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Genus: Hepatovirus

Species: Hepatovirus A (formerly named Hepatitis A virus)

Serotype: Hepatitis A virus 1 (HAV-1)    
   Biotype: Human hepatitis A virus (HHAV)  
5' UTR VP4 VP2 VP3 VP1 pX 2B 2C 3A 3B 3C 3D 3' UTR
   Biotype: Simian hepatitis A virus (SHAV)  
5' UTR VP4 VP2 VP3 VP1 pX 2B 2C 3A 3B 3C 3D 3' UTR
     

(White areas indicate genes which haven't yet been sequenced completely; grey areas are where only partial sequences exist)

Virus Strain Region Length

Accession No.

 Reference Comments

Human hepatitis A virus (HHAV)
HHAV ? P1+ 3274 M14114 Baroudy et al., 1985  
3D+3'ncr 1590 M14115 Baroudy et al., 1985  
HHAV HM-175 (Victoria, Australia/76) CG 7478 M14707 Cohen et al., 1987a wild type - p35 AGMK
HHAV HM-175 CG 7473 M16632 Cohen et al., 1987b attenuated
HHAV HM-175 p59 (p42 BS-C-1) ? ? ? Ross et al., 1986  
HHAV HM-175 p16 CG 7472 ? Jansen et al., 1988  
HHAV HM-175 (HPA18F) CG* 7423 M59808 Lemon et al., 1991 * ~29nt & 35nt missing from the termini
HHAV HM-175 (HPA24A) CG* 7436 M59810 Lemon et al., 1991 * ~29nt & 23nt missing from the termini
HHAV HM-175 (HPA43C) CG* 7419 M59809 Lemon et al., 1991 * ~29nt & 39nt missing from the termini
HHAV LA CG 7478 K02990 Najarian et al., 1985  
HHAV CR326 5' half of genome 3054 M10033 Linemeyer et al., 1985  
HHAV HAS-15 P1+P2 4136 X15464 Sverdlov et al., 1987  
2C+P3 2676 X15463  
P1+ 3372 X04200 Ovchinnikov et al., 1986  
HHAV ? P1+NS 3372 A11312 Ovchinnikov et al., 1988  
3C 925 A11313  
HHAV MBB CG 7470 M20273 Paul et al., 1987  
HHAV LCDC-1 1D 1023 X14666 Andonov et al., 1989  
HHAV GA76 1B-1D+2A (p) 2426 M66695 Khanna et al., 1992  
HHAV GBM CG* 7427 X75214 Graff et al., 1994 FRhK *(~46nt missing from the 5' end)
CG* 7431 X75215 WT *(~46nt missing from the 5' end)
CG* 7431 X75216 HFS *(~46nt missing from the 5' end)
HHAV FG 5' NCR 709 X70846 Morace et al., 1993  
2B-3B 2264 X70845  
CG* 7421 X83302 Morace, unpublished * 25nt missing at the 5' end
HHAV S10 5' NCR ? ? N/A Morace et al., 1993  
2B-3B ? ? N/A  
HHAV LSH/S 1D-3C/3D 272 S44068 Fineschi et al., 1991  
266 S44069  
341 S44086  
339 S44094  
336 S44105  
293 S44109  
302 S44110  
HHAV RGSB n11 1D 800 X75446 Argentini et al., 1995  
HHAV RGSB n16 1D 800 X75447 Argentini et al., 1995  
HHAV ? ? ? ? Beneduce et al., 1995  
HHAV strain ISR-05, Afula District, Israel, 1993 VP1/2A junction 168 Z77243 Karetnyi et al., 1996, unpublished.  
HHAV strain ISR-10, Afula District, Israel, 1993 VP1/2A junction 168 Z77244 Karetnyi et al., 1996, unpublished.  
HHAV strain ISR-12, Afula District, Israel, 1993 VP1/2A junction 168 Z77245 Karetnyi et al., 1996, unpublished.  
HHAV strain ISR-15, Afula District, Israel, 1993 VP1/2A junction 168 Z77246 Karetnyi et al., 1996, unpublished.  
HHAV strain ISR-70, Akko District, Israel, 1993 VP1/2A junction 168 Z77247 Karetnyi et al., 1996, unpublished.  
HHAV strain ISR-79, Akko District, Israel, 1993 VP1/2A junction 168 Z77248 Karetnyi et al., 1996, unpublished.  
