However, hcv exhibits a high genetic diversity, the isolates. Hcv is a member of the flaviviridae family and has a single stranded rna genome that is 9. The first complete genome sequence of hcv1a from pakistan and a phylogenetic. The hepatitis c virus is the cause of hepatitis c and some cancers such as liver cancer hepatocellular carcinoma, abbreviated hcc and lymphomas in humans. If the primary mechanism by which mir122 stabilizes the hcv genome is by base pairing with the singlestranded sequence at the very distal viral rna 5. Alignments curated sequence and reference alignments for all genes. The comparison was made in order to identify evolutionary and molecular phylogenetic relationships among hcv strains belonging to genotype 1a. Genome polyprotein hepatitis c virus genotype 1a isolate 1 hcv. Geography geographic distribution of hcv database sequences. Because of the extraordinary genetic diversity of hcv, 8 genotypes and 86 confirmed subtypes have been reported and have shown different geographic distributions, pathogenesis, and responses to antihcv therapy. This resource provides viral genome sequence data and related information. The polypeptide has 30 potential nglycosylation sites. Identification of a novel hepatitis c virus genotype from.
Genotype and subtypeindependent fullgenome sequencing. These genotypes are subtyped according to sequence characteristics. Within that directory a readme file will describe the various files available. Amino acid and nucleotide sequence comparisons of flaviviruses and pestiviruses with hcv suggest that. A bootscan and b grouping scan of bak1 as reference sequence with representative complete genome sequences of hcv genotypes 1 to 7. Mar 17, 2016 hepatitis c virus hcv is a significant human pathogen affecting nearly 3 % of the worlds population, and is a leading cause of chronic liver diseases including cirrhosis and hepatocellular carcinoma. The first fulllength genome sequence of hcv was reported in 1989, which promoted the development of hcv diagnosis and antiviral treatment. Pepmap this tool can be used to map epitopes, functional domains, or any protein region of interest. Oct 31, 2018 the rna genome of the hepatitis c virus hcv encodes a single open reading frame orf containing numerous functional elements. The present study was conducted to determine the first fulllength. There are 8 recognized main variants of hcv genotypes 1 to 8 with up to 35% nucleotide. Once a month the new sequences are downloaded and the available.
The chaperonelike activity of the hepatitis c virus ires. A global consensus sequence was constructed using the multiple alignment feature of the clc workbench for hcv e1 figure 1 and e2 figure 2 proteins. Here, we describe a subtypeindependent full genome. To design effective peptides, a consensusbased approach was used. Genome sequence of an unknown subtype of hepatitis c virus. The nearly complete viral genome sequence of qc69 was derived from a serum sample drawn in 2003 that displayed an hcv rna level of 7,210,000 iuml in the cobas amplicor hcv monitor. We wanted to test the contribution of these seed sequence base pairs, as well as that from base pairs that form downstream of the canonical seed sequence p8p9, figure 1a, to the stability of the mir122.
In many cases, the sequence data is segregated into directories for each chromosome. Hepatitis c virus hcv exhibits a high genetic diversity and is classified into 6 genotypes, which are further divided into 66 subtypes. The first complete genome sequence of hcv1a from pakistan and. Pairing highthroughput sequencing technologies with highthroughput mutagenesis enables genome wide investigations of pathogenic organisms. Due to high conservation of the 5 untranslated region of the hcv genome, this test has limitations in differentiating subtype 1a from 1b. Current sequencing strategies require prior knowledge of the hcv genotype and subtype for efficient amplification, making it difficult to sequence samples with a rare or unknown genotype andor subtype. Subtype information is available in the majority of cases. Fulllength sequence of the genome of hepatitis c virus. 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. Its distribution, natural history and exact rule of this viral group in human. Unconventional mir122 binding stabilizes the hcv genome. Table 1 confirmed hcv genotypessubtypes may 2019 confirmed hcv genotypessubtypes. Phil sharps lab contains the insert firefly luciferase, hepatitis c virus ires sequence, renilla, and 3utr short rna binding sites and is published in mol cell. Since the discovery of hcv in 1989, a large number of genetic analyses of hcv have been reported, and the viral genome structure has been elucidated.
Knowledge of the specific functions of protein domains encoded by the genome of the hepatitis c virus hcv, a major human pathogen that contributes to liver disease worldwide, remains limited to insight from smallscale studies. A structure of dnvr2 and pv rnas, which differ only in 5. The first complete genome sequences of hepatitis c virus. Population sequencing of the hcv coding region of interest may be performed using reverse transcription polymerase chain reaction pcr and standard sanger sequencing of the bulk pcr product. The results will contain some of the fields we annotate, such as subtype, sampling country and isolation year. Core protein packages viral rna to form a viral nucleocapsid, and promotes virion budding. We retrieved 77 complete genomic sequences of all available genotypes genbank accession numbers in table s1 and conducted bioinformatics analysis to assess the level of sequence conservation.
