41.8%), A3/E (3.8%), A1/E (1.3%) and some drug resistance mutations were identified. Disturbances of HDL-cholesterol, direct bilirubin, transaminases (ASAT and ALAT), PAL, GGT and albumin have been observed in HBsAg positive blood donors. The results of our study indicated that Lubumbashi is in a region with high endemicity for HBV and report for the first time HBV of genotypes A, E, A1/E and A3/E. They highlight the need to implement strategies to improve transfusion safety in blood transfusion centers and hospital blood banks in Lubumbashi in order to reduce HBV infection in recipients. They could also contribute to the implementation of treatment strategies and the development of mapping of circulating HBV genotypes in the DRC.

Quadruple mutation GCAC1809-1812TTCT acts as a biomarker in healthy European HBV carriers.

Many mutation analyses of the HBV genome have been performed in the search for new prognostic markers. However, the Kozak sequence preceding precore was covered only infrequently in these analyses. In this study, the HBV core promoter/precore region was sequenced in serum samples from European inactive HBV carriers. Quadruple mutation GCAC1809-1812TTCT was found with a high prevalence of 42% in the Kozak sequence preceding precore among all HBV genotypes. GCAC1809-1812TTCT was strongly associated with coexistence of basal core promoter (BCP) double mutation A1762T/G1764A and lower HBV DNA levels. In vitro GCAC1809-1812TTCT lead to drastically diminished synthesis of pregenomic RNA (pgRNA), precore mRNA, core, HBsAg, and HBeAg. Calculation of the pgRNA secondary structure suggests a destabilization of the pgRNA structure by A1762T/G1764A that was compensated by GCAC1809-1812TTCT. In 125 patients with HBV-related cirrhosis, GCAC1809-1812TTCT was not detected. While a strong association of GCAC1809-1812TTCT with inactive carrier status was observed, BCP double mutation was strongly correlated with cirrhosis, but this was only observed in absence of GCAC1809-1812TTCT. In conclusion, our data reveal that GCAC1809-1812TTCT is highly prevalent in inactive carriers and acts as a compensatory mutation for BCP double mutation. GCAC1809-1812TTCT seems to be a biomarker of good prognosis in HBV infection.

Prevalence and genetic variability of occult hepatitis B virus in a human immunodeficiency virus positive patient cohort in Gondar, Ethiopia.

Occult hepatitis B (OHB) is a major concern in HIV infected patients as it associates with a high risk of HBV reactivation and disease progression. However, data on the prevalence of OHB among HIV positive patients in Ethiopia is lacking. This study aims to determine the prevalence of OHB in HBV/HIV co-infected patients from Gondar, Ethiopia. A total of 308 consented HIV positive patients were recruited from the University of Gondar Teaching Hospital, Ethiopia. Clinical and demographic data of the participants were recorded. Plasma was tested for HBsAg and anti-HBc using commercial assays (Abbott Architect). In HBsAg negative anti-HBc positive patient samples, total DNA was isolated and amplified using nested PCR with primers specific to HBV polymerase, surface and pre-core/core regions, followed by Sanger sequencing and HBV mutational analysis using MEGA 7.0. Of the total study subjects, 62.7% were female, median age 38.4 years, interquartile range (IQR): 18-68, and 208 (67.5%) had lifestyle risk factors for HBV acquisition. Two hundred and ninety-one study subjects were HIV+/HBsAg-, out of which 115 (39.5%) were positive for anti-HBc. Occult hepatitis B was detected in 19.1% (22/115) of anti-HBc positive HIV patients. HBV genotype D was the predominant genotype (81%) among OHB positive patients. Mutations associated with HBV drug resistance, HBV reactivation, and HCC risk were detected in 23% (5/22), 14% (3/22) and 45.5% (10/22) of patients, respectively. This study found a high rate of occult hepatitis B in HIV patients. Further, high rates of mutations associated with HBV reactivation, drug resistance, and HCC risk were detected in these patients. These data highlighted the need for integrating OHB screening for proper management of liver diseases in HIV patients.

Unexpected findings of hepatitis B and delta infection in northeastern Brazil: A public health alert

