Special Issue "Structural Variations and Molecular Genetics of Hepatitis Virus and Related Viruses".

In this special issue, we present collected updated data on the hepatitis viruses [...].

Viral Hepatitis: Etiology, Epidemiology, Transmission, Diagnostics, Treatment, and Prevention.

Viral hepatitis is a major global public health problem affecting hundreds of millions of people and is associated with significant morbidity and mortality. Five major biologically unrelated hepatotropic viruses cause most of the global burden of viral hepatitis. Hepatitis B and hepatitis C are associated with a significant number of chronic infections. Most deaths from viral hepatitis are due to hepatitis B and hepatitis C. An estimated 257 million people were living with HBV and 71 million people were living with HCV. Most people are asymptomatic. New diagnostics and highly effective, pangenotypic direct-acting antivirals provide opportunities to cure and eradicate chronic hepatitis C virus infection.

Electronic health record year and country of birth testing and patient navigation to increase diagnosis of chronic viral hepatitis.

The United States Preventive Services Task Force recommends hepatitis C testing people born from 1945 to 1965, "birth cohort" as well as hepatitis C and hepatitis B testing people from countries of birth with endemic infection risk. We automated the hospital electronic health record system to test birth cohort and those born in countries with endemic infection risk. A script is launched searching the laboratory database upon registration for any hepatitis C antibody, hepatitis C RNA and/or hepatitis B surface antigen result. If no positive result was found, a hepatitis C antibody/reflex RNA and/or hepatitis B surface antigen were ordered. A patient navigator received weekly results and assisted patients with positive serology to schedule an appointment with their primary care provider or treatment specialist. A total of 10 726 participants were hepatitis C antibody tested, with 6.9% antibody positive. Monthly hepatitis C testing from January to July 2016 compared to August 2016-August 2017 increased 342% as a result of "birth cohort" testing. Following country of birth testing, monthly hepatitis B and hepatitis C testing increased 91%, and 44%, respectively, during June-August 2017 compared to September 2017-March 2018. 67% of hepatitis C-positive patients were linked to care. If the navigator contacted the patient, 92% were linked to care, and 32% were treated. Of hepatitis B surface antigen-positive patients, 43% were linked to care, 5% were on treatment, and 15% started treatment. Automated electronic health record ordering of hepatitis C and/or hepatitis B testing is feasible and increases testing. In the population tested, much improvement is needed with linkage to care and treatment.

Evolutionary biology of human hepatitis viruses.

Hepatitis viruses are major threats to human health. During the last decade, highly diverse viruses related to human hepatitis viruses were found in animals other than primates. Herein, we describe both surprising conservation and striking differences of the unique biological properties and infection patterns of human hepatitis viruses and their animal homologues, including transmission routes, liver tropism, oncogenesis, chronicity, pathogenesis and envelopment. We discuss the potential for translation of newly discovered hepatitis viruses into preclinical animal models for drug testing, studies on pathogenesis and vaccine development. Finally, we re-evaluate the evolutionary origins of human hepatitis viruses and discuss the past and present zoonotic potential of their animal homologues.

Detection and Characterization of Homologues of Human Hepatitis Viruses and Pegiviruses in Rodents and Bats in Vietnam.

Rodents and bats are now widely recognised as important sources of zoonotic virus infections in other mammals, including humans. Numerous surveys have expanded our knowledge of diverse viruses in a range of rodent and bat species, including their origins, evolution, and range of hosts. In this study of pegivirus and human hepatitis-related viruses, liver and serum samples from Vietnamese rodents and bats were examined by PCR and sequencing. Nucleic acids homologous to human hepatitis B, C, E viruses were detected in liver samples of 2 (1.3%) of 157 bats, 38 (8.1%), and 14 (3%) of 470 rodents, respectively. Hepacivirus-like viruses were frequently detected (42.7%) in the bamboo rat, Rhizomys pruinosus, while pegivirus RNA was only evident in 2 (0.3%) of 638 rodent serum samples. Complete or near-complete genome sequences of HBV, HEV and pegivirus homologues closely resembled those previously reported from rodents and bats. However, complete coding region sequences of the rodent hepacivirus-like viruses substantially diverged from all of the currently classified variants and potentially represent a new species in the Hepacivirus genus. Of the viruses identified, their routes of transmission and potential to establish zoonoses remain to be determined.

