TABLE 1.

Assays and primers used in this study^a

Assay	Primer	Genome position	5′→3′ sequenceb	Concn (nM)
E1 assay
1st round (649 bp)	CHIKV-E1-S1	10141–10160	GTYATCCCSTCYCCGTACGT	480
	CHIKV-E1-S1B	10142–10160	TYATCCCGTCTCCGTACGT	200
	CHIKV-E1-AS1	10790–10768	TTYAYMGCTCTTACCGGGTTTGT	480
	CHIKV-E1-AS1B	10787–10768	AYCGCTCTTACCGGGTTTGT	200
2nd round (536 bp)	CHIKV-E1-S2	10228–10248	GGMGTCTACCCATTYATGTGG	400
	CHIKV-E1-S2B	10226–10248	CTGGMGTCTACCCATTTATGTGG	200
	CHIKV-E1-AS2	10763–10744	ATTTGRCAGCCRAAHGGTGC	600
E2 assay
1st round (438 bp)	CHIKV-E2-S1	8973–8993	CCTTGCAGCACNTAYGYGCA	600
	CHIKV-E2-AS1	9410–9391	AGTGTTGGGTGRTCVGGRTA	600
2nd round (365 bp)	CHIKV-E2-S2	9046–9065	CCAGAYACYCCWGAYCRCAC	600
	CHIKV-E2-AS1	9410–9391	AGTGTTGGGTGRTCVGGRTA	600

^aAssay sizes and primer positions are shown relative to a CHIKV reference genome (GenBank accession no. MG967666).

^bH = A/C/T, M = A/C, N = A/C/G/T, R = A/G, W = A/T, V = A/C/G, and Y = C/T.