Recent advances in molecular diagnostics of hepatitis Bvirus

Hepatitis B virus(HBV)is one of the important global health problems today.Infection with HBV can lead to a variety of clinical manifestations including severe hepatic complications like liver cirrhosis and hepatocellular carcinoma.Presently,routine HBV screening and diagnosis is primarily based on the immuno-detection of HBV surface antigen(HBsAg).However,identification of HBV DNA positive cases,who do not have detectable HBsAg has greatly encouraged the use of nucleic acid amplification based assays,that are highly sensitive,specific and are to some extent tolerant to sequence variation.In the last few years,the field of HBV molecular diagnostics has evolved rapidly with advancements in the molecular biology tools,such as polymerase chain reaction(PCR)and real-time PCR.Recently,apart of PCR based amplification methods,a number of isothermal amplification assays,such as loop mediated isothermal amplification,transcription mediated amplification,ligase chain reaction,and rolling circle amplification have been utilized for HBV diag-nosis.These assays also offer options for real time detection and integration into biosensing devices.In this manuscript,we review the molecular technologies that are presently available for HBV diagnostics,with special emphasis on isothermal amplification based technologies.We have also included the recent trends in the development of biosensors and use of next generation sequencing technologies for HBV.

Next-generation sequencing in clinical virology: Discovery of new viruses

Viruses are a cause of significant health problem world-wide, especially in the developing nations. Due to different anthropological activities, human populations are exposed to different viral pathogens, many of which emerge as outbreaks. In such situations, discovery of novel viruses is utmost important for deciding prevention and treatment strategies. Since last century, a number of different virus discovery methods, based on cell culture inoculation, sequence-independent PCR have been used for identification of a variety of viruses. However, the recent emergence and commercial availability of nextgeneration sequencers(NGS) has entirely changed the field of virus discovery. These massively parallel sequencing platforms can sequence a mixture of genetic materials from a very heterogeneous mix, with high sensitivity. Moreover, these platforms work in a sequenceindependent manner, making them ideal tools for virus discovery. However, for their application in clinics, sample preparation or enrichment is necessary to detect low abundance virus populations. A number of techniques have also been developed for enrichment or viral nucleic acids. In this manuscript, we review the evolution of sequencing; NGS technologies available today as well as widely used virus enrichment technologies. We also discuss the challenges associated with their applications in the clinical virus discovery.

Epstein-Barr virus is associated with gastric carcinoma: The question is what is the significance?

AIM: To examine the possible role of the Epstein- Barr Virus (EBV) in the development of gastric adenocarcinoma (GC). It is unclear whether EBV is involved in GC development or is a consequence of gastric inflammation secondary to immunosuppressive treatments. METHODS: A systematic review was carried out of all published observational studies on the temporal association between EBV and GC, with a view to determine a causal relationship. RESULTS: The present study showed that the worldwide crude prevalence of EBV in gastric adenocarcinoma was 8.29%. The prevalence varied from 7.08% for intestinal type and 9.82% for diffuse type of GC. It was observed that Western and Central Asian countries had a significantly higher frequency of EBV positive cases compared to South-Eastern countries. America had the highest EBV-GC prevalence whereas Europe had the lowest. CONCLUSION: The present review has demonstrated a high prevalence of EBV in gastric adenocarcinoma. However, studies designed to assess a temporal relationship and histological association using sensitive techniques should be carried out to establish the role of EBV in GC carcinogenesis.

Compartmentalization of hepatitis B virus: Looking beyond the liver

Hepatitis B virus(HBV) is classically considered to be hepatotropic, but accumulating evidences strongly support its extra-hepatotropic nature too. HBV nucleicacids and proteins have long been reported in a variety of extra-hepatic tissues. Of these, HBV has been studied in details in the peripheral blood mononuclear cells(PBMCs), due to its accessibility. From these studies, it is now well established that PBMCs are permissive to HBV infection, replication, transcription and production of infective virions. Furthermore, molecular evolutionary studies have provided definite evidences towards evolution of HBV genome in PBMCs, which is independent of evolution occurring in the liver, leading to the emergence and selection of compartment specific escape variants or drug resistant strains. These variants/resistant strains of HBV remain restricted within the PBMCs and are rarely detected in the serum/plasma. In addition, HBV infected PBMCs have been reported to be directly transmitted through intrauterine modes, and this infection does not correlate significantly with serum HBV surface antigen or HBV DNA markers. This editorial briefly reviews the current knowledge on this topic, emphasizes and delineates the gaps that are required to be filled to properly understand the biological and clinical relevance of extrahepatic tropism of HBV.

