TABLE 1.

Agreement of the three rapid subtyping tools with phylogenetic analysis for the study population

Subtype defined by phy of PRa	No. of PR sequences	Concordanceb with phy (%) for PR			No. of RT sequences	Concordanceb with phy (%) for RT
		Stanford	NCBI	REGAc		Stanford	NCBI	REGAc
A	27	63	44.4	52	18	22.2	33.3	44.4
Bd	2	100	100	50	7	100	100	71.4
C	16	62.5	56.3	12.5	9	77.8	77.8	55.6
D	5	100	80	20	2	100	100	0
F	4	75	100	50	3	100	100	66.7
G	32	87.5	72	37.5	20	80	65	25
H	4	100	100	25	1	100	100	100
J	1	0	100	0	0
CRF01_AE	2	50	50	0	0
CRF02_AG	141	97.2	99.3	18.4	81	92.5	96.3	32
CRF03_AB	2	0	100	0	0
CRF06_cpx	11	0	81.8	18.2	5	0	60	40
CRF10_CD	2	0	0	0	3	0	0	0
CRF11_cpx	5	0	100	40	4	0	75	50
CRF12_BF	9	0	66.7	22.2	7	0	57.1	28.6
CRF13_cpx	1	0	100	0	1	0	0	0
CRF14_BG	13	0	100	0	10	0	100	0
Pure subtypes	91	75.8	64.8	36.2	60	66.7	65	43.3
All CRFs	186	74.2	95.1	17.5	111	67.6	85.6	28.8
CRFs without CRF02_AG	45	2.2	82.2	13.3	30	0	56.7	20
Total	277	74.7	85.2	23.5	171	67.2	78.4	33.9
Clade B controle	33	100	100	90.9	33	100	100	90.9

^aSubtypes in the pol coding region are as follows: CRF01_AE, subtype A; CRF02_AG, subtypes A and G; CRF03_AB, subtypes A and B; CRF06_cpx, subtypes G, K, A, and J; CRF10_CD, clades C and D; CRF11_cpx, subtypes J, G, and A; CRF12_BF, subtypes F and B; CRF13_cpx, subtypes G and J; CRF14_BG, subtype G.

^bItalicized values indicate significant differences (P < 0.05) between Stanford and NCBI results.

^cIncluding all the sequences not assigned to a subtype by the REGA tool (194 PR and 95 RT sequences).

^dSpecimens carrying non-B sequences at the pol coding region.

^eSpecimens carrying clade B sequences at both PR and RT.