HHAV 412991 VP1/2A junction 168 U68689 Taylor, 1996, unpublished.  
HHAV 96001190 VP1/2A junction 168 U68690 Taylor, 1996, unpublished.  
HHAV 406909 VP1/2A junction 168 U68691 Taylor, 1996, unpublished.  
HHAV JVR VP1/2A junction 168 U68692 Taylor, 1996, unpublished.  
HHAV 503712 VP1/2A junction 168 U68693 Taylor, 1996, unpublished.  
HHAV 96002382 VP1/2A junction 168 U68694 Taylor, 1996, unpublished.  
HHAV 406808 VP1/2A junction 168 U68695 Taylor, 1996, unpublished.  
HHAV 923359 VP1/2A junction 168 U68696 Taylor, 1996, unpublished.  
HHAV VDM VP1/2A junction 168 U68697 Taylor, 1996, unpublished.  
HHAV 2333 VP1/2A junction 168 U68698 Taylor, 1996, unpublished. -
HHAV 314274 VP1/2A junction 168 U68699 Taylor, 1996, unpublished. -
HHAV 504184 VP1/2A junction 168 U68700 Taylor, 1996, unpublished. -
HHAV Nor-1 (Grimstad, Norway 1996) VP1/2A junction 349 AF050223 Grinde et al., 1997; Stene-Johansen et al., 1998  
HHAV Nor-2 (Loerenskog, Norway 1996) VP1/2A junction 349 AF050224 Grinde et al., 1997; Stene-Johansen et al., 1998  
HHAV Nor-3 (Bergen, Norway 1996) VP1/2A junction 349 AF050225 Grinde et al., 1997; Stene-Johansen et al., 1998  
HHAV Nor-4 (Meraaker, Norway 1995) VP1/2A junction 349 AF050226 Grinde et al., 1997; Stene-Johansen et al., 1998  
HHAV Nor-5 (Levanger, Norway 1995) VP1/2A junction 349 AF050227 Grinde et al., 1997; Stene-Johansen et al., 1998  
HHAV Nor-7 (Trondheim, Norway 1995) VP1/2A junction 348 AF050228 Grinde et al., 1997; Stene-Johansen et al., 1998  
HHAV Nor-8 (Oslo, Norway 1995) VP1/2A junction 349 AF050229 Grinde et al., 1997; Stene-Johansen et al., 1998  
HHAV Nor-9 (Oslo, Norway 1995) VP1/2A junction 349 AF050230 Grinde et al., 1997; Stene-Johansen et al., 1998  
HHAV Nor-10 (Fredrikstad, Norway 1996) VP1/2A junction 349 AF050231 Grinde et al., 1997; Stene-Johansen et al., 1998  
HHAV Nor-11 (Oslo, Norway 1995) VP1/2A junction 349 AF050232 Grinde et al., 1997; Stene-Johansen et al., 1998  
HHAV Nor-12 (Oslo, Norway 1995) VP1/2A junction 349 AF050233 Grinde et al., 1997; Stene-Johansen et al., 1998  
HHAV Nor-13 (Oslo, Norway 1996) VP1/2A junction 349 AF050234 Grinde et al., 1997; Stene-Johansen et al., 1998  
HHAV Nor-14 (Oslo, Norway 1995) VP1/2A junction 349 AF050235 Grinde et al., 1997; Stene-Johansen et al., 1998  
HHAV Nor-15 (Oslo, Norway 1995) VP1/2A junction 349 AF050236 Grinde et al., 1997; Stene-Johansen et al., 1998  
HHAV Nor-16 (Verdal, Norway 1995) VP1/2A junction 349 AF050237 Grinde et al., 1997; Stene-Johansen et al., 1998  
HHAV Nor-17 (Norway 1995-97) VP1/2A junction 349 AF050238 Grinde et al., 1997; Stene-Johansen et al., 1998  
HHAV AH1 CG 7477 AB020564 K. Fujiwara, unpublished.  
HHAV AH2 CG 7477 AB020565 K. Fujiwara, unpublished.  
HHAV AH3 CG 7445 AB020566 K. Fujiwara, unpublished.  
HHAV FH1 CG 7477 AB020567 K. Fujiwara, unpublished.  
HHAV FH2 CG 7478 AB020568 K. Fujiwara, unpublished.  
HHAV FH3 CG 7477 AB020569 K. Fujiwara, unpublished.  
HHAV HAF-203 (Brazil, 1992) CG