Introduction and objectivesResearch has shown that hepatitis B (HBV) and Delta virus (HDV) are a worldwide public health problem. This study aims to estimate the prevalence rates of HBV and HDV infection in five municipalities of Maranhão, Northeastern Brazil. Materials and methodsA total sample between 3856 and 4000 individuals. Questionnaires were used to register sociodemographic characteristics and factors associated with transmission. Patients were tested for hepatitis B virus surface antigen (HBsAg), anti-hepatitis B core antigen (anti-HBc), and antibodies against hepatitis Delta virus (anti-HDV). Factors associated with HBV were detected by means of multivariate Poisson regression. ResultsOverall, 3983 subjects were included. Ninety-two of the participants were HBsAg-positive (2.30%, 95% CI 1.80–2.80), and anti-HBc was detected in 1535 (38.50%, 95% CI 37–40). The factors associated with the presence of anti-HBc were: (1) Municipality (P<0.001); Age (P<0.001); School education (P<0.001); Illicit drug use (P=0.001); non-HBV vaccine (P=0.041). Among the HBsAg carriers, eight were anti-HDV-positive (8.69%, 95% CI 2.90–14.40). The most frequent HBV genotype was D4. The only HDV genotype was HDV-8. ConclusionHBV exhibited intermediate endemicity in the studied region. Traditional factors were associated with exposure to the virus. The presence of the HDV was confirmed. The most frequent HBV and HDV genotypes were unlike the ones currently described in Brazil.

Using Quasispecies Patterns of Hepatitis B Virus to Predict Hepatocellular Carcinoma With Deep Sequencing and Machine Learning.

Hepatitis B virus (HBV) infection is one of the main leading causes of hepatocellular carcinoma (HCC) worldwide. However, it remains uncertain how the reverse-transcriptase (rt) gene contributes to HCC progression. We enrolled a total of 307 patients with chronic hepatitis B (CHB) and 237 with HBV-related HCC from 13 medical centers. Sequence features comprised multidimensional attributes of rt nucleic acid and rt/s amino acid sequences. Machine-learning models were used to establish HCC predictive algorithms. Model performances were tested in the training and independent validation cohorts using receiver operating characteristic curves and calibration plots. A random forest (RF) model based on combined metrics (10 features) demonstrated the best predictive performances in both cross and independent validation (AUC, 0.96; accuracy, 0.90), irrespective of HBV genotypes and sequencing depth. Moreover, HCC risk scores for individuals obtained from the RF model (AUC, 0.966; 95% confidence interval, .922-.989) outperformed α-fetoprotein (0.713; .632-.784) in distinguishing between patients with HCC and those with CHB. Our study provides evidence for the first time that HBV rt sequences contain vital HBV quasispecies features in predicting HCC. Integrating deep sequencing with feature extraction and machine-learning models benefits the longitudinal surveillance of CHB and HCC risk assessment.

Optimization of the algorithm diagnosis chronic hepatitis B markers in patients with newly diagnosed HIV infection.

The possibility of modifying the algorithms for chronic viral hepatitis B laboratory diagnosis in individuals with newly diagnosed HIV infection is analyzed. Plasma samples were used from 196 patients residing in the Northwestern Federal District. Serological HBV markers were found in 79.6% of cases. However, HBsAg was detected in 5.6% of patients. Anti-HBcore IgG antibodies are found in 62.24% of cases, anti-HBe IgG antibodies in 27.55%, anti-HBs IgG antibodies in 52.55% of cases. Using a commercial kit with a 100 IU / ml sensitivity, HBV DNA was detected in 4.6% of patients, that is, 81.8% of HBsAg-positive individuals. Using the method developed by us, HBV DNA was found in 18.36% of HIV-infected individuals, including 12.75% of cases was HBsAg-negative (latent) disease form. In the examined group, HBV of genotype D prevailed (91.7%), genotype A was detected in 8.3% of cases. The distribution of subgenotypes is presented in the following ratios: D2 - 55.6%, D1 - 22.2%, D3 - 13.9%, A2 - 8.3%. Mutations were detected in the reverse transcriptase (RT) region in 91.6% of patients, in the SHB region in 83.3%, in the Core and Precore regions in 72.2% and in 27.7% of patients, respectively. Three HBV isolates (8.3%) were identified with drug resistance mutations to lamivudine, entericavir, telbivudine and tenofovir, which are amino acid substitutions in the HBV polymerase gene at positions L180M, T184A, M204V. Vaccine escape mutations were detected in 61.1% of patients. In all samples with drug resistance mutations, escape-mutants were simultaneously present. When analyzing the basal nucleus promoter, Precore and Core regions, 22.2% of patients with the double mutation A1762T / G1764A, 25% with the mutation G1896A were identified. In one person, all three substitutions were found. In the Core region, 77.7% of patients showed mutations in one of the hot spots (codons 87, 97, 112, and 130 substitution), which can play a role in immunomodulation in CHB. Analysis of the HBV genetic structure, mutations detection early in the virus in patients with HBV can help predict the clinical course and disease progression, and ART complications. To reduce the HIV HBV co-infection burden and to appointer anti-HBV therapy, it is necessary to introduce detection the occult HBV to modify the algorithm for CHB laboratory diagnosis.