Detection of newly discovered KIs virus in India.

KIs virus (KIs-V) is a putative new hepatitis virus recently identified from Japan. Prevalence of this virus was found to be significantly higher in individuals with past exposure to hepatitis E virus and having moderately raised alanine aminotransferase levels. The present work was undertaken to see the circulation of this virus in India. Blood samples (n=648) collected during hepatitis E outbreaks from different states (1990-2014) were screened by PCR. One anti- HEV IgM positive serum was found to be positive for two closely related viruses, one with 100% and other with 94.4% homology with the KIs-V sequence reported from Japan. This is the first evidence of KIs-V occurrence in India. Significance of association between KIs-V and hepatitis E virus still remains unanswered. Further studies are needed for understanding pathogenesis of KIs-V in humans.

Hepatitis Virus Infections in Poultry.

Viral hepatitis in poultry is a complex disease syndrome caused by several viruses belonging to different families including avian hepatitis E virus (HEV), duck hepatitis B virus (DHBV), duck hepatitis A virus (DHAV-1, -2, -3), duck hepatitis virus Types 2 and 3, fowl adenoviruses (FAdV), and turkey hepatitis virus (THV). While these hepatitis viruses share the same target organ, the liver, they each possess unique clinical and biological features. In this article, we aim to review the common and unique features of major poultry hepatitis viruses in an effort to identify the knowledge gaps and aid the prevention and control of poultry viral hepatitis. Avian HEV is an Orthohepevirus B in the family Hepeviridae that naturally infects chickens and consists of three distinct genotypes worldwide. Avian HEV is associated with hepatitis-splenomegaly syndrome or big liver and spleen disease in chickens, although the majority of the infected birds are subclinical. Avihepadnaviruses in the family of Hepadnaviridae have been isolated from ducks, snow geese, white storks, grey herons, cranes, and parrots. DHBV evolved with the host as a noncytopathic form without clinical signs and rarely progressed to chronicity. The outcome for DHBV infection varies by the host's ability to elicit an immune response and is dose and age dependent in ducks, thus mimicking the pathogenesis of human hepatitis B virus (HBV) infections and providing an excellent animal model for human HBV. DHAV is a picornavirus that causes a highly contagious virus infection in ducks with up to 100% flock mortality in ducklings under 6 wk of age, while older birds remain unaffected. The high morbidity and mortality has an economic impact on intensive duck production farming. Duck hepatitis virus Types 2 and 3 are astroviruses in the family of Astroviridae with similarity phylogenetically to turkey astroviruses, implicating the potential for cross-species infections between strains. Duck astrovirus (DAstV) causes acute, fatal infections in ducklings with a rapid decline within 1-2 hr and clinical and pathologic signs virtually indistinguishable from DHAV. DAstV-1 has only been recognized in the United Kingdom and recently in China, while DAstV-2 has been reported in ducks in the United States. FAdV, the causative agent of inclusion body hepatitis, is a Group I avian adenovirus in the genus Aviadenovirus. The affected birds have a swollen, friable, and discolored liver, sometimes with necrotic or hemorrhagic foci. Histologic lesions include multifocal necrosis of hepatocytes and acute hepatitis with intranuclear inclusion bodies in the nuclei of the hepatocytes. THV is a picornavirus that is likely the causative agent of turkey viral hepatitis. Currently there are more questions than answers about THV, and the pathogenesis and clinical impacts remain largely unknown. Future research in viral hepatic diseases of poultry is warranted to develop specific diagnostic assays, identify suitable cell culture systems for virus propagation, and develop effective vaccines.

Multiplex qPCR for serodetection and serotyping of hepatitis viruses: A brief review.

