Interdisciplinary Collaboration to Develop a Custom Genomic Analysis Pipeline for the Clinical Laboratory: Hepatitis B Virus and Cytomegalovirus Antiviral Resistance Genotyping.

Pre-S Deletion and Complex Mutations of Hepatitis B Virus Related to Advanced Liver Disease in HBeAg-Negative Patients

Hepatitis B virus (HBV) is a highly variable DNA virus due to its unique life cycle, which involves an error-prone reverse transcriptase. The high substitution rate drives the evolution of HBV by generating genetic variants upon which selection operates. HBV mutants with clinical implications have been documented worldwide, indicating the potential for spreading and developing their own epidemiology. However, the prevalence of such mutants among the different HBV genotypes and subgenotypes has not been systematically analyzed. In the current study, we performed large-scale analysis of 6,479 full-length HBV genome sequences from genotypes A-H, with the aim of gaining comprehensive insights into the relationships of relevant mutations associated with immune escape, antiviral resistance and hepatocellular carcinoma (HCC) development with HBV (sub)genotypes and geographic regions. Immune escape mutations were detected in 10.7% of the sequences, the most common being I/T126S (1.8%), G145R (1.2%), M133T (1.2%), and Q129R (1.0%). HBV genotype B showed the highest rate of escape mutations (14.7%) while genotype H had no mutations (P < 0.001). HCC-associated mutations were detected in 33.7% of the sequences, with significantly higher frequency of C1653T, T1753V and A1762T/G1764A in genotype G than C (P < 0.001). The overall frequencies of lamivudine-, telbivudine-, adefovir-, and entecavir-resistant mutants were 7.3, 7.2, 0.5, and 0.2%, respectively, while only 0.05% showed reduced susceptibility to tenofovir. In particular, the highest frequency of lamivudine-resistant mutations was observed in genotype G and the lowest frequency in genotype E (32.5 and 0.3%; P < 0.001). The prevalence of HBV mutants was also biased by geographic location, with North America identified as one of the regions with the highest rates of immune escape, antiviral resistance, and HCC-associated mutants. The collective findings were discussed in light of natural selection and the known characteristics of HBV (sub)genotypes. Our data provide relevant information on the prevalence of clinically relevant HBV mutations, which may contribute to further improvement of diagnostic procedures, immunization programs, therapeutic protocols, and disease prognosis.

The direct cytopathic effects of the hepatitis B virus (HBV) on subsequent liver damage are not fully understood in HBV-infected patients. However, associations between the prevalence of various HBV genotypes and the extent of liver damage have been reported from different parts of the world. The purpose of this study was to determine the distribution of HBV genotypes in patients with chronic HBV infection in Bangladesh, a country of 160 million people, of which approximately 3–6 million are chronically infected HBV patients. In addition, whole and partial genome sequencing of HBV was performed to evaluate the relationship between HBV mutations and genotypes. We found that 42% of the patients with low HBV DNA and normal levels of alanine aminotransferase (ALT) had HBV genotype D. In contrast, the HBV genotype C was dominant among patients with high HBV DNA levels (>2000 IU/ml) and elevated ALT and in patients with liver cirrhosis (LC) and hepatocellular carcinomas (HCC). Whole and partial genome sequences of HBV revealed that most patients with LC and HCC had HBV genotype C with mutations at the T1762/A1764 positions. It seems that Bangladesh represents a borderline country, situated within East Asia, which mainly consists of individuals with HBV genotypes B and C, whereas in the western parts of Asia, HBV genotypes A and D are prevalent. Bangladesh is, therefore, an excellent model for the comparison of the pathophysiology of three major HBV genotypes in a single population. The findings of this study suggest a possible association between HBV viral factors and the extent of liver damage in chronic HBV-infected patients.

Preventing Infection-Associated Cancer: From Bench to Hillside

Hepatitis D and B virus genotypes in chronically infected patients from the Eastern Amazon Basin

Although chronic infection with hepatitis B virus (HBV) has been established as a cause of hepatocellular carcinoma (HCC), the roles of viral load and HBV genotype remain unclear. From 1988 through 1992, baseline blood samples were collected from 4841 Taiwanese men who were HBV carriers but had not been diagnosed with HCC. We used real-time polymerase chain reaction assays of plasma DNA samples to quantify HBV DNA levels (a measure of viral load) and determine HBV genotypes for 154 case patients who were diagnosed with HCC during 14 years of follow-up and 316 control subjects. Unconditional logistic regression was used to assess odds ratios (ORs) of HCC for HBV-related factors. All statistical tests were two-sided. The risk of HCC increased with increasing HBV viral load (adjusted OR for the highest versus the lowest quintile of HBV DNA copies/mL = 7.26, 95% confidence interval [CI] = 3.54 to 14.89; P(trend)<.001). Genotype C HBV was associated with an increased risk of HCC compared with other HBV genotypes (adjusted OR = 5.11, 95% CI = 3.20 to 8.18). Both viral load and genotype were positively associated with HCC within 10-year age categories among subjects aged 30 years old to older than 60 years. Genotype C HBV was associated with increased viral load, and associations of HBV genotype and viral load with HCC risk were additive. The adjusted OR of HCC for those carrying genotype C HBV and with viral load in the highest quintile was 26.49 (95% CI = 10.41 to 67.42) compared with HBV carriers with other HBV genotypes and viral load in the lowest two quintiles. Measurements of HBV viral load and genotype may help to define which male HBV carriers aged 30 years or older are at high risk for HCC.

