A universal protocol to generate consensus level genome sequences for foot-and-mouth disease virus and other positive-sense polyadenylated RNA viruses using the Illumina MiSeq

Table 2 Primers and probes used in quantitation and WGS of FMDV and other RNA viruses

	Primer name	Primer sequence
RT-qPCR	Callahan 3DF [24]	ACT GGG TTT TAC AAA CCT GTG A
	Callahan 3DR [24]	GCG AGT CCT GCC ACG GA
	Callahan 3DP [24]	TCC TTT GCA CGC CGT GGG AC
First-strand synthesis	UKFMD Rev 6 [25]	GGC GGC CGC TTT TTT TTT TTT TTT
	NK72 [26]	GAA GGG CCC AGG GTT GGA CTC
	UKFMD UKG 4926R	AAG TCC TTC CCG TCG GGG T
	EMC-2B65R [27]	TCG GCA GTA GGG TTT GAG
	ERAV-2A22R [28]	GGG TTG CTC TCA ACA TCT CCA GCC AAT TT
	Vesi-3D1R	CKN GTN GGY TTN ARN CC
	Vesi-3D2R	TAN CAN CCR TCR TCN CCR TAN GT

International Union of Pure and Applied Chemistry (IUPAC) nucleotide ambiguity codes:
N: G or T or A or C; K: G or T; Y: T or C; R: G or A.

ISSN: 1471-2164