The present review describes the current status of multiplex quantitative real time polymerase chain reaction (qPCR) assays developed and used globally for detection and subtyping of hepatitis viruses in body fluids. Several studies have reported the use of multiplex qPCR for the detection of hepatitis viruses, including hepatitis A virus (HAV), hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis D virus (HDV), and hepatitis E virus (HEV). In addition, multiplex qPCR has also been developed for genotyping HBV, HCV, and HEV subtypes. Although a single step multiplex qPCR assay for all six hepatitis viruses, i.e., A to G viruses, is not yet reported, it may be available in the near future as the technologies continue to advance. All studies use a conserved region of the viral genome as the basis of amplification and hydrolysis probes as the preferred chemistries for improved detection. Based on a standard plot prepared using varying concentrations of template and the observed threshold cycle value, it is possible to determine the linear dynamic range and to calculate an exact copy number of virus in the specimen. Advantages of multiplex qPCR assay over singleplex or other molecular techniques in samples from patients with co-infection include fast results, low cost, and a single step investigation process.

[Microbiological diagnosis of viral hepatitis]. / Diagnóstico microbiológico de las hepatitis virales.

Liver inflammation or hepatitis has many different causes, both infectious and non-infectious. Among the former, viral infection is responsible for at least half of all hepatitis worldwide. Different viruses have been described with primary tropism for liver tissue. These microorganisms have been successively named with letters of the alphabet: A, B, C, D, E and G. The aim of this paper is to review this heterogeneous group of viruses in its most basic aspects, including clinical implications, treatment, main control, and prophylactic measures and, of special interest, diagnostic approaches, both serological and molecular, which are used for their detection, quantification and characterization.

Rapid and sensitive approach to simultaneous detection of genomes of hepatitis A, B, C, D and E viruses.

BACKGROUND: Five viruses have been etiologically associated with viral hepatitis. Nucleic acid testing (NAT) remains the gold standard for diagnosis of viremic stages of infection. NAT methodologies have been developed for all hepatitis viruses; however, a NAT-based assay that can simultaneously detect all five viruses is not available. OBJECTIVES: We designed TaqMan card-based assays for detection of HAV RNA, HBV DNA, HCV RNA, HDV RNA and HEV RNA. STUDY DESIGN: The performances of individual assays were evaluated on TaqMan Array Cards (TAC) for detecting five viral genomes simultaneously. Sensitivity and specificity were determined by testing 329 NAT-tested clinical specimens. RESULTS: All NAT-positive samples for HCV (n = 32), HDV (n = 28) and HEV (n = 14) were also found positive in TAC (sensitivity, 100%). Forty-three of 46 HAV-NAT positive samples were also positive in TAC (sensitivity, 94%), while 36 of 39 HBV-NAT positive samples were positive (sensitivity, 92%). No false-positives were detected for HBV (n = 32), HCV (n = 36), HDV (n = 30), and HEV (n = 31) NAT-negative samples (specificity 100%), while 38 of 41 HAV-NAT negative samples were negative by TAC (specificity 93%). CONCLUSIONS: TAC assay was concordant with corresponding individual NATs for hepatitis A-E viral genomes and can be used for their detection simultaneously. The TAC assay has potential for use in hepatitis surveillance, for screening of donor specimens and in outbreak situations. Wider availability of TAC-ready assays may allow for customized assays, for improving acute jaundice surveillance and for other purposes for which there is need to identify multiple pathogens rapidly.

MicroRNAs: role and therapeutic targets in viral hepatitis.

MicroRNAs regulate gene expression by binding to the 3'-untranslated region (UTR) of target messenger RNAs (mRNAs). The importance of microRNAs has been shown for several liver diseases, for example, viral hepatitis. MicroRNA-122 is highly abundant in the liver and is involved in the regulation of lipid metabolism. MicroRNA-122 is also an important host factor for the HCV and promotes HCV replication. In contrast to HCV, microRNA-122 inhibits replication of the HBV. MicroRNA-122 acts as a tumour suppressor and reduced levels of microRNA-122 are associated with hepatocellular carcinoma. MicroRNAs other than microRNA-122 have been linked to viral hepatitis, fibrosis and inflammation. In this review, we discuss function and clinical implications of microRNA-122 and other microRNAs in liver diseases, especially viral hepatitis.