Distribution of hepatitis B virus genotypes in the general population of Myanmar via nationwide study

BackgroundHepatitis B virus (HBV) infections are a severe health concern worldwide. HBV is a DNA virus with a rapid rate of mutation. Based on heterogeneity of the nucleotide sequence, the HBV strains are divided into nine genotypes, each with a characteristic geographical distribution. Identifying and tracking alterations of HBV genotypes is important in epidemiological and transmission studies, and contributes to predicting the risk for development of severe liver disease and response to antiviral treatment. The present study was undertaken to detect HBV genotypes and sub-genotypes in the general population of different states and regions in Myanmar.MethodsIn 2015, a total of 5547 adults of the general population, residing in seven states, seven regions and the Nay Pyi Taw Union Territory, were screened for Hepatitis B Surface antigen (HBsAg) by the immunochromatographic test (ICT). Of the 353 HBsAg positive samples, the HBVDNA was identified using polymerase chain reactions (PCR) targeting the DNA sequences encoding the Pre-S region. A total of 153 PCR positive samples were subsequently subjected to genotyping by partial genome sequencing in both directions. The resulting sequences were then edited, aligned, and compared with reference sequences using the National Centre for Biotechnology Information (NCBI) web-based genotyping tool.ResultsThree HBV genotypes (HBV genotype B, genotype C and genotype D) were detected in Myanmar, of which genotype HBV genotype C (66.7%) was the most prevalent, followed by HBV genotype D (32%) and HBV genotype B (1.3%). Sub-genotyping revealed a total of 7 variants within the B, C and D genotypes: 2 (B4 and B5) in HBV genotype B, 3 (C1, C5 and C7) in HBV genotype C, and 2 (D3 and D6) in HBV genotype D.ConclusionHBV genotype C, sub-genotype C1 was predominantly distributed in all states and regions of Myanmar. This study is the first report on the nationwide distribution of HBV genotypes and sub-genotypes in Myanmar. We believe our findings will enable huge support for the hepatitis disease surveillance program, since HBV infection is one of the National Priority Diseases in Myanmar.

Clinical significance and mutation characteristics in the core promoter/pre-C region of different HBV genotypes in children

Objective: To understand the clinical significance and mutation characteristics in the basic core promoters and pre-C region (BCP/PC) of different hepatitis B virus genotypes samples of infected children. Methods: A total of 294 children and 92 adults with CHB infection who were treated at four hospitals in Chongqing from 2011 to 2018 were collected. The BCP / PC region of HBV was amplified by PCR and sequenced directly to comparatively analyze the gene mutation conditions in this region. The two sample means were compared by the t-test, and the nonparametric data was compared by Wilcoxon-Mann-Whitney test. χ2 test or Fisher's exact test was used to compare the data rates of the two groups. Results: Children and adult patients were dominated by genotype B; accounting for 76.9% and 71.7%, respectively, and genotype C accounted for 23.1% and 28.3%, respectively. In the children group, the mutation rates of ten nucleotide sites containing nt 1679, 1721, 1753, 1757, 1758, 1762, 1764, 1775, 1856 and 1858 of the genotype C samples was significantly higher than that of genotype B samples. The mutation rates of G1721a, C1856t and T1858c of genotype C samples were 30.9%, 16.2% and 30.9%, respectively, while the mutation rates of genotype B samples were 0.4%, 0, 0, P < 0.001, respectively. In the adult group, the only three sites containing nt 1679, 1758, and 1775 of the genotype C sample had a higher mutation rate than the genotype B samples. The combined mutations pattern were only detected in children with genotype C samples, but not in children and adult with genotype B samples. Further analysis showed that the age of G1721A/A1775G/T1858C containing combined mutation group was significantly lower than that of the non-mutation group [(4.58 ± 2.53) years vs. (6.53 ± 4.02) years, P = 0.012]. Serum HBV DNA titer was significantly higher in combined mutation group than that of the non-mutation group [(7.57 ± 2.03) log10 copies / ml vs. (6.61 ± 2.11) log10 copies / ml, P = 0.045]. Conclusion: The frequencies of mutations in the BCP/PC region of HBV-infected children in genotype C samples were significantly higher than that of genotype B samples. Genotype-related combined site mutations were only found in children with genotype C samples, and were also associated with younger patients and high HBV-DNA titers.

Excavating new facts from ancient Hepatitis B virus sequences

Recently, two independent studies discovered 15 ancient Hepatitis B virus (aHBV) sequences, of which 7 dated back to the Neolithic age (NA) and the Bronze Age (BA). In the present research, all the available aHBV sequences were collectively re-analysed with reference to extant HBV diversity to understand the role of these aHBV genotypes in evolution of extant HBV genetic diversity. Several intergenotype recombination events were documented, which corroborated well with population admixture and ancient human migration. Present analyses suggested replacement of HBV genotype associated with early Neolithic European farming cultures by the migrating steppe people, during Bronze Age Steppe migration. Additionally, detailed analyses of recombinations revealed evolution of a number of extant genotypes and suggested their possible site of origin. Through this manuscript, novel and important findings of the analyses are communicated.