Variable and hypervariable domains are found in the regions of HCV corresponding to the flavivirus envelope and NS1 proteins and the pestivirus envelope glycoproteins

Weiner, Amy J.; Brauer, Matthew J.; Rosenblatt, Jody; Richman, K H; Tung, James W.; Crawford, Kevin; Bonino, Ferruccio; Saracco, Giorgio Maria; Choo, Qui Lim; Houghton, Michael; Han, Jang H.

doi:10.1016/0042-6822(91)90104-j

Cited by 589 publications

(322 citation statements)

References 26 publications

Supporting

Mentioning

314

Contrasting

Unclassified

Order By: Relevance

“…E1 and E2 consist of 192 and 426 amino acids, respectively (Kato et al 1990). The protein region encompassing the amino-terminal 27-31 amino acids of E2 is the most variable throughout the amino acid sequences of all HCV proteins and called hypervariable region 1 (HVR1) (Hijikata et al 1991;Weiner et al 1991). HVR1 is known as the major neutralization epitope of HCV (Weiner et al 1992).…”

Section: Discussionmentioning

confidence: 99%

New Methods for Detecting Positive Selection at Single Amino Acid Sites

Suzuki

2004

J Mol Evol

View full text Add to dashboard Cite

Inferring positive selection at single amino acid sites is of particular importance for studying evolutionary mechanisms of a protein. For this purpose, Suzuki and Gojobori (1999) developed a method (SG method) for comparing the rates of synonymous and nonsynonymous substitutions at each codon site in a protein-coding nucleotide sequence, using ancestral codons at interior nodes of the phylogenetic tree as inferred by the maximum parsimony method. In the SG method, however, selective neutrality of nucleotide substitutions cannot be tested at codon sites, where only termination codons are inferred at any interior node or the number of equally parsimonious inferences of ancestral codons at all interior nodes exceeds 10,000. Here I present a modified SG method which is free from these problems. Specifically, I use the distance-based Bayesian method for inferring the single most likely ancestral codon from 61 sense codons at each interior node. In the computer simulation and real data analysis, the modified SG method showed a higher overall efficiency of detecting positive selection than the original SG method, particularly at highly polymorphic codon sites. These results indicate that the modified SG method is useful for inferring positive selection at codon sites where neutrality cannot be tested by the original SG method. I also discuss that the p-distance is preferable to the number of synonymous substitutions for inferring the phylogenetic tree in the SG method, and present a maximum likelihood method for detecting positive selection at single amino acid sites, which produced reasonable results in the real data analysis.

show abstract

Section: Discussionmentioning

confidence: 99%

New Methods for Detecting Positive Selection at Single Amino Acid Sites

Suzuki

2004

J Mol Evol

View full text Add to dashboard Cite

show abstract

“…A hot start, nested PCR was then performed using identical cycling conditions and internal primers, as previously described (Weiner et al, 1991), which yielded a 176 bp amplified product. For nested PCR, the lower reaction mixture contained 3 mM-MgC12, 200 gmol each dNTP, 10 mM-Tris HC1 pH 8.3, 15 mM-KCI and 100 pmol each primer and was separated by a wax layer (Ampliwax; Perkin Elmer) from an upper reaction mixture containing 40mM-Tris-HC1 pH 8.3, 60mM-KC1, 1.5 U AmpliTaq polymerase (Perkin Elmer) and 0.1% of the first round product.…”

Section: Methodsmentioning

confidence: 99%

“…HCV has been demonstrated to exist as a quasispecies in infected individuals based on the finding of multiple mutations within the second envelope gene hypervariable region (HVR1) (Weiner et al, 1991;Martell et aL, 1992;Kato et al, 1994). Virus quasispecies have been defined as a variable mixture of a master nucleotide sequence and a spectrum of mutant molecules isolated from a given host and are characteristic of certain classes of RNA viruses, such as lentiviruses and picornaviruses (Holland et al, 1992).…”

Section: Introductionmentioning

confidence: 99%

Characterization of simple and complex hepatitis C virus quasispecies by heteroduplex gel shift analysis: correlation with nucleotide sequencing