Prevalence of hepatitis A virus, hepatitis B virus, hepatitis C virus, hepatitis D virus and hepatitis E virus as causes of acute viral hepatitis in North India: a hospital based study.

CONTEXT: Acute viral hepatitis (AVH) is a major public health problem and is an important cause of morbidity and mortality. AIM: The aim of the present study is to determine the prevalence of hepatitis A virus (HAV), hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis D virus (HDV) and hepatitis E virus (HEV) as causes of AVH in a tertiary care hospital of North India. SETTINGS AND DESIGN: Blood samples and clinical information was collected from cases of AVH referred to the Grade I viral diagnostic laboratory over a 1-year period. SUBJECTS AND METHODS: Samples were tested for hepatitis B surface antigen, anti-HCV total antibodies, anti-HAV immunoglobulin M (IgM) and anti-HEV IgM by the enzyme-linked immunosorbent assay. PCR for nucleic acid detection of HBV and HCV was also carried out. Those positive for HBV infection were tested for anti-HDV antibodies. STATISTICAL ANALYSIS USED: Fisher's exact test was used and a P < 0.05 was considered to be statistically significant. RESULTS: Of the 267 viral hepatitis cases, 62 (23.22%) patients presented as acute hepatic failure. HAV (26.96%) was identified as the most common cause of acute hepatitis followed by HEV (17.97%), HBV (16.10%) and HCV (11.98%). Co-infections with more than one virus were present in 34 cases; HAV-HEV co-infection being the most common. HEV was the most important cause of acute hepatic failure followed by co-infection with HAV and HEV. An indication towards epidemiological shift of HAV infection from children to adults with a rise in HAV prevalence was seen. CONCLUSIONS: To the best of our knowledge, this is the first report indicating epidemiological shift of HAV in Uttar Pradesh.

Base-calling algorithm with vocabulary (BCV) method for analyzing population sequencing chromatograms.

Sanger sequencing is a common method of reading DNA sequences. It is less expensive than high-throughput methods, and it is appropriate for numerous applications including molecular diagnostics. However, sequencing mixtures of similar DNA of pathogens with this method is challenging. This is important because most clinical samples contain such mixtures, rather than pure single strains. The traditional solution is to sequence selected clones of PCR products, a complicated, time-consuming, and expensive procedure. Here, we propose the base-calling with vocabulary (BCV) method that computationally deciphers Sanger chromatograms obtained from mixed DNA samples. The inputs to the BCV algorithm are a chromatogram and a dictionary of sequences that are similar to those we expect to obtain. We apply the base-calling function on a test dataset of chromatograms without ambiguous positions, as well as one with 3-14% sequence degeneracy. Furthermore, we use BCV to assemble a consensus sequence for an HIV genome fragment in a sample containing a mixture of viral DNA variants and to determine the positions of the indels. Finally, we detect drug-resistant Mycobacterium tuberculosis strains carrying frameshift mutations mixed with wild-type bacteria in the pncA gene, and roughly characterize bacterial communities in clinical samples by direct 16S rRNA sequencing.

[Genotyping and molecular marking of bacteria and viruses in epidemiological surveillance of actual infections].

AIM: Determination of genetic and molecular features of pathogens circulating in Russia, in the northwest of the country and in St. Petersburg to resolve the problems of spread of diseases caused by these pathogens. MATERIALS AND METHODS: Complete and limited gene sequencing, DNA restriction fragment length polymorphism analysis, spoligotyping, VNTR-typing, resistotyping and other methods were used. RESULTS: Data on population structure and dominant genotypes of tuberculosis mycobacteria, corynebacteria, helicobacteria, hepatitis A, B, C, human papilloma viruses circulating in Russia, in the northwest of the country and in St. Petersburg were obtained. Genetic divergence of rubella virus and poliovirus vaccine strains under mass vaccination conditions was detected. Evidence of higher effectiveness of pathogen genotyping methods in epidemiologic diagnostics compared with traditional epidemiological investigation was obtained. CONCLUSION: Microorganism genotyping methods were helpful in resolving strategic problems of contemporary epidemiology. Perspectives of further development of these methods are related to obtaining data on circulating genotypes in all regions of the world, establishment of complete databases on circulating genotypes and integration of this methodology into daily diagnostics and epidemiological surveillance.