7468

 AF268396 Baptista et al., unpublished  
HHAV SLF88 CG*

7414

AY032861 Ching et al., 2002 * 5' end missing
HHAV LU38/WT (China) CG

7477

AF357222 Hu et al., 2002  
HHAV LY6 (China) CG 7477 AF485328 Hu et al., 2002  
HHAV P27 VP2+VP3+VP1 2304 AJ519486 Costa-Mattioli et al., unpub.  
HHAV 9F94 VP2+VP3+VP1 2304 AJ519487 Costa-Mattioli et al., unpub.  
HHAV DL3 CG 7476 AF512536 Liu et al., unpub.  
HHAV HepA-293 (Russia, 2007) CG 7487 HQ437707 Bondarenko et al., 2010  

Simian hepatitis A virus (SHAV)

(I'm not sure if all these are true simian HAVs)
SHAV Simian ?(Russian) 3D ? 1443 ? Balayan et al., 1989?  
? 1248 X15461 Balayan et al., 1989?  
? 156 X15462 Balayan et al., 1989  
SHAV PA21 (simian strain) P1 2373 M34084 Brown et al., 1989  
SHAV AGM-27 (African green monkey) CG* 7400 D00924 Tsarev et al., 1991 * ~58 nt & 22nt missing from the termini
SHAV CY-145 (cynomolgus macaque) P1+2A 2521 M59286 Nainan et al., 1991  
SHAV JM55/CY-55 (cynomolgus macaque) P1 (p) 1611 N/A Nainan et al., 1991  
SHAV not named (Macaca mulatta) CG 7425 EU140838 Arankalle, V.A. and Ramakrishnan, J., unpub.  
CG = complete genome; (p) = partial gene sequence

Molecular Epidemiological Studies

Robertson, B.H., Jansen, R.W., Khanna, B., Totsuka, A., Nainan, O.V., Siegl, G., Widell, A., Margolis, H.S., Isomura, S., Ito, K., Ishizu, T., Moritsugu, T. (1992). Genetic relatedness of hepatitis A virus strains recovered from different geographical regions. J. Gen. Virol. 73: 1365-1377.

References

Andonov, A.P., Lau, P. and Chaudhary, R. (1989). Nucleotide sequence of the VP1 gene from a Chinese strain of hepatitis A virus (HAV). Nucleic Acids Res. 17: 3594-3594.

Argentini, C., D'ugo, E., Bruni, R., Gluck, R., Giuseppetti, R., Rapicetta, M. (1995). Sequence and phylogenetic analysis of the VP1 gene in two cell culture adapted HAV strains from a unique pathogenic isolate. Virus Genes 10: 37-43.

Balayan, M.S., Kusov, Yu. Yu., Andjarparidze, A.G., Tsarev, S.A., Sverdlov, E.D., Chizhikov, V.E., Blinov, V.M., Vasilenko, S.K. (1989). Variations in genome fragments coding for RNA polymerase in human and simian hepatitis A viruses. FEBS Letters, ????????

Baptista, M.L., Silva, M., de Lima, M.A., Yoshida, C.F., Gaspar, A.M., Pires Lopes, M.Q. and Galler, R. Nucleotide sequence of the HAF-203 hepatitis A virus strain isolated in Brazil and expression of the VP1 gene in a bacterial system. Unpublished. [Virology, Oswaldo Cruz Foundation, Av. Brasil 4365, Rio de Janeiro, RJ 21040-900, Brazil]

Baroudy, B.M., Ticehurst, J.R., Miele, T.A., Maizel, J.V.Jr., Purcell, R.H. and Feinstone, S.M. (1985). Sequence analysis of hepatitis A virus cDNA coding for capsid proteins and RNA polymerase. Proc. Natl. Acad. Sci. USA 82: 2143-2147.

