TABLE 1

Assays and primers used in this studya

AssayPrimerGenome
position
5′→3′ sequencebConcn
(nM)
E1 assay
    1st round (649 bp)CHIKV-E1-S110141–10160GTYATCCCSTCYCCGTACGT480
CHIKV-E1-S1B10142–10160TYATCCCGTCTCCGTACGT200
CHIKV-E1-AS110790–10768TTYAYMGCTCTTACCGGGTTTGT480
CHIKV-E1-AS1B10787–10768AYCGCTCTTACCGGGTTTGT200
    2nd round (536 bp)CHIKV-E1-S210228–10248GGMGTCTACCCATTYATGTGG400
CHIKV-E1-S2B10226–10248CTGGMGTCTACCCATTTATGTGG200
CHIKV-E1-AS210763–10744ATTTGRCAGCCRAAHGGTGC600
E2 assay
    1st round (438 bp)CHIKV-E2-S18973–8993CCTTGCAGCACNTAYGYGCA600
CHIKV-E2-AS19410–9391AGTGTTGGGTGRTCVGGRTA600
    2nd round (365 bp)CHIKV-E2-S29046–9065CCAGAYACYCCWGAYCRCAC600
CHIKV-E2-AS19410–9391AGTGTTGGGTGRTCVGGRTA600
  • a Assay sizes and primer positions are shown relative to a CHIKV reference genome (GenBank accession no. MG967666).

  • b H = 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.