Dynamic epidemiology of acute viral hepatitis in Japan.

The epidemiology of acute viral hepatitis (AVH) is dynamic and affected by many factors including hygiene, socioeconomic status and vaccination coverage. A total of 4,302 cases of AVH were sequentially enrolled in this nationwide study between 1980 and 2008. Of the cases of AVH, acute hepatitis A (AHA) accounted for 1,583 (36.8%), acute hepatitis B (AHB) for 1,197 (27.8%), acute hepatitis C (AHC) for 359 (8.3%), and non-A, non-B and non-C (non-ABC) for 1,163 (27.0%). Between 1980 and 1995, the proportions of AHA, AHB, AHC and non-ABC were approximately 40, 25, 10 and 25%; between 1996 and 2003, they were approximately 30, 30, 10 and 30%, and this shifted to approximately 10, 40, 10 and 40% in the last 5 years. The number of AHB caused by genotype A, which is not indigenous to Japan, was 6.0% between 1991 and 1996 but has been markedly increasing since 2000, to reach 52% in 2008. Autochthonous acute hepatitis E (AHE) accounted for 10-15% of non-ABC hepatitis after 2002. The etiology of AVH in Japan has been drastically changing. A marked increase of AHB genotype A and constant occurrence of autochthonous AHE require attention, and necessary measures should be taken.

A review of hepatitis viral infections in Pakistan.

A review of published literature on viral hepatitis infections in Pakistan is presented. A total of 220 abstracts available in the Pakmedinet and Medline have been searched. All relevant articles were reviewed to determine the prevalence of hepatitis viral infections in Pakistan. Two hundred and three (203) relevant articles/abstracts including twenty nine supporting references are included in this review. Of the articles on prevalence of hepatitis infection, seven were related to Hepatitis A, fifteen to Hepatitis E while the remaining articles were on frequency of hepatitis B and C in different disease and healthy population groups. These included eight studies on healthy children, three on vertical transmission, nineteen on pregnant women, fifteen on healthy individuals, six on army recruits, thirty one on blood donors, thirteen on health care workers, five on unsafe injections, seventeen on high risk groups, five on patients with provisional diagnosis of hepatitis, thirty three on patients with chronic liver disease, four on genotypes of HBV and five on genotypes of HCV. This review highlights the lack of community-based epidemiological work as the number of subjects studied were predominantly patients, high risk groups and healthy blood donors. High level of Hepatitis A seroconversion was found in children and this viral infection accounts for almost 50%-60% of all cases of acute viral hepatitis in children in Pakistan. Hepatitis E is endemic in the country affecting mostly the adult population and epidemic situations have been reported from many parts of the country. The mean results of HBsAg and Anti-HCV prevalence on the basis of data aggregated from several studies was calculated which shows 2.3% and 2.5% prevalence of HBsAg and Anti-HCV in children, 2.5% and 5.2% among pregnant women, 2.6% and 5.3% in general population, 3.5% and 3.1% in army recruits, 2.4% and 3.6% in blood donors, 6.0% and 5.4% in health care workers, 13.0% and 10.3% in high risk groups, 12.3% and 12.0% in patients with provisional diagnosis of hepatitis and 25.7% and 54% in patients with chronic liver disease respectively. This review has illustrated the high endemicity of hepatitis viral infections in Pakistan where hepatitis B and C potentially account for a serious burden of the disease. This review has triggered the launching of a network intervention for the control of hepatitis viral infectious. This review was used as the basis for the launch of hepatitis programme, but putting it into a formal review took time and the hepatitis program was initiated.