Beneduce, F., Pisani, G., Divizia, M., Pana, A. and Morace, G. (1995). Complete nucleotide sequence of a cytopathic hepatitis-A virus strain isolated in Italy. Virus Research 36: 299-309.

Brown, E.A., Jansen, R.W. and Lemon, S.M. (1989). Characterization of a simian hepatitis A virus (HAV): antigenic and genetic comparison with human HAV. J. Virol. 63: 4932-4937.

Ching, K.Z., Nakano, T., Chapman, L.E., Demby, A. and Robertson, B.H. (2002). Genetic characterization of wild-type genotype VII hepatitis A virus. J. Gen. Virol. 83: 53-60.

Cohen, J.I., Ticehurst, J.R., Purcell, R.H., Buckler-White, A. and Baroudy, B.M. (1987a). Complete nucleotide sequence of wild-type hepatitis A virus: comparison with different strains of hepatitis A virus and other picornaviruses. J. Virol. 61: 50-59.

Cohen, J.I., Rosenblum, B., Ticehurst, J.R., Daemer, R.J., Feinstone, S.M. and Purcell, R.H. (1987b). Complete nucleotide sequence of an attenuated hepatitis A virus: comparison with wild-type virus. Proc. Natl. Acad. Sci., USA 84: 2497-2501.

Costa-Mattioli, M., Ferre, V., Casane, D., Perez-Bercoff, R., Coste-Burel, M., Imbert-Marcille, B.M., Andre, E., Bressollette-Bodin, C., Billaudel, S. and Cristina, J. Evidence of recombination in natural populations of hepatitis A virus. Unpublished. [Laboratorio de Virologia Molecular, CIN - Facultad de Ciencias, Igua 4225, 11400 Montevideo, URUGUAY]

Fineschi, N., Cavalieri, F., Garelick, H., Prugnola, A., Pellegrini, V. and Zuckerman A.J. (1991). Characterization of a hepatitis A virus strain suitable for vaccine production. J. Hepatol. 0:51-51.

Fujiwara K. Hepatitis A virus. Unpublished. [Keiichi Fujiwara, Chiba University School of Medicine, First Department of Internal Medicine; 1-8-1 Inohana, Chuo-ku, Chiba, Chiba 260-8670, Japan (E-mail:fujiwark@ho.chiba-u.ac.jp, Tel:81-43-226-2083, Fax:81-43-226-2088)]

Graff, J., Normann, A., Feinstone, S.M. and Flehmig, B. (1994). Nucleotide sequence of wild-type hepatitis A virus GBM in comparison to two cell culture adapted variants. J. Virol. 68: 548-554.

Grinde, B., Stene-Johansen, K., Sharma, B., Hoel, T., Jensenius, M. and Skaug K. (1997). Characterisation of an epidemic of hepatitis A virus involving intravenous drug abusers--infection by needle sharing? J. Med. Virol. 53: 69-75.

Hu, Y., Hu, N. and Liu, G. (2002). Complete genomes of two Human hepatitis A virus isolates from China: analysis and comparison with other isolates. Acta Virol. 46: 153-157.

Karetnyi, Y.V., Shulman, L.M., Manor, J., Leitner, L., Shehab, S. and Mendelson, E. (1996). Genetic classification of hepatitis A virus strains isolated in Israel, based on their VP1/2A necleotide sequence. Unpublished. (Central Virology Laboratory, Sheba Medical Center, Tel Hashomer, 52621, Israel).

Khanna, B., Spelbring, J.E., Innis, B.L. and Robertson, B.H. (1992). Characterization of a genetic variant of human hepatitis A. virus. J. Med. Virol. 36: 118-124.

Lemon, S.M., Murphy, P.C., Shields, P.A., Ping, L.H., Feinstone, S.M., Cromeans, T. and Jansen, R.W. (1991). Antigenic and genetic variation in cytopathic Hepatitis A virus variants arising during persistent infection: evidence for genetic recombination. J. Virol. 65: 2056-2065.

Liu, G., Hu, N. and Hu, Y. A complete genome of a wild-type hepatitis A virus strain DL3. Unpublished. [Department of Vaccine Research, Institute of Medical Biology, Chinese Academy of Medical Sciences, 379 Jiaoling, Kunming, Yunnan 650118, P.R. China]

Linemeyer, D.L., Menke, J.G., Martin-Gallardo, A., Hughes, J.V., Young, A. and Mitra, S.W. (1985). Molecular cloning and partial sequencing of hepatitis A viral cDNA. J. Virol. 54: 247-255.