Hepatitis viruses (hepatotropic viruses) are classified into five ‎kinds, denoted by the letters A, B, C, D, and E, each with its ‎own unique genotypes, clinical implications, and geographic ‎distribution. Viral hepatitis is a type of liver inflammation that ‎can resolve on its own or proceed to cirrhosis or hepatocellular ‎cancer. Hepatitis A, B, and C infections are the most common ‎types of infectious viral hepatitis. Over the previous five ‎decades, hepatitis B virus (HBV) infection has exhibited an ‎intermediate or high endemicity level in low-income nations. ‎HBV genotype variation is thought to be crucial in regulating ‎disease development, infection outcome, antiviral therapy ‎response, and illness prognosis. HBV is divided into ten ‎genotypes (A-J) and roughly 40 sub-genotypes, correlated with ‎different geographic distributions, transmission routes, and ‎disease progression. The goal of this study was to figure out ‎the current status of HBV prevalence and genotype distribution ‎in West African countries. HBV genotypes A, D, and E have ‎been reported the most widely prevalent genotypes in Africa so ‎far, while there are limited reports of genotypes B and C. HBV ‎genotype A is shown to be more prevalent in Africa than on ‎other continents, implying that it has an African origin. ‎Genotype D has been found across Africa, particularly in the ‎Mediterranean and North African regions. Except in Africa, HBV ‎genotype E infection is extremely rare, even when infection ‎with this genotype has been recorded outside of Africa, it has ‎virtually always been in African origin people. Within Africa, ‎HBV genotype E is abundant and broad across the continent, ‎reaching from Senegal's west coast to Namibia's southwestern ‎tip and eastward to the Central African Republic. These ‎epidemiological findings and differences have important ‎implications for the immunization, antiviral therapy, and clinical ‎outcomes of HBV on a national and regional level.‎

Genetic variability of hepatitis B virus and response to antiviral treatments: Searching for a bigger picture

Hepatitis delta virus (HDV) and hepatitis B virus (HBV) have been identified as major causes of morbidity and mortality in Pakistan because HDV causes infection only in the presence of HBV. Coinfection with both hepatitis viruses can lead to a more severe acute form of disease and to an increased risk of fulminant hepatitis. HDV infection differs in its distribution and severity depending on the geographical distribution, and several genotypes of HDV have been identified so far. The aim of the present study was to establish the HDV and HBV genotypes in chronically infected Pakistani patients and to determine whether there is any correlation between HDV and HBV genotypes. We studied samples from a total of 46 chronically infected HBV and HDV patients for HBV and HDV genotype analysis out of a total of 75 chronic HBV carriers enrolled. HBV and HDV genotypes were determined using type-specific PCR, followed by sequencing of PCR amplified products. The results of HBV genotyping showed that 33 of 46 (71.7%) patients had genotype D, five (10.9%) had A+D mixed genotypes, whereas eight (17.3) samples were untypable. We could detect only one HDV genotype (HDV-1) prevalent in the Pakistani population. The HDV-1 genotype isolate was associated with HBV genotype D alone or in combination with A (HBV-A+D). The present study concludes that HDV/HBV coinfection is very high in the Pakistani population and was previously underestimated. The most prevalent circulating genotypes of HBV and HDV are HDV-1 and HBV-D, respectively, in the studied area. There is no specific interaction between HBV and HDV genotypes as suggested by HDV-1/HBV-D or HDV-1/HBV-A+D coinfection. Coinfection of HDV-1 and HBV-D simply reflects the most frequent genotypes circulating in this specific geographical region of the world.

