Complete genome sequence of a precoredefective hepatitis. The complete nucleotide sequence of the genome of a hepatitis b virus isolated from a naturally infected chimpanzee article pdf available in journal of general virology 69 pt 66. The highly heterogenic characteristic of viruses is the major obstacle to efficient dna amplification. Here, we present the first characterization and complete genome sequence of a strain belonging to genotype e in mexico, obtained from a foreign carrier with chronic infection. May 10, 2018 the two neolithic hbv genomes clustered phylogenetically with, but distinctly from, african nonhuman primate hbv sequences, and the medieval hbv clustered with contemporary hbv d4 genome sequences. The database contains genomic sequence data from representative viruses. There is limited information regarding characterization and mutational analysis of hbv isolated in bangladesh. Complete genome sequence of hepatitis b virus hbv from a patient with fulminant hepatitis without precore and core promoter mutations. Dna extraction, amplification, and sequence determination and analysis. The hepatitis b virus hbv hbx regulatory protein is required for hbv replication and involved in hbv related carcinogenesis.
Hepatitis b virus hbv is among the most common causes of liver cirrhosis. The virus tool assigns taxonomic names to sequences from eukaryotic viruses and phages. Hepatitis b virus hbv remains a major public health problem worldwide. Identification of host factors that support viral replication is. This has additional annotation, for use with noncommercial sequence browsers e.
Neolithic and medieval virus genomes reveal complex. Hbv genome is optimized, being circular and encoding four overlapping reading frames. Deep sequencing of the hepatitis b virus in hepatocellular. An estimated 350 million people worldwide have chronic hbv infection.
Chronic infection is associated with an increased risk to develop severe liver diseases, including liver cirrhosis, and. Subcloning was done in three parts of hbv dna from patients fh1 and ah1. Hbv is an enveloped dna virus that replicates by reverse transcription of an rna intermediate. Forty treatmentnaive hbv infected patients were enrolled, including 10 cases of acute hepatitis b ahb, 9 cases of. An efficient method to detect hbv integration using. Plasmid sequence and snapgene enhanced annotations. The hbv genome is also highlighted, showing the relevance of the overlap between the polymerase and envelope, so that mutations in one reading frame can affect the other. Machinelearning based patient classification using. Fullgenome sequence analyses of hepatitis b virus hbv strains recovered from chimpanzees infected in the wild. Idea shamelessly stolen from mick watsons kraken downloader scripts that can also be found in micks github repo. We report the full genome sequences of seven molecular clones of hbv genotype a, amplified from an hbv infected north indian patient. The nucleotide sequence and reading frames of a mutant hepatitis b virus subtype adr.
Nucleotide sequence of the hepatitis b virus genome subtype ayw cloned. Analysis of the complete genome of hepatitis b virus. To circumvent this problem, we modeled the hbv by duplicating the sequence of each reference genome from. Hepatitis b virus infection is currently a global public health problem. Sitespecific rna bindding by a hepatitis b virus reverse transcriptase initiates two reactions. Quantification hepatitis b virus hbv dna plays a critical role in the management of chronic hbv infections. Sequence variations of fulllength hepatitis b virus. Fullgenome sequence analyses of hepatitis b virus hbv. The genome was 3215 nucleotides long, and differed in dna sequence by 10 from that of subtypes adw or ayw, but by only 2 90 from that of subtype adr. Cloning and sequencing of hbv dna has provided evidence that the gene coding for hbv env proteins has the capacity to code for proteins larger than the 226 amino acid chain of p25 tiollais et al. It was found an important presence of hbva1 and hbve.
Hbvseq accepts usersubmitted hbv rt sequences, determines their genotypes, and compares them to the genotype consensus reference sequences. Search interface retrieves hiv and siv sequences, which can then be aligned and used to build trees. Jun 28, 2008 by cloning and sequencing polymerase chain reaction. Hepatitis b virus hbv is a unique, tiny, partially doublestranded, reversetranscribing dna virus with proteins encoded by multiple overlapping reading frames. In colombia, our group reported recently the presence of subgenotypes f3, a2 and genotype g in bogota. The entire nucleotide sequence of genomic dna was determined for hepatitis b virus hbv of subtype ayr, which had been derived from the blood of a japanese asymptomatic carrier. All three comprised 3215 bp and differed in sequence by only 3. The current practice of using overlapping conserved primer sets to amplify a complete hbv genome in a clinical. Here we use hepatitis b virus as an example to introduce a simple and efficient way for. Tools for working with sequences lists all our online tools, organized by function. Pdf the complete nucleotide sequence of the genome of a.
