Real-time RT-PCR high-resolution melting curve analysis and multiplex RT-PCR to detect and differentiate grapevine leafroll-associated virus 3 variant groups I, II, III and VI

Table 2 Pairwise comparison of LR3.HRM4 amplicon (226 nt segment of Hsp70h) for each variant group

		Variant group representative isolates
		1	2	3	4	5	6	7	8	9	10
Group I_GU983863.1_GLRaV-3_Isolate_WA-MR	1		0	1	1	9	10	24	50	50	53
Group I_AF037268.2_GLRaV-3_Isolate_NY-1	2	100		1	1	9	10	24	50	50	53
Group I_EU344893.1_GLRaV-3_Isolate_Cl-766	3	99.56	99.56		2	9	10	24	50	50	53
Group I_GQ352631.1_GLRaV-3_Isolate_621	4	99.56	99.56	99.12		10	11	25	49	49	52
Group II_GQ352632.1_GLRaV-3_Isolate_623	5	96.02	96.02	96.02	95.58		2	27	49	49	53
Group II_EU259806.1_GLRaV-3_Isolate_GP18	6	95.58	95.58	95.58	95.13	99.12		27	51	51	53
Group III_GQ352633.1_GLRaV-3_Isolate PL-20	7	89.38	89.38	89.38	88.94	88.05	88.05		58	58	61
Group VI_JQ655295_GLRaV-3_Isolate GH11	8	77.88	77.88	77.88	78.32	78.32	77.43	74.34		0	10
Group VI_JQ655296_GLRaV-3_Isolate_GH30	9	77.88	77.88	77.88	78.32	78.32	77.43	74.34	100		10
Group VI_EF508151.1_GLRaV-3_Isolate_NZ-1	10	76.55	76.55	76.55	76.99	76.55	76.55	73.01	95.58	95.58

The upper comparison in bold is the number of nucleotide differences between variant sequences and the lower comparison is the percent identity (%) between variant sequences.