Aim: Hepatitis B virus (HBV) is not uncommon among animal and non-animal handlers. The brutality of HBV infection and the outcome of treatment is linked with exact HBV genotypes. No study on the circulation of HBV genotypes has been reported among animal and non-animal handlers in Nigeria. This study was intended to evaluate the genotypic distribution among animal and non-animal handlers in Osun State, Nigeria.&#x0D; Study Design: Cross-sectional study.&#x0D; Place and Duration of Study: Ladoke Akintola University of Technology (LAUTECH), Nigeria, between June 2015 and July 2019.&#x0D; Methods: Blood samples were obtained from HBsAg positive individuals and screened for HBV-DNA from cohorts of animal and non-animal handlers. HBV-DNA was extracted, amplified and genotyped using a multiplex PCR technique with primers specific for six genotypes of HBV (Genotype A, B, C, D, E and F).&#x0D; Results: Results showed that a total of 11 (6.1%) of the 180 animal and non-animal handlers evaluated were positive to HBsAg and 4.4% were positive for HBV-DNA by a semi-nested PCR using HBV specific primer pairs. The molecular analysis of the sera of 11 HBsAg positive animal and non-animal handlers showed that 72.7% of them had a true HBV infection. Results further show that genotype E (75.0%) was predominant over genotype A (12.5%) and mix genotypes (D and E) with 12.5% prevalence. Other genotypes were not detected. Of the 8 positive HBV-DNA samples, 7 (87.5%) were males and one (12.5%) was a female. All animal and non-animal handlers with true HBV infection were found to harbour HBV genotype E predominantly.&#x0D; Conclusion: The molecular analysis of HBV-DNA and genotypes circulating among animal and non-animal handlers shows that the majority of the subjects with true HBV infection were found to predominantly harbour HBV genotype E in Osun state, Nigeria. The study further highlights the predominance HBV genotype E in Nigeria.

Lamivudine Plus Low-Dose Hepatitis B Immunoglobulin to Prevent Recurrent Hepatitis B Following Liver Transplantation

Infection with hepatitis B virus (HBV) is a major global public health problem, with an estimated prevalence of 350 million chronic carriers worldwide, and 1.5 million in the United States. The majority of HBV-infected individuals are concentrated in Asia and subSaharan Africa, but the incidence is rising is Western countries as a result of changing migration patterns. Chronic HBV infection can lead to liver cirrhosis, hepatic decompensation, and premature death. As many as 25% of HBV-infected patients will develop hepatocellular carcinoma (HCC), which is the fourth most common solid tumor worldwide. As much as a 50% reduction in the incidence of HBV transmission has been achieved in certain countries through widespread vaccination programs. Reduction in the morbidity and mortality of HBV-related HCC has been achieved as a result of intensive screening programs and through antiviral treatment with agents such as lamivudine and interferon. Because the majority of HCC cases worldwide are HBV-associated, HCC is truly a preventable malignancy. Given the considerable number of patients who are at risk for developing chronic HBV infection and its deadly sequelae, the costs associated with screening and treatment are similarly enormous. The challenge, therefore, is to select those patients most likely to benefit from HBV treatment and HCC screening to maximize the benefit-cost ratio of such programs. Any opportunity to optimize selection of patients for HBV treatment and HCC screening, and thereby reduce the incidence of HCC, should result in a significant public health benefit. HBV has been classified into eight genotypes, designated by capital letters A through H. HBV genotypes have distinct geographic distributions, with genotypes B and C being the most prevalent in Asia. Several studies have demonstrated that genotype C is associated with a higher prevalence of hepatitis B e antigen (HBeAg), more active hepatitis, and more advanced liver disease than genotype B. In a cross-sectional study of 270 Taiwanese HBV carriers with various forms of liver disease, genotype C was more prevalent in patients with cirrhosis and in those with HCC older than 50 years compared with age-matched asymptomatic carriers. Furthermore, HBV genotype C has been shown to be an independent risk factor for development of HCC. In a study of 426 Chinese patients infected with HBV, 25 patients developed HCC during a median follow-up of 121 weeks. Cirrhosis and HBV genotype C infection were independently associated with HCC development. In a study of 4,841 Taiwanese male hepatitis B s antigen (HBsAg) carriers, there were 154 cases of HCC diagnosed during a 14-year follow-up period. HBV DNA levels and HBV genotypes were determined for all patients with HCC and 316 control subjects. Results indicated that the risk of HCC increased with increasing HBV viral load. Moreover, genotype C was associated with an increased risk of HCC compared with other HBV genotypes (adjusted odds ratio [OR] 5.11; 95% CI, 3.20 to 8.18). In that study, the association of HBV genotype C and HBV viral load with HCC risk appeared to be additive. The adjusted OR of HCC for those carrying genotype C and with viral load in the highest quintile was 26.49 (95% CI, 10.41 to 67.42) compared with those carrying other HBV genotypes and lower viral loads. These and other recent studies have been paramount in our understanding of the factors that influence clinical outcome in HBV infection. However, it appears that HBV genotype is only one of the elements associated with hepatocarcinogenesis. Mutations in the basic core promoter (BCP) and precore regions carry an increased risk of HCC. In a cross-sectional, retrospective study of 160 chronic HBV carriers and 200 patients with HCC, advanced age, male sex, the precore A1896 mutation, the BCP T1762/A1764 mutation, and a high HBV load were significantly associated with development of HCC. There has also been recent interest in studying the relationship among HBV genotypes, subgenotypes, and mutations encountered in HBV carriers. Whether these have additive or synergistic effects on the risk of HCC development remains unclear. It has been reported that patients with genotype B have a higher chance of harboring precore mutations when compared with patients with genotype C. In the same study, core promoter mutations, T1653 mutations, HBV DNA levels of at least 4 log10 copies/mL, and cirrhosis were shown on to be independent risk factors for HCC. HBV genotype C has been classified into four subgenotypes: HBV/C1-C4. The designation of the two most widely disseminated subgenotypes is controversial. HBV/C1 (or Cs) is commonly found in Southeast Asia. HBV/C2 (or Ce) is found in East Asia including Japan and China. There are limited data on the clinical implications and JOURNAL OF CLINICAL ONCOLOGY E D I T O R I A L VOLUME 26 NUMBER 2 JANUARY 1

