Table 1.

Primer and Probe Sequences for RT-ddPCR assays. Each assay is identified by the amino acid(s) in Spike RBD it targets. For each probe name, bold letters indicate the amino acid detected by that probe. For each probe sequence, bold/underlined letters indicate the mutation that results in the amino acid change. Primer and probe sequences for 501Y are the same as the S1B set listed in [36].

Reaction	Primer/Probe Name	Sequence
417	S417Forward	GAGGTGATGAAGTCAGACAAATCG
	S417Reverse	GCAGCCTGTAAAATCATCTGGTAA
	S417NProbe	FAM_CTGGAAATATTGCTGATTAT_MGB
	S417TProbe	VIC_CTGGAACGATTGCTG_MGB
484	S484Forward	TTAGGAAGTCTAATCTCAAACCTTTTGAG
	S484Reverse	CTGTATGGTTGGTAACCAACACCAT
	S484KProbe	FAM_CCTTTAACACCATTACAAGGT_MGB
	S484EProbe	VIC_CCTTCAACACCATTACAAGG_MGB
452/501	S452Forward	CAATCTTGATTCTAAGGTTGGTGGTA
	S452Reverse	CGGCCTGATAGATTTCAGTTGAA
	S452RProbe	FAM_ACCGGTATAGATTGTTTAGGAA_MGB
	S501Forward	ATGGTGTTGAAGGTTTTAATTGTTACTTT
	S501Reverse	GTGCATGTAGAAGTTCAAAAGAAAGTACTA
	S501YProbe	VIC_ATGGTTTCCAACCCACTTAT_MGB

Abbreviations: FAM, 6-carboxyfluorescein; MGB, Minor Groove Binder; VIC, 2′‑chloro-7′-phenyl-1,4-dichloro-6-carboxy-fluoroscein.