Production and application of recombinant haemagglutinin neuraminidase of Newcastle disease virus

Objective:To discuss the possibility of expressing the haemagglutinin-neuraminidase（HN） protein in prokaryotic system such as Escherichia coli（E.coli） cells by cloning the full length HN gene.Methods:The full length HN gene of Newcastle Disease Virus（NDV） of size 1 734 bp was preciously isolated by RT-PCR.The sequence was assessed and submitted to Nucleic Acid Databank（NCBI） and the gene ID was EU215390.1 after cloning and sequencing.Now the assessed HN gene was subcloned into pET 32 a+ expression vector for production the HN protein in E.coli, BL21（DE3） PLYSS cells following standard protocols.The crude lysate protein from the induced positive clone was size assessed by sodium dodecyl sulfale-polyacrylamide gel electrophoresis （SDS-PAGE） and their haemagglutination（HA） property against chicken RBC was assessed by standard micro HA test.Results:The molecular size of the full HN gene of NDV as assessed by cloning and digesting the positive clone to release the insert was 1.7 kb.The expressed protein in both crude and pure form was assessed to be 63 kDa and 81 kDa,respectively.The HA activity of the crude protein of the positive clone was 1 in 40.Conclusions:This finding indicates that the fusion protein retains the biological activity of native protein in the crude form and therefore could be used as a diagnostic reagent for antibody detection and for routine assessment of immune status in commercial layer forms.

Role of RNA secondary structure in emergence of compartment specific hepatitis B virus immune escape variants

AIM To investigate the role of subgenotype specific RNA secondary structure in the compartment specific selection of hepatitis B virus(HBV)immune escape mutations.METHODS This study was based on the analysis of the specific observation of HBV subgenotype A1 in the serum/plasma,while subgenotype A2 with G145R mutation in the peripheral blood leukocytes(PBLs).Genetic variability found among the two subgenotypes was used for prediction and comparison of the full length pregenomic RNA(pgRNA)secondary structure and base pairings.RNA secondary structures were predicted for 37℃using the Vienna RNA fold server,using default parameters.Visualization and detailed analysis was done using RNA shapes program.RESULTS In this analysis,using similar algorithm and conditions,entirely different pgRNA secondary structures for subgenotype A1 and subgenotype A2 were predicted,suggesting different base pairing patterns within the two subgenotypes of genotype A,specifically,in the HBV genetic region encoding the major hydrophilic loop.We observed that for subgenotype A1 specific pgRNA,nucleotide 358U base paired with 1738A and nucleotide 587G base paired with 607C.However in sharp contrast,in subgenotype A2 specific pgRNA,nucleotide 358U was opposite to nucleotide 588G,while 587G was opposite to 359U,hence precluding correct base pairing and thereby lesser stability of the stem structure.When the nucleotides at 358U and 587G were replaced with 358C and 587A respectively(as observed specifically in the PBL associated A2 sequences),these nucleotides base paired correctly with 588G and 359U,respectively.CONCLUSION The results of this study show that compartment specific mutations are associated with HBV subgenotype specific alterations in base pairing of the pgRNA,leading to compartment specific selection and preponderance of specific HBV subgenotype with unique mutational pattern.

KIR and a specific HLA-C gene are associated with susceptibility and resistance to hepatitis B virus infection in a Brazilian population

BRIEF REPORT The activity of natural killer （NK） cells is partially regulated by killer cell immunoglobulin-like receptors （KIRs） interacting with human leukocyte antigen C （HLA-C） ligands.1 The ligands of several inhibitory （2DL and 3DL） and activating （2DS and 3DS） KIR have been described.

Unraveling the Dynamic Role of Microtubules in the HBV Life Cycle

Acute hepatitis B virus(HBV)infection can progress to chronicity and development of cirrhosis and hepatocellular carcinoma(HCC).Current antiviral drugs offer long-term virological and biochemical response in patients with chronic HBV infection but they are unable to cure HBV.1,2 Many viruses,including HBV,exploit the host microenvironment for their efficient replication and persistence.Although the dynamic interactions between viruses and host cytoskeletal proteins vary,the microtubular network always provides a mode of directed transport for the invading pathogens.Following viral entry,the microtubular network undergoes structural reorganization,indicating that invading pathogens not only utilize,but also alter the host cell cytoskeleton during replication and egress.The network is regulated by several post-translational modifications of tubulin along with microtubule(MT)-associated proteins(MAPs).3 It is well known that MAP1S links autophagic cytoplasmic components to MTs and mitochondria,affecting autophagosome biogenesis and degradation.Moreover,depletion of the MAP1S gene in mice causes deficiencies of both basal autophagy for subsequent clearance of abnormal mitochondria and nutritional stress-induced autophagy for cell longevity and nutrient recycling.Autophagic defects that result from oxidative stress can subsequently either suppress tumorigenesis by triggering cell death or,support tumorigenesis if the cells survive the effects of oxidative stress.