Copyright
©The Author(s) 2003.
World J Gastroenterol. Mar 15, 2003; 9(3): 499-504
Published online Mar 15, 2003. doi: 10.3748/wjg.v9.i3.499
Published online Mar 15, 2003. doi: 10.3748/wjg.v9.i3.499
Table 1 The primers used for amplification of DL3 genomic RNA
Clones | Primers | Sequences |
A (0.8kb) | 5’RACE RT-primer | 5-(P)GCAGAATGAATC-3 |
5’RACE A1 | 5-AGTCCGTTGATAGGACTGAG-3 | |
5’RACE S1 | 5-TGTTCTTCCTCAATATCTGCC-3 | |
5’RACE A2 | 5-TTCTAAGAAGACTCAGGGGG-3 | |
5’RACE S2 | 5-CTGGAAAATTCCTTGTTTGGCC-3 | |
B (0.5kb) | B1 | 5-GCTGAGGTACTCAGGGGC-3 |
B2 | 5-AGGATAAACAGTCAAGGATGC-3 | |
C (1.1kb) | C1 | 5-ACATATGCAAGATTTGGCATTG-3 |
C2 | 5-ATCCATAGCATGATAAAGAGG-3 | |
D (1.0kb) | D1 | 5-CCTGGATTTCTGACACTCC-3 |
D2 | 5-CAGTGGATAACATGGCATTTG-3 | |
E (1.1kb) | E1 | 5-TCTGTCACAGAACAATCAGAG-3 |
E2 | 5-AATCCCTGAACAAATGTCTCC-3 | |
F (1.2kb) | F1 | 5-TCCAGAATGATGGAGCTGAG-3 |
F2 | 5-CTTCGACAAGCACTCCAAG-3 | |
G (1.2kb) | G1 | 5-AGTTCCTTAGTAATGACAGTTG-3 |
G2 | 5-GCCATTGGATCAATCTCAGC-3 | |
H (1.1kb) | H1 | 5-AAGTGGAATTTTCTCAGTGTTC-3 |
H2 | 5-GTCCAATCAAGTCAAGATTATC-3 | |
I (o.5kb) | I1 | 5-GATTCTCTGTTATGGAGATG-3 |
I2 | 5-TTTTTTTTTTTTTTTTTTTTTATTT-3 |
Table 2 Nucleotide identities of full-length genomes between DL3 and reference isolates
Numbers of nucleotide differences/identity | |||||||||||
AH1 | AH2 | AH3 | FH1 | FH2 | FH3 | GBM | LA | HM175 | MBB | SLF88 | |
Full | 185/97.5 | 263/96.5 | 307/95.9 | 282/96.2 | 200/97.3 | 199/97.3 | 323/95.7 | 344/95.4 | 642/91.4 | 659/91.2 | 1066/85.7 |
5’NTR | 15/98.0 | 29/96.0 | 25/96.6 | 16/97.8 | 13/98.2 | 13/98.2 | 18/97.4 | 14/98.1 | 38/94.8 | 50/93.1 | 84/88.5 |
VP4 | 1/98.6 | 2/97.1 | 4/94.2 | 2/97.1 | 2/97.1 | 2/97.1 | 3/95.7 | 2/97.1 | 7/89.9 | 7/89.9 | 8/88.4 |
VP2 | 15/97.7 | 25/96.2 | 28/95.8 | 24/96.4 | 18/97.3 | 24/96.4 | 39/94.1 | 28/95.8 | 58/91.3 | 58/91.3 | 98/85.3 |
VP3 | 15/98.0 | 25/96.6 | 28/96.2 | 27/96.3 | 13/98.2 | 23/96.9 | 35/95.3 | 40/94.6 | 67/90.9 | 63/91.5 | 114/84.6 |
VP1 | 23/97.2 | 27/96.7 | 25/97.0 | 23/97.2 | 22/97.3 | 13/98.4 | 30/96.4 | 44/94.6 | 76/90.8 | 78/90.5 | 124/84.9 |
2A | 5/97.7 | 10/95.3 | 11/94.8 | 9/95.8 | 3/98.6 | 9/95.8 | 9/95.8 | 12/94.4 | 17/92.0 | 14/93.4 | 27/87.3 |
2B | 13/98.3 | 26/96.5 | 29/96.1 | 46/93.9 | 18/97.6 | 28/96.3 | 33/95.6 | 37/95.1 | 75/90.0 | 73/90.3 | 99/86.9 |
