Complete Nucleotide Sequence of Wild-type Hepatitis A Virus: Comparison with Different Strains of Hepatitis A Virus and Other Picornaviruses

Overview

Journal J Virol

Publisher American Society for Microbiology

Date 1987 Jan 1

PMID 3023706

Citations 112

Authors

J I Cohen

J R Ticehurst

R H Purcell

A Buckler-White

B M Baroudy

Affiliations

Soon will be listed here.

Abstract

The complete nucleotide sequence of wild-type hepatitis A virus (HAV) HM-175 was determined. The sequence was compared with that of a cell culture-adapted HAV strain (R. Najarian, D. Caput, W. Gee, S.J. Potter, A. Renard, J. Merryweather, G.V. Nest, and D. Dina, Proc. Natl. Acad. Sci. USA 82:2627-2631, 1985). Both strains have a genome length of 7,478 nucleotides followed by a poly(A) tail, and both encode a polyprotein of 2,227 amino acids. Sequence comparison showed 624 nucleotide differences (91.7% identity) but only 34 amino acid differences (98.5% identity). All of the dipeptide cleavage sites mapped in this study were conserved between the two strains. The sequences of these two HAV strains were compared with the partial sequences of three other HAV strains. Most amino acid differences were located in the capsid region, especially in VP1. Whereas changes in amino acids were localized to certain portions of the genome, nucleotide differences occurred randomly throughout the genome. The most extensive nucleotide homology between the strains was in the 5' noncoding region (96% identity for cell culture-adapted strains versus wild type; greater than 99% identity among cell culture-adapted strains). HAV proteins are less homologous with those of any other picornavirus than the latter proteins are when compared with each other. When the sequences of wild-type and cell culture-adapted HAV strains are compared, the nucleotide differences in the 5' noncoding region and the amino acid differences in the capsid region suggest areas that may contain markers for cell culture adaptation and for attenuation.

Citing Articles

Hepatitis a Vaccine as Opportunity of Primary Prevention for Food Handlers: A Narrative Review.

Fallucca A, Restivo V, Sgariglia M, Roveta M, Trucchi C Vaccines (Basel). 2023; 11(7).

PMID: 37515087 PMC: 10383099. DOI: 10.3390/vaccines11071271.

Development and Evaluation of a Molecular Hepatitis A Virus Assay for Serum and Stool Specimens.

Kozak R, Rutherford C, Richard-Greenblatt M, Chau N, Cabrera A, Biondi M Viruses. 2022; 14(1).

PMID: 35062362 PMC: 8777614. DOI: 10.3390/v14010159.

Heme Oxygenase-1 Exerts Antiviral Activity against Hepatitis A Virus In Vitro.

Kim D, Ahn H, Go H, Kim D, Kim J, Lee J Pharmaceutics. 2021; 13(8).

PMID: 34452191 PMC: 8401830. DOI: 10.3390/pharmaceutics13081229.

Dissemination of Internal Ribosomal Entry Sites (IRES) Between Viruses by Horizontal Gene Transfer.

Arhab Y, Bulakhov A, Pestova T, Hellen C Viruses. 2020; 12(6).

PMID: 32512856 PMC: 7354566. DOI: 10.3390/v12060612.

A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites.

Koirala D, Shao Y, Koldobskaya Y, Fuller J, Watkins A, Shelke S Nat Commun. 2019; 10(1):3629.

PMID: 31399592 PMC: 6689051. DOI: 10.1038/s41467-019-11585-z.

References

Lundquist R, EHRENFELD E, Maizel Jr J . Isolation of a viral polypeptide associated with poliovirus RNA polymerase. Proc Natl Acad Sci U S A. 1974; 71(12):4773-7. PMC: 433979. DOI: 10.1073/pnas.71.12.4773. View

Diamond D, Wimmer E, von der Helm K, Deinhardt F . The genomic map of hepatitis A virus: an alternate analysis. Microb Pathog. 1986; 1(2):217-9. DOI: 10.1016/0882-4010(86)90023-9. View

Maxam A, Gilbert W . Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980; 65(1):499-560. DOI: 10.1016/s0076-6879(80)65059-9. View

Lamb R, Lai C . Sequence of interrupted and uninterrupted mRNAs and cloned DNA coding for the two overlapping nonstructural proteins of influenza virus. Cell. 1980; 21(2):475-85. DOI: 10.1016/0092-8674(80)90484-5. View