Importantly, the authenticity of these hbv was also confirmed by the detection of a peptide of hbv core protein from two of the samples. Complete genome sequence of the who international standard. Hepatitis b virus subtype adw2, genotype a, complete genome. Annotation, comparison, detection and visualization of. A short cisacting sequence is required for hepatitis b virus pregome encapsidation and sufficient for packaging of foreign rna. The number of hepatitis b virus hbv whole genomic sequences in public nucleotide databases genbank, embl, and ddbj had reached 866 by january 1, 2007.
This article is from middle east journal of digestive diseases, volume 4. If the match length on both hbv genome reference and human genome reference for one peassembled read was larger than 30 bp, the peassembled read alignment result was reported to detect a precise breakpoint. Within that directory a readme file will describe the various files available. Evidence of transmission of hepatitis b virus to spouses from. Dna, we analysed the sequences of the conserved region of the surface gene nucleotide nt 3055, representing 6. The complete nucleotide sequence of hepatitis b virus genome subtype ayw cloned in escherichia coli has been determined using the maxam and gilbert method and the dideoxynucleotide method. Nucleotide sequence variation in the genome has been used to classify hbv into different genotypes a to j 3, 4. Here, we report the complete nucleotide sequence of a precoredefective hbv genotype d2 strain isolated in bangladesh. A the annotation procedure starts with the computation of a pairwise alignment between the query sequence q and the most similar duplicated reference genome sequence r1, r2. Hbv infection and epidemic in asia appear more severe. The hepatitis b virus hbv is a major health problem worldwide with more than 350 million people being chronic carriers. We report the full genome sequences of seven molecular clones of hbv genotype a, amplified from an hbvinfected north indian patient. However, associations between the prevalence of various hbv genotypes and the extent of liver damage have been reported from different parts of the world. One was fragment c nt 11258, amplified using primers ss1 and ss2, the second was fragment d nt 2459248, amplified using primers sp6 and as3 and the last was fragment e nt 991946, amplified using primers b3 and b2.
Complete genome sequence of the who international standard for. This is probably the first report of the hbv genome sequencing using ion torrent from india. D6 hbvd6, based on the s gene sequences of isolates in papua. Characterization of fulllength genomes of hepatitis b virus. Mandart, e, fitoussi, f, tiollais, p and charnay, p. Coming from 46 countries and regions, these sequences were categorized as eight genotypes ah. We analyzed hbvlike sequences from three chimpanzees pan troglodytes that were most likely infected during their life in africa in the wild. Complete genome sequence of hepatitis b virus genotype e. In bangladesh, the rate of hbv chronicity is 26% 4, which makes it relatively higher risk than. Each hepatitis b virus hbv genotype and subgenotype is associated with a particular geographic distribution, ethnicity, and anthropological history. Complete genome sequence and phylogenetic relatedness of. Illumina and nanopore methods for whole genome sequencing of. The conventional practice of using a single set of primers to amplify a nearcomplete hbv genome is hampered by its low analytical sensitivity. The specialized hepatitis b virus hbv database, hbvdb, allows the researchers to investigate the genetic variability of the virus and the viral.
Hepatitis b virus hbv, a causative agent for acutechronic hepatitis and hepatocellular carcinoma hcc, has a circular partially doublestranded dna genome, is about 3. Globally, more than 2 billion people have been infected by hbv 2,3 and, according to the world health organization who approximately 257 million were living with hbv in 2017. Download the ebv hhv4 consensus genome sequence download the ebv annotated genes. The direct cytopathic effects of the hepatitis b virus hbv on subsequent liver damage are not fully understood in hbv infected patients. To construct hbvspecific grnas, we searched for a potential 20base target sequence on the genome of the genotype a hbvexpression vector paavhbv1. This highly annotated nucleotide sequence can be downloaded from. The world health organization who international standard is for hepatitis b virus hbv dna for use in nucleic acid amplification assays was characterized by determining the complete genome sequence, which was assigned genotype a. If a mutation caused a sequence mismatched in the primer or probe of a commercial dna quantification kit, this would lead to an.
Fullgenome sequence analyses of hepatitis b virus hbv strains. Genomic analysis of hepatitis b virus and its association. Use with snapgene software or the free viewer to visualize additional data and align other sequences. Complete genome sequences of seventy hbv variants obtained from fifty syrian patients sera were determined and. The burden of chronic liver disease caused by hepatitis b virus hbv is increasingly detected at present 1. In many cases, the sequence data is segregated into directories for each chromosome. Hepatitis b virus hbv infects the liver and is a key risk factor for hepatocellular carcinoma. Deep sequencing of full length hepatitis b virus hbv. See the readme file in that directory for general information about the organization of the ftp files. Universal primers for hbv genome dna amplification across. Complete genome sequence of a precoredefective hepatitis b.
