TABLE 1.

Primers and probes in the VEEV and MADV/EEEV rRT-PCRs ^a

Name	Sequence b	Concentration (nM) c	Location (5′−3′) d	Sequences fully matching e
VEEV
VEEV forward 1	GAAAGTTCACGTTGAYATCGAGGA	200	44–67	156/159 (98)
VEEV forward 2	GAAGGTTCACGTTGAYATCGAGGA	200
VEEV reverse 1	GCTCTGGCRTTAGCATGGTC	200	144–163	159/159 (100)
VEEV reverse 2	GCTCTAGCRTTAGCATGGTC	200
VEEV probe	5′-FAM-TTGAGGTAGAAGCHAAGCAGGTC-BHQ-1–3′	400	112–134	158/159 (99)
MADV/EEEV
ME forward	GAGATAGAAGCMACGCAGGTC	400	121–141; 99–119	31/32 (97); 1/449 (100)
ME reverse	TGYTTGGAATGCGTGTGC	400	255–272; 233–250	32/32 (100); 9/449 (98)
MADV probe	5′-FAM-CATCGAAAGCGAAGTGGACC-BHQ-1–3′	200	195–214	31/32 (97)
EEEV probe	5′-CFO560-TGAGGGAGAAGTGGAYACAGACC-BHQ-1–3′	400	176–198	6/449 (99)

^a BHQ, black hole quencher; CFO560, CAL Fluor Orange 560; and FAM, Fluorescein.

^b Probe sequences listed 5’′-fluorophore-sequence-quencher-3’′.

^c Concentration in the final reaction mixture.

^d Location in the following complete genome sequences: VEEV strain VEEV/Homo sapiens/GTM/69Z1/1969/IAB (Aaccession number KC344505.2); MADV strain Homo sapiens/Haiti-1901/2016 (MH359233.1); EEEV strain EEEV/Culiseta melanura/USA/SL13-0764-C/2013 (Aaccession number KX029319.1).

^e Displayed as number of complete genome sequences without a mismatch in the primer/probe sequence over all complete genome sequences aligned (%). Genomes downloaded on 22 Sept. 2021. Data shown for the combination of forward and reverse VEEV primers.