Zuker M, Stiegler P . Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 1981; 9(1):133-48. PMC: 326673. DOI: 10.1093/nar/9.1.133. View

Kitamura N, Semler B, Rothberg P, Larsen G, Adler C, Dorner A . Primary structure, gene organization and polypeptide expression of poliovirus RNA. Nature. 1981; 291(5816):547-53. DOI: 10.1038/291547a0. View

Racaniello V, Baltimore D . Molecular cloning of poliovirus cDNA and determination of the complete nucleotide sequence of the viral genome. Proc Natl Acad Sci U S A. 1981; 78(8):4887-91. PMC: 320284. DOI: 10.1073/pnas.78.8.4887. View

GOAD W, Kanehisa M . Pattern recognition in nucleic acid sequences. I. A general method for finding local homologies and symmetries. Nucleic Acids Res. 1982; 10(1):247-63. PMC: 326131. DOI: 10.1093/nar/10.1.247. View

Maizel Jr J, Lenk R . Enhanced graphic matrix analysis of nucleic acid and protein sequences. Proc Natl Acad Sci U S A. 1981; 78(12):7665-9. PMC: 349330. DOI: 10.1073/pnas.78.12.7665. View

10.

Palmenberg A, Rueckert R . Evidence for intramolecular self-cleavage of picornaviral replicase precursors. J Virol. 1982; 41(1):244-9. PMC: 256745. DOI: 10.1128/JVI.41.1.244-249.1982. View

11.

Hanecak R, Semler B, Anderson C, Wimmer E . Proteolytic processing of poliovirus polypeptides: antibodies to polypeptide P3-7c inhibit cleavage at glutamine-glycine pairs. Proc Natl Acad Sci U S A. 1982; 79(13):3973-7. PMC: 346558. DOI: 10.1073/pnas.79.13.3973. View

12.

Coulepis A, Locarnini S, WESTAWAY E, Tannock G, Gust I . Biophysical and biochemical characterization of hepatitis A virus. Intervirology. 1982; 18(3):107-27. DOI: 10.1159/000149314. View

13.

Takegami T, Semler B, Anderson C, Wimmer E . Membrane fractions active in poliovirus RNA replication contain VPg precursor polypeptides. Virology. 1983; 128(1):33-47. DOI: 10.1016/0042-6822(83)90316-1. View

14.

Nomoto A, Omata T, Toyoda H, Kuge S, Horie H, Kataoka Y . Complete nucleotide sequence of the attenuated poliovirus Sabin 1 strain genome. Proc Natl Acad Sci U S A. 1982; 79(19):5793-7. PMC: 346996. DOI: 10.1073/pnas.79.19.5793. View

15.

Ticehurst J, Racaniello V, Baroudy B, Baltimore D, Purcell R, Feinstone S . Molecular cloning and characterization of hepatitis A virus cDNA. Proc Natl Acad Sci U S A. 1983; 80(19):5885-9. PMC: 390180. DOI: 10.1073/pnas.80.19.5885. View

16.

Lemon S, Binn L . Antigenic relatedness of two strains of hepatitis A virus determined by cross-neutralization. Infect Immun. 1983; 42(1):418-20. PMC: 264574. DOI: 10.1128/iai.42.1.418-420.1983. View

17.

Feinstone S, Daemer R, Gust I, Purcell R . Live attenuated vaccine for hepatitis A. Dev Biol Stand. 1983; 54:429-32. View

18.

Kozak M . Compilation and analysis of sequences upstream from the translational start site in eukaryotic mRNAs. Nucleic Acids Res. 1984; 12(2):857-72. PMC: 318541. DOI: 10.1093/nar/12.2.857. View

19.

Palmenberg A, Kirby E, Janda M, DRAKE N, Duke G, Potratz K . The nucleotide and deduced amino acid sequences of the encephalomyocarditis viral polyprotein coding region. Nucleic Acids Res. 1984; 12(6):2969-85. PMC: 318719. DOI: 10.1093/nar/12.6.2969. View

20.

Stanway G, Hughes P, Mountford R, Reeve P, Minor P, Schild G . Comparison of the complete nucleotide sequences of the genomes of the neurovirulent poliovirus P3/Leon/37 and its attenuated Sabin vaccine derivative P3/Leon 12a1b. Proc Natl Acad Sci U S A. 1984; 81(5):1539-43. PMC: 344872. DOI: 10.1073/pnas.81.5.1539. View