Our study aimed to characterize hbv fulllength genome quasispecies qs in patients with different phases of infection to better understand its pathogenesis. Chronic infection is associated with an increased risk to develop severe liver. Hbv dna was extracted from serum specimens by using a modification of the master pure procedure epicentre technologies, madison, wi in which 50. Hepatitis b virus hbv has been divided into 10 genotypes, a to j, based on an 8% nucleotide sequence divergence between genotypes. Our group includes molecular biologists, sequence analysts, computer technicians, postdocs and graduate research assistants. At the moment 8889 distinct taxonomic names are assigned based on 11845 reference. Illumina and nanopore methods for whole genome sequencing. Taking advantage of the large number of virus dna sequences in public databases to select conserved sites for primer design is an optimal way to tackle the difficulties in virus genome amplification. Although the diagnosis of acute and chronic hbv infection is usually made by serologic methods, detection and. More than 260 million people worldwide have chronic hbv infection, which causes 0. A prior to correction one fulllength read per concatemer, b concatemers corrected by consensus. Use text editor or plasmid mapping software to view sequence.
This information will aid the design, development, and evaluation of hbv dna amplification assays. The combination of double and singlestranded dna in a single molecule can cause. The reads included concatemers of the fulllength hbv genome as illustrated in fig. This dataset was further supplemented with hepadnavirus isolates from chimpanzees, orangutans, and gorillas. Full genome sequences of hbv were performed in 38 patients with chronic hbv infection 11, 11, and 16 patients with hbv genotypes a, d, and c, respectively.
Hepatitis b virus hbv infection is one of the most prevalent viral infections in humans and represents a serious public health problem. Complete genome sequence of a 2019 novel coronavirus sars. Similar in public databases, sequence number from mainland china ranks the highest, and then in order are china hong kong, japan, africa, europe, and north america. Insights from deep sequencing of the hbv genomeunique, tiny. Hbv has an unusual, circular, partially doublestranded ds dna genome of approximately 3. Fulllength hbv genome amplification, cloning and sanger sequencing. Although the findings of the study is limited and like a genome announcement, it signifies to be documented. The phylogenetic tree was constructed with the data from these 38 isolates. Distinct hepatitis b virus dynamics in the immunotolerant and early immunoclearance phases. Our previous study showed the novel hbv subgenotypes c6 hbv c6 and d6 hbv d6, based on the s gene sequences of isolates in papua, indonesia. The purpose of this study was to determine the distribution of hbv genotypes in patients with chronic. May 10, 2018 consensus sequence of the petersberg hbv genome.
The complete nucleotide sequence of hepatitis b virus genome subtype ayw cloned in escherichia coli has been determined using the maxam and gilbert method and. Hepatitis b virus hbv can integrate into the human genome, contributing to genomic instability and hepatocarcinogenesis. Locate the directory for your organism of interest. However, hbv is a dna virus with high levels of genetic variation, and drugresistant mutations have emerged with the use of antiviral drugs. Some script to download bacterial and fungal genomes from ncbi after they restructured their ftp a while ago. Nov 29, 2019 download one protein sequence per gene. Hbv is a major health problem worldwide with more than 350 million individuals being chronically infected. It is strongly recommended that you also download the original genbank file if you want to obtain a more complete picture of the ebv coding regions. Identification of hepatitis b virus indigenous to chimpanzees. The new genome sequence was obtained by first mapping reads to a reference sarscov2 genome using bwamem 0. Geography search interface retrieves hiv sequences based on geographical distribution.
Complete genome sequences of hepatitis b virus from north. An hbv recombinant strain subgenotype f3a1 was found for the first time. Neolithic and medieval virus genomes reveal complex evolution. Pdf comparative analysis of hepatitis b virus genome. The aim of this study was to characterize the hbv genotypes circulating in quibdo, the largest afrodescendant community in colombia. Here we use hepatitis b virus as an example to introduce a simple and efficient way for virus. Overview of hbv whole genome data in public repositories. Nucleotide sequence of the hepatitis b virus genome. Here by conducting highthroughput viral integration detection and rna. The genome was 3215 nucleotides long, and differed in dna sequence by 10% from that of subtypes adw or ayw, but by only 2% from that of subtype adr. The number of hepatitis b virus hbv whole genomic sequences in public nucleotide databases. Phylogenetic analysis of complete genome sequences of. The taxonomic rank which gets assigned is based on availability of reference genomes in refseq, and is mostly at species level. Sep 10, 2018 the manuscript talks about the complete genome analysis of hepatitis b virus and represent the complete genome sequence of hbv subgenotype c2 in bangladesh.