Morace, G., Pisani, G., Beneduce, F., Divizia, M. and Panà, A. (1993). Mutations in the 3A genomic region of two cytopathic strains of hepatitis A virus isolated in Italy. Virus Res. 28: 187-194.

Nainan, O.V., Margolis, H.S., Robertson, B.H., Balayan, M. and Brinton, M.A. (1991). Sequence analysis of a new hepatitis A virus naturally infecting cynomolgus macaques (Macaca fascicularis). J. gen. Virol. 72: 1685-1689.

Najarian, R., Caput, D., Gee, W., Potter, S.J., Renard, A., Merryweather, J., Van Nest, G. and Dina, D. (1985). Primary structure and gene organization of human hepatitis A virus. Proc. Nat. Acad. Sci., USA 82: 2627-2631.

Ovchinnikov, Y.A., Sverdlov, E.D., Tsarev, S.A., Arsenyan, S.G., Rokhlina, T.O., Chizhikov, V.E., Petrov, N.A., Prikhod'ko, G.G., Blinov, V.M., Vasilenko, S.K., Sandakhchiev, L.S., Kusov, Yu Yu, Grabko, V.I., Fleer, G.P., Balayan, M.S. and Drozdov, S.G. (1986). The sequence of 3372 nucleotide units of hepatitis a virus RNA, coding for the capsid VP4-VP1 and certain nonstructural proteins. Dokl-Biochem. Sect. (English Translation) 285: 379-383.

Ovchinnikov, J.A., Sverdlov, E.D., Tsarev, S.A., Frolova, E.I., Rokhlina, T.O., Rostapshov, V.M., Azhikina, T.L., Arsenian, S.G., Snezhkov, E.V., Markova, S.V., Kovriga, I.E., Kusov, J.J., Nastashenko, T.A., Valyano, N.M., Balaian, M.S., Drozdov, S.G., Chizhikov, V.E., Petrov, N.A. and Vasilenko S.K. (1988). Recombinant plasmid DNAs, coding for synthesis of polypeptide substances for a vaccine against hepatitis A. Patent numbers EP0276330-A/19 & EP0276330-A/20, 03-AUG-1988. Institut Bioorganicheskoi Khimii Imeni M.M. Shemyakina Akademii nauk SSR; Institut Poliomielita i Virusnykh Entsefalitov Akad. Med. Nauk SSSR; Vsesojuzny Nauchno-Issledovatelsky Institut Molekulyarnoi Biologii; Moskovsky Nauchno-Issledovatelsky Institut Virusnykh Preparatov.

Paul, A.V., Tada, H., von der Helm, K., Wissel, T., Kiehn, R., Wimmer, E. and Deinhardt, F. (1987). The entire nucleotide sequence of the genome of human hepatitis A virus (isolate MBB). Virus Res. 8: 153-171.

Stene-Johansen, K., Skaug, K., Blystad, H. and Grinde B. (1998). An unique hepatitis A virus strain caused an epidemic in Norway associated with intraveous drug abuse. Scand. J. Infect. Dis. 0: 0-0.

Sverdlov, S.D., Tsarev, S.A., Markova, S.V., Vasilenko, S.K., Chizhikov, V.E., Petrov, N.A., Kusov Yu.Yu., Nastashenko, T.A. and Balayan, M.S. (1987). Cloning and expression of hepatitis A virus genome in E. coli cells. Mol. Gen. Microbiol. Virol. 6: 129-133.

Taylor, M.B. (1996). Molecular epidemiology of South African strains of hepatitis A virus: 1982-1996. Unpublished. (M.B. Taylor, Institute of Pathology, University of Pretoria, Medical Virology, Dr Savage Rd, Pretoria, Gauteng, 0001, South Africa).

Tsarev, S.A., Emerson, S.U., Balayan, M.S., Ticehurst, J.R. and Purcell R.H. (1991). Simian hepatitis a virus (HAV) strain AGM-27: Comparison of genome structure and growth in cell culture with other HAV strains. J. gen. Virol. 72: 1677-1683.