Wilson

Polyak

Day

et al. 1995

Journal of General Virology

View full text Add to dashboard Cite

In infected humans, hepatitis C virus (HCV) exists as a quasispecies typically characterized by multiple nucleotide substitutions within the second envelope gene hypervariable region 1 (HVR1). In the current study, we used heteroduplex gel shift analysis (GSA) of HVR1 sequences amplified directly from patients' sera to define two patterns of HCV quasispecies: (i) simple quasispecies, which gave a mostly homogeneous gel shift profile with a single predominant band and (ii) complex quasispecies, which gave a gel shift profile with multiple bands. Recombinant HVRI libraries were generated from two patients with complex HCV quasispecies (cases 1 and 2) and two patients with simple HCV quasispecies (cases 3 and 4), and 129 individual clones were analysed by either GSA, nucleotide sequencing or both techniques. In case I we identified a highly complex HCV quasispecies with 11 distinct HVR1 variants differing by 1-51 nucleotide changes. We found a general but not absolute correlation between GSA pattern and the number or position of nucleotide changes within HVR1. In case 2, the complex HCV quasispecies consisted of three distinct major variants; GSA of individual HVR1 clones allowed us to reconstruct the complex quasispecies pattern in vitro. In case 3, the simple quasispecies comprised 66 % homogeneous clones and 33 % unique minor variants differing by 1-3 nucleotides from the consensus sequence. In case 4, the simple quasispecies was 84 % homogeneous, but six unique major shift variants were identified among 31 clones by GSA. In summary, HCV quasispecies can be characterized based on GSA profiles following direct PCR amplification of HVR1 sequences from patients' serum; the GSA profiles approximate the clonal population of HCV as determined by clonal analysis. GSA of HVR1 clones showed a strong correlation with nucleotide sequencing.

show abstract

“…Immunohistochemical analysis that this region is subjected to immune selection. 4,9 This rerevealed a predominantly cytoplasmic presence of core gion exhibits significant variation not only among HCV isoprotein with occasional nuclear staining, and both cytolates but also within infected individuals over the course of plasmic and membrane expression of the E2 protein in time. 10 the transgenic livers.…”

mentioning

confidence: 91%

“…3,4 In general, the genome is flanked in its 5 -untranslated Although hepatitis C virus (HCV) is a leading cause region by a highly conserved (ú98%) 341 nucleotide seof morbidity and mortality worldwide, the role of viral quence, which appears to play a key role in translational cytopathic effects remains unclear. To study the biosyncontrol.…”

mentioning

confidence: 99%

Transgenic expression of hepatitis C virus structural proteins in the mouse

et al. 1997

View full text Add to dashboard Cite

lies. 3,4 In general, the genome is flanked in its 5 -untranslated Although hepatitis C virus (HCV) is a leading cause region by a highly conserved (ú98%) 341 nucleotide seof morbidity and mortality worldwide, the role of viral quence, which appears to play a key role in translational cytopathic effects remains unclear. To study the biosyncontrol. 1,5,6 The coding region encodes structural proteins in thesis of HCV structural proteins and their pathogenic its N-terminal portion that include a nonglycosylated core role, we constructed transgenic mice, expressing type protein (p22), which associates with genomic RNA to form 1b HCV structural proteins (core, E1, and E2) in liver the nucleocapsid. The C-terminal 20 amino acids of the core tissues. Two liver-specific promoters were used. The protein are highly hydrophobic and may act as a signal semouse major urinary protein (MUP) promoter has been quence for processing of adjacent polypeptides. 7,8 Immedishown to be developmentally regulated with little or no ately downstream from the core are two proteins, designated expression in utero but high-level expression after birth.E1 and E2/NS1, which correspond to the putative envelope The albumin (Alb) promoter provides constitutive, high glycoproteins. These proteins, designated gp33 and gp70 levels of transgenes in liver. Expression of both HCV respectively, are extensively N-glycosylated and appear to transgenes was detected in several lines by Northern function as membrane-associated proteins essential for virion blots, HCV-specific reverse transcriptase-polymerase assembly. The presence of a hypervariable region in the Nchain reactions (RT-PCR), and Western immunoblotting.terminal portion of the E2/NS1 domain to which an active Alb HCV lines showed higher levels of HCV expression humoral response is directed in infected individuals suggests than the MUP HCV lines. Immunohistochemical analysis that this region is subjected to immune selection. 4,9 This rerevealed a predominantly cytoplasmic presence of core gion exhibits significant variation not only among HCV isoprotein with occasional nuclear staining, and both cytolates but also within infected individuals over the course of plasmic and membrane expression of the E2 protein in time. 10 the transgenic livers. In both transgenes, the highest lev-HCV is an important cause of morbidity and mortality els of both antigens were seen in perivenular hepatoworldwide, causing a spectrum of liver disease ranging from cytes, suggesting potential processing specificity in the asymptomatic carrier state to end-stage liver disease. those cells. At six months of age, the livers of allCompared to other hepatotropic viruses, there is a higher transgenic lineages remained histologically normal. We rate of chronicity after HCV infection, with at least 70% of concluded that HCV structural proteins are not directly those infected developing chronic liver disease. 11 In addition cytopathic in this animal model. (HEPATOLOGY 1997;25: to the morbidity and mortality caused by chronic l...

show abstract

Variable and hypervariable domains are found in the regions of HCV corresponding to the flavivirus envelope and NS1 proteins and the pestivirus envelope glycoproteins

Cited by 589 publications

References 26 publications

New Methods for Detecting Positive Selection at Single Amino Acid Sites

New Methods for Detecting Positive Selection at Single Amino Acid Sites

Characterization of simple and complex hepatitis C virus quasispecies by heteroduplex gel shift analysis: correlation with nucleotide sequencing

Transgenic expression of hepatitis C virus structural proteins in the mouse

Contact Info

Product

Resources

About