This study is the first analysis of complete hbv genome sequences from afrocolombian population. Neolithic and medieval virus genomes reveal complex evolution of hepatitis b. Aiming to identify genes and noncoding rnas ncrnas directly. Hepatitis b is caused by the hepatitis b virus hbv, an enveloped virus containing a partially double stranded, circular dna genome, and classified within the family hepadnavirus. Hepatitis b virus hbv genomic mutations affect viral replication, disease progression, and diagnostic and vaccination efficiency. Hepatitis b virus hbv infection results in different clinical presentation due to different levels of immune response. The association between hepatitis b virus hbv mutations and.
They were classified as hbvb 10 strains, hbvc 9 strains, and hbvd 3 strains. Complete genome sequence of hepatitis b virus hbv from a. Organization of overlapping open reading frames and approximate location of singlestranded portion of plus strand are indicated. Early minion nanopore singlemolecule sequencing technology. Regulation of the hepatitis b virus replication and gene. Identification of hbv genotype and consensus sequences coverage across the genome results nanopore data figure 8. This alignment is split up into cds alignments that are optimized. The substitution rate is surprisingly high for a dna virus, but lower than that of other reverse transcribing organisms. Overview of hbv whole genome data in public repositories and the. Citeseerx nucleotide sequence of a cloned hepatitis b virus. Summary the entire nucleotide sequence of genomic dna was determined for hepatitis b virus hbv of subtype ayr, which had been derived from the blood of a japanese asymptomatic carrier.
The crisprcas9 system facilitates clearance of the. Maximum likelihood trees of fulllength hbv sequences from sample 31 sequenced by nanopore. For successful hbv genome reconstruction, we mapped all metagenomic sequences to 16 hbv reference genomes eight human genotypes ah and 8 nhps from africa and asia that are representative of the current hbv strain diversity supplementary file 6. The cobas hbv is a fdaapproved in vitro nucleic acid amplification test for the quantification of hepatitis b virus hbv dna in human serum, using the using the cobas 6800 or 8800 instrument for automated viral nucleic acid extraction silicabased capture technique, purification, amplification, and detection of the viral nucleic acid target. The complete nucleotide sequences of the dna of three hepatitis b virus hbv genomes of subtype adw, cloned from plasma samples of asymptomatic carriers living in the mainland and okinawa prefecture of japan and indonesia were determined. The underlying mechanism of hbsagnegative hepatitis b virus hbv infection is notoriously. Hbv is a relaxed circular, partially doublestranded dna virus, with a unique genomic organization four overlapping reading frames encoding 7 proteins in 3. Association of hbv genome sequences with neighboring countries. Sep 24, 2007 the highly heterogenic characteristic of viruses is the major obstacle to efficient dna amplification.
The hepatitis virus database includes hbv and provides information on. Full length hbv dna was amplified according to the protocol described by gunther et al. Diagnosis of acute or chronic hepatitis b virus hbv infection is based on the presence of hbv serologic markers such as hepatitis b surface antigen hbsag and hepatitis b core igm antibody antihbc igm, or the presence of hbv dna detected by molecular assays. Ono y, onda h, sasada r, igarashi k, sugino y, nishioka k. The mutations defined as differences between the submitted sequence and the consensus reference sequence are used as query parameters for interrogating a local hbv rt drug resistance database hbvrt db to retrieve the prevalence of each mutation. Highthroughput sequence data for neolithic and medieval virus genomes reveal complex evolution of hepatitis b. Pdf complete genome sequence and phylogenetic relatedness. Hbv causes hepatitis b, a serious and common infectious disease of the liver.
Genomewide identification of direct hbx genomic targets. Genomic and oncogenic preference of hbv integration in. Nucleotide sequence of a cloned hepatitis b virus genome. Advancing interventions to tackle the huge global burden of hepatitis b virus hbv infection depends on improved insights into virus epidemiology, transmission, withinhost diversity, drug resistance and pathogenesis, all of which can be advanced through the largescale generation of fulllength virus genome. Implications for an origin of hbv1 kazuaki takahashi, betsy brotman, sadakazu usuda, shunji mishiro,2 and alfred m. Hbx interacts with chromatin modifying enzymes and transcription factors to modulate histone posttranslational modifications and to regulate viral cccdna transcription and cellular gene expression.
The first step of the automated annotation procedure is a similarity search, using the fasta program 28 figure 1 a in order to identify the most similar reference genome to the sequence to annotate. The human papillomaviruses database collects, curates, analyzes, and publishes genetic sequences of papillomaviruses and related cellular proteins. Amino acid sequences coded for by the s, c, p and x genes. The joint position of human and hbv sequence was the breakpoints for hbv integration fig. Overview of hbv whole genome data in public repositories and. The viral genomes resource is a collection of viral genomic sequences that is a part of the entrez genomes, which provides curated sequence data and annotations of complete genomes to. Hepatitis b virus hbv phylogenetic analysis was completed with reference strains ai as previously described, and hbv escape and resistance mutations were evaluated using geno2pheno hbv 2.