Full-length genome of wild-type hepatitis A virus (DL3) isolated in China

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