The full hcv genome sequencing approach generated complete 5utr sequence in 3 of 4 patients 94. Modulates viral translation initiation by interacting with hcv ires and 40s ribosomal subunit. Virus pathogen database and analysis resource vipr. The rna genome of the hepatitis c virus hcv encodes a single open reading frame orf containing numerous functional elements. Stabilization of hepatitis c virus rna by an ago2mir122. Fulllength sequence of the genome of hepatitis c virus type 3a. Jan 29, 20 if the primary mechanism by which mir122 stabilizes the hcv genome is by base pairing with the singlestranded sequence at the very distal viral rna 5. The hepatitis c virus hcv is a small 5565 nm in size, enveloped, positivesense singlestranded rna virus of the family flaviviridae. A comprehensive functional map of the hepatitis c virus.
The hepatitis c virus hcv has remarkable genetic diversity and exists as eight genotypes 1 to 8 with distinct geographic distributions. Hcv infection frequently causes chronic hepatitis, which progresses to liver cirrhosis and hepatocellular carcinoma. Bioinformatics analysis to reveal hcv grich sequences. Genome sequence of an unknown subtype of hepatitis c virus genotype 6. Quickalign formerly epilign and primalign aligns short nucleotide or protein sequences e. Hepatitis c virus hcv infection is a leading cause of liver diseases and liver diseaserelated death. No complete genome sequence of hcv subtype 2b hcv2b is. After cleavage, the membrane sequence is retained at the cterminus of the protein, serving as er membrane anchor. Worldwide prevalence of substitutions in hcv genome. Locate the directory for your organism of interest. Hepatitis c virus hcv is a significant human pathogen affecting nearly 3 % of the worlds population, and is a leading cause of chronic liver diseases including cirrhosis and hepatocellular. Source hepatitis c virus genotype 1 organism hepatitis c virus. Annotate hepatitis c virus hcv genome sequences for this exercise, you will use vipr. The length and diversity of the hcv genome has resulted in analysis of certain regions of the virus, however there has been little standardisation of protocols.
Pairing highthroughput sequencing technologies with highthroughput mutagenesis enables genomewide investigations of pathogenic organisms. Current sequencing strategies require prior knowledge of. The hepatitis c virus is the cause of hepatitis c and some cancers such. The results will contain some of the fields we annotate. Human pegivirus hpgv is structurally similar to hepatitis c virus hcv and was discovered 20 years ago. Hepatitis c virus hcv is a significant human pathogen affecting nearly 3 % of the worlds population, and is a leading cause of chronic liver diseases including cirrhosis and hepatocellular carcinoma.
Amino acid and nucleotide sequence comparisons of flaviviruses and pestiviruses with hcv suggest. Hepatitis c virus genotype by sequencing arup lab test. Signals involved in regulation of hepatitis c virus rna. Complete genome sequence of a 2019 novel coronavirus sars. Nov 01, 2019 hepatitis c virus hcv infection is a leading cause of liver diseases and liver diseaserelated death. Complete genome sequencing and evolutionary analysis of. As a standard, substitutions are reported as differences. Hepatitis c virus genotype 2a isolate hcj6 hcv uniprot. Our aim was to determine, by deep nextgeneration sequencing ngs, the entire genome sequence of hpgv that was discovered in an egyptian patient while analyzing hcv sequence from the same. The genome contains a single openreading frame and encodes. However, hcv exhibits a high genetic diversity, the isolates from the different areas showed heterogeneity at the nucleotide level. Analysis by both methods used sliding window of 300 bases, incrementing by 15 bases across genome. A bootscan and b grouping scan of bak1 as reference sequence with representative complete genome sequences of hcv genotypes 1. The hepatitis c virus hcv genome shows remarkable sequence variability, leading to the classification of at least six major genotypes, numerous subtypes and a myriad of quasispecies within a.