2C | 30/97.0 | 42/95.8 | 42/95.8 | 44/95.6 | 35/96.5 | 35/96.5 | 52/94.8 | 55/94.5 | 114/88.7 | 120/88.1 | 152/84.9 |
3A | 1/99.5 | 4/98.2 | 4/98.2 | 9/95.9 | 4/98.2 | 3/98.6 | 13/94.1 | 8/96.4 | 14/93.7 | 18/91.9 | 23/89.6 |
3B | 1/98.6 | 1/98.6 | 2/97.1 | 3/95.7 | 3/95.7 | 0 | 2/97.1 | 3/95.7 | 6/91.3 | 7/89.9 | 12/82.6 |
3C | 14/97.9 | 20/97.0 | 24/96.3 | 25/96.2 | 16/97.6 | 21/96.8 | 30/95.4 | 27/95.9 | 56/91.5 | 50/92.4 | 98/85.1 |
3D | 51/96.5 | 51/96.5 | 84/94.3 | 53/96.4 | 52/96.5 | 27/98.2 | 57/96.1 | 64/95.6 | 113/92.3 | 114/92.2 | 209/85.8 |
3’NTR | 1/98.4 | 1/98.4 | 1/98.4 | 1/98.4 | 1/98.4 | 1/98.4 | 2/96.8 | 10/84.4 | 1/98.4 | 7/88.9 | 18/71.4 |
Table 3 Amino acid identities of full-length genomes between DL3 and reference isolates
Numbers of amino acid differences/identity | |||||||||||
AH1 | AH2 | AH3 | FH1 | FH2 | FH3 | GBM | LA | HM175 | MBB | SLF88 | |
Full | 21/99.1 | 18/99.2 | 36/98.4 | 28/98.7 | 21/99.1 | 18/99.2 | 36/98.4 | 34/98.5 | 35/98.4 | 49/97.8 | 72/96.8 |
VP4 | 1/95.7 | 1/95.7 | 1/95.7 | 1/95.7 | 1/95.7 | 1/95.7 | 1/95.7 | 1/95.7 | 1/95.7 | 1/95.7 | 2/91.3 |
VP2 | 0 | 0 | 0 | 1/99.5 | 0 | 0 | 1/99.5 | 0 | 2/99.1 | 2/99.1 | 1/99.5 |
VP3 | 1/99.6 | 1/99.6 | 1/99.6 | 2/99.2 | 1/99.6 | 1/99.6 | 1/99.6 | 1/99.6 | 2/99.2 | 2/99.2 | 4/98.4 |
VP1 | 0 | 0 | 0 | 1/99.6 | 0 | 1/99.6 | 2/99.3 | 13/95.3 | 1/99.6 | 2/99.3 | 2/99.3 |
2A | 1/98.6 | 1/98.6 | 1/98.6 | 1/98.6 | 1/98.6 | 0 | 1/98.6 | 0 | 1/98.6 | 2/97.2 | 1/98.6 |
2B | 2/99.2 | 2/99.2 | 3/98.8 | 5/98.0 | 5/98.0 | 5/98.0 | 3/98.8 | 4/98.4 | 4/98.4 | 6/97.6 | 6/97.6 |
2C | 6/98.2 | 5/98.5 | 4/98.8 | 6/98.2 | 5/98.5 | 4/98.8 | 7/97.9 | 5/98.5 | 11/96.7 | 17/94.9 | 14/95.8 |
3A | 0 | 1/98.6 | 1/98.6 | 1/98.6 | 0 | 0 | 5/93.2 | 1/98.6 | 1 /98.6 | 3/95.9 | 1/98.6 |
3B | 0 | 0 | 0 | 0 | 0 | 0 | 1/95.7 | 0 | 0 | 0 | 0 |
3C | 2/99.1 | 2/99.1 | 3/98.6 | 2/99.1 | 2/99.1 | 2/99.1 | 3/98.6 | 2/99.1 | 2/99.1 | 2/99.1 | 8/96.3 |
3D | 8/98.4 | 5/99.0 | 22/95.5 | 8/98.4 | 6/98.8 | 4/99.2 | 11/97.8 | 7/98.6 | 10/98.0 | 12/97.5 | 33/93.3 |
- Citation: Liu GD, Hu NZ, Hu YZ. Full-length genome of wild-type hepatitis A virus (DL3) isolated in China. World J Gastroenterol 2003; 9(3): 499-504
- URL: https://www.wjgnet.com/1007-9327/full/v9/i3/499.htm
- DOI: https://dx.doi.org/10.3748/wjg.v9.i3.499