Table 2.

Specificity (%) of different genomic regions in clustering genogroups, genotypes, variants, and outbreak events as a group separated from others, as derived from bootstrapped ML trees

Group	N	Full	Windows (center 1,150)						PCR regions
		1–1,620 (1,620 nt) full Capsid	900–1,400 (500 nt) window-500	950–1,350 (400 nt) window-400	1,000–1,300 (300 nt) window-300	1,025–1,275 (250 nt) window-250	1,050–1,350 (200 nt) window-200	1,100–1,200 (100 nt) window-100	1–282 (282 nt) G2SK region C	5–284 (280 nt) G1SK region C	301–577 (277 nt) region E	795–1,253 (459 nt) P2 domain	1,372–1,585 (214 nt) CapC/D1/D3 region D	1,439–1,581 (143 nt) CapA/B1/B2 region D
On the basis of criterion 1: pure branches with support values >70
Genogroups	4	100	75	75	50	50	25	25	25	50	50	75	75	75
GI genotypes	8	100	100	88	63	63	63	38	75	75	75	100	63	63
GII genotypes	20	100	95	90	70	80	65	45	100	100	80	95	63	75
GIII genotypes	2	100	100	100	50	50	50	100	50	50	100	100	50	0
Variants	12	83	67	58	50	42	50	25	33	33	17	58	42	17
Outbreak events	11	100	64	64	55	45	45	27	0	0	55	64	27	9
On the basis of criteria 1 and 2: pure branches irrespective of support values
Genogroups	4	100	75	75	75	75	50	75	50	75	75	75	75	75
GI genotypes	8	100	100	100	100	88	88	75	75	75	100	100	75	63
GII genotypes	20	100	100	95	85	80	75	70	100	100	95	95	100	95
GIII genotypes	2	100	100	100	50	50	100	100	50	50	100	100	50	50
Variants	12	83	75	83	75	58	67	67	67	33	42	75	58	50
Outbreak events	11	100	91	82	73	64	64	64	36	36	82	73	45	36

Nucleotide position was chosen from the reference strain AB220921, and nt position 1 of the capsid gene corresponds with nt position 5,085 of the GII-4 strain Lordsdale/1,995/UK (GenBank X86557)