A truncated form hepatitis c virus gene wherein part of the gene region encoding from the core protein to the ns2 protein of hepatitis c virus has been deleted while retaining the translation frame. The present study describes a unifying approach for hcv full genome sequencing, based on sequenceindependent amplification combined with next generation sequencing. The gene encoding the spike glycoprotein of the human coronavirus hcv 229e has been cloned and sequenced. The nearly complete viral genome sequence of qc69 was derived from a serum sample drawn in 2003 that displayed an hcv rna level of 7,210,000 iuml in the cobas amplicor hcv monitor test version 2. A single sequence can be in fasta format or raw sequence. Hepatitis c virus hcv is a worldwide pathogen that belongs to the genus hepacivirus within the flaviviridae family. Hepatitis c virus hcv is the major etiologic agent of nona, nonb hepatitis. Sequencing data is compared to a database of characterized sequences. The sensitivity for detection of resistance substitutions varies but is generally 15% to 25%. Hepatitis c virus database and bioinformatics analysis tools in the virus pathogen resource vipr. Interactive view of the hiv genome and proteome for juxtaposition and exploration of multiple types of data. This analysis predicts an s polypeptide of 1173 amino acids with an m r of 128600. The first complete genome sequence of hcv1a from pakistan. Current sequencing strategies require prior knowledge of the hcv.
Gene cutter clip genes from a nucleotide alignment, codonalign and translate. Comparative study of the amino acid sequence of hepatitis c virus hcv with those of flaviviruses and pestiviruses and gene expression experiments in bacteria, yeast, and animal cells have revealed that. A measure of genome diversity calculated by qiu et al 10 illustrates the ranges of low and high genetic variation at regions frequently sequenced. Comprehensive evolutionary and phylogenetic analyses were conducted. Hepatitis c virus hcv preferentially replicates in the human liver and frequently causes chronic infection, often leading to cirrhosis and liver cancer.
Hcv fulllength genome reconstruction with sequence. Wholegenome sequencing of human pegivirus variant from an. The subtype which is identified using the reference genomes provided in smith et al. Jun 27, 20 here, we report the first patient derived hepatitis c virus hcv complete genome from pakistan as is not available from this region of the world. One nucleotide or amino acid sequence, or a bulk set of sequences. Our dna database contains most of the same hcv sequences found in genbank, but a blast search here gives more informative output.
Since the identification of hepatitis c virus hcv, viral sequencing has been important in understanding hcv classification, epidemiology, evolution, transmission clustering, treatment response and natural history. Hcv recombinant protein c200 is encoded by the putative ns3 and ns4 regions of the hcv genome. See the readme file in that directory for general information about the organization of the ftp files. Here, we report the first patient derived hepatitis c virus hcv complete genome from pakistan as is not available from this region of the world. The cre and the ires regions influence genomic dimer formation. Nucleotide sequences of the genomic rna of hepatitis c virus isolated from a human carrier. We generated a consensus sequence of 29,811 bp with no gap and high average coverage 77,000. Prevents the establishment of cellular antiviral state by blocking the interferonalphabeta ifnalphabeta and ifngamma. Use of whole genome sequencing in the dutch acute hcv in. B mir122 slows decay of dnvr2 rna in hela s10 lysate. The hcv sequence database collects and annotates sequence data and provides. The global consensus sequence is shown at the base of the alignments in figures 1 and 2.
We first assessed the ability of the mutated mir122 rnas, p3p4 and p8p9, to form a stable complex with hcv dom i rna using an. We wanted to test the contribution of these seedsequence base pairs, as well as that from base pairs that form downstream of the canonical seed sequence p8p9, figure 1a, to the stability of the mir. The viral genome is positivesense, singlestranded rna, approximately 9,600 nucleotides long, with a single open reading frame orf about 9,000 nucleotides long. The clade type which is reported in case the subtype is 1a.
In particular, the gene according to claim 1 wherein said part of the gene region is present in a region encoding at least the e1 protein and the e2 protein. A global consensus sequence was constructed using the multiple. Among these, the cisacting replication element cre at the 3. Since the identification of hepatitis c virus hcv, viral sequencing has been important in understanding hcv classification, epidemiology, evolution, transmission clustering, treatment response and natural. Genotypes old and new hcv genotypes in the database. Please use the form to submit dna sequences of hcv strains covering ns3 region, ns5a region andor ns5b region. Isolates of hepatitis c virus are grouped into six major genotypes 16. No complete genome sequence of hcv subtype 2b hcv 2b is available from latin american countries, and the factors underlying its emergence and spread within the continent remain unknown. Hcv genome dimeric complex formation is initiated at the highly conserved palindromic sequence motif dls in the 3. A number of structural features typical of coronavirus s proteins can be recognized, including a signal sequence, a membrane anchor, heptad repeat. Because of the extraordinary genetic diversity of hcv, 8 genotypes and 86. Comparative study of the amino acid sequence of hepatitis c virus hcv with those of flaviviruses and pestiviruses and gene expression experiments in bacteria, yeast, and animal cells have revealed that the proteins of hcv are processed by a host derived signalase and cleaved by viruscoded proteases. Nov 11, 2019 human pegivirus hpgv is structurally similar to hepatitis c virus hcv and was discovered 20 years ago.