Most cases of hepatocellular carcinoma (HCC) are associated with cirrhosis related to chronic hepatitis B virus (HBV) or hepatitis C virus (HCV) infection. Changes in the time trends of HCC and most variations in its age-, sex-, and race-specific rates among different regions are likely to be related to differences in hepatitis viruses that are most prevalent in a population, the timing of their spread, and the ages of the individuals the viruses infect. Environmental, host genetic, and viral factors can affect the risk of HCC in individuals with HBV or HCV infection. This review summarizes the risk factors for HCC among HBV- or HCV-infected individuals, based on findings from epidemiologic studies and meta-analyses, as well as determinants of patient outcome and the HCC disease burden, globally and in the United States.

Hepatitis B Virus (HBV) infection is a global health concern. HBV genotypes differ in disease potential and geographical distribution. These genotypes impact the diagnostic and preventive strategies. Furthermore, limited data are available on Torque Teno Virus (TTV) co-infections with HBV. Hence, this study evaluated HBV infection prevalence, genotype distribution, and the presence of TTV among HBV-positive patients. During the study period, a total of 1820 serum samples were collected and tested for HBsAg using ELISA method. Of this, 43 (2.36%) were HBsAg positive. These HBsAg-positive samples were further subjected to conventional PCR followed by Sanger sequencing for HBV and TTV genotype detection. In this study, only HBV genotypes D (subgenotype D2) (97%) and A (subgenotype A1) (3%) were detected. 15% of HBV-infected patients were positive for TTV in which genotype 1A was detected in 66.67% of cases and 1B in 33.33% of cases. To the best of our knowledge, this study represents the first of its kind from Puducherry to document Torque Teno Virus (TTV) co-infection in HBV-positive cases from the non-renal transplant population. This study underscores the significance of HBV genotypes and TTV co-infection in HBV patients. Further studies and surveillance are needed to monitor circulating HBV genotypes and explore TTV's role in co-infection, particularly its pathogenesis and clinical implications.

Objective To study the relationship between Hepatitis B virus (HBV) genotypes and antiviral efficacy of adefovir dipivoxil (ADV). Methods Sixteen patients with chronic hepatitis B (CHB) received ADV therapy for 92 weeks. Blood samples were collected at week 0, 12, 16, 28, 40,48, 52, 68, 80 and 92. Alanine aminotransferase (ALT) and HBV DNA titer were determined by automatic biochemistry analysator and fluorescence quantitative real-time PCR respectively. HBV genomes were retrieved with full-length PCR from sera samples of week 0, 28, 52 and 92. And then the genomes were sequenced and genotyped. The curative effects were compared in different gcnotypes at all time points. Results (1) There were no statistically significant differences in levels of HBV DNA and ALT of different genotype patients with CHB before A DV treatment (all P>0.05 ) . There were no statistically significant differences in changes of HBV DNA load , normalization of ALT and seroconversion of HBeAg at all time points between the HBV genotype B and HBV genotype C patients with CHB (all P>0.05). The effective inhibition rates of HBV DNA were both 100% in the HBV genotype B and HBV genotype C patients at week 92. (2) In all the 16 patients with CHB, 9 patients were genotype B,6 patients were genotype C and 1 patient was co-infected by genotype B and C. HBV genotype switching was observed in 5 patients (from B to C, or from C to B) after ADV treatment. Conclusions There is no significant difference in response to ADV treatment between the HBV genotype B and HBV genotype C patients with CHB in terms of virology, serology and biochemistry. It indicates that the HBV genotypes may have no influence on the antiviral efficacy of ADV treatment. Key words: Hepatitis B virus; Genotype; Adefovir dipivoxil; Antiviral therapy; Treatment effectiveness