Table 1.

Primer sets for targeted multiplex PCR

Clade	Position in the genome	Primer sequence	Amplicon size (bp)	Melting temperature Tm (°C)
G614	241	GF-1: 5’- TGTCGTTGACAGGACACGAG-3’ GR-1: 5’- TCCTCCACGGAGTCTCCAAA-3’	228	60.94 59.33
G614	3037	GF-2: 5’- ATGAGTTCGCCTGTGTTGTG-3’ GR-2: 5’- TGTCTGATTGTCCTCACTGCC-3’	392	58.77 60.00
G614	14408	GF-3: 5’ - TGGGATCAGACATACCACCCA - 3’ GR-3: 5’ - GTGCAGCTACTGAAAAGCACG - 3’	334	60.27 60.40
G614	23403	GF-4: 5’ -CTGATGCTGTCCGTGATCCA - 3’ GR-4: 5’ - ACTAGCGCATATACCTGCACC - 3’	302	59.82 60.00
S84	8782	SF-1: 5’- GCGTCATATTAATGCGCAGGT-3’ SR-1: 5’- GCAGCCAAAACACAAGCTGA-3’	663	59.47 59.90
S84	28144	SF-2: 5’ - CGTGGATGAGGCTGGTTCTA - 3’ SR-2: 5’ - CCCACTGCGTTCTCCATTCT - 3’	300	59.18 60.04
V251	26144	VF-1: 5’- TCAGGTGATGGCACAACAAGT-3’ VR-1: 5’- GTACGCACACAATCGAAGCG-3’	468	60.13 60.25
I378	1397	IF-1: 5’ – GAAACTTCATGGCAGACGGG-3’ IR-1: 5’ – GCTAGCACGTGGAACCCAAT-3’	303	59.20 60.68
I378	28688	IF-2: 5’ - ACCGCTCTCACTCAACATGG - 3’ IR-2: 5’ - GCAGTACGTTTTTGCCGAGG - 3’	632	60.04 60.11
D392	1440	DF-1: 5’ - AGGTGCCACTACTTGTGGTT - 3’ DR-1: 5’ - AGTTTCAAGAGTGCGGGAGA - 3’	607	59.16 58.95
D392	2891	DF-2: 5’ - CGGTGCACCAACAAAGGTTAC - 3’ DR-2: 5’ - GCAGAAGTGGCACCAAATTCC - 3’	450	60.27 60.34