Table 2.

Primers used for detecting CMBs and CBSIs in uniplex, duplex and multiplex RT-PCR assays.

Primer name	Primer sequence (5′–3′)	Targeta	Reference
Primers used for amplifying CMBs
Deng A	TAATATTACCKGWKGVCCSC	Begomovirus	[31]
Deng B	TGGACYTTRCAWGGBCCTTCACA	Begomovirus	[31]
CMBRep/F	CRTCAATGACGTTGTACCA	ACMV & EACMV	[29]
CMBCP/F	GKCGAAGCGACCAGGAGAT	ACMV & EACMV-Ug	[29]
ACMVCP/R	CCCTGYCTCCTGATGATTATA	ACMV	[29]
EACMV-UG/R	CGCCTAAGCAAGGAATGGCGT	EACMV-Ug	[25]
EACMVRep/R	GGTTTGCAGAGAACTACATC	EACMV	[29]
Primers used for amplifying CBSIs
RT-PCR
CBSVF3	GGARCCRATGTAYAAATTTGC	CBSIs	[25]
CBSVR3	AGGAGCWGCTARWGCAAA	CBSIs	[25]
RT-qPCR
CBSVR4 + CBSVF3	GCWGCTTTTATYACAAAMGC	CBSIs	[28]
Primers used for amplifying CBSV and UCBSV individually
CBSVF2	GGRCCATACATYAARTGGTT	CBSIs	[25]
CBSVR7	CCCTTTGCAAARCTRAAATARC	CBSV	[25]
CBSVR8	CCATTRTCTYTCCAMADCTTC	UCBSV	[25]
Primers used for amplifying cassava housekeeping genes
RubiscoLF	CTTTCCAAGGCCCGCCTCA	RubiscoL	[32]
RubiscoLR	CATCATCTTTGGTAAAATCAAGTCCA	RubiscoL	[29]
L2F	TGGTGTTGCCATGAACCCTGTAGA	Ribosomal protein (L2)	[33]
L2R	CGACCAGTCCTCCTTGCAGC	Ribosomal protein (L2)	[33]

^aACMV – African cassava mosaic virus; EACMV – East African cassava mosaic virus; EACMV-Ug – East African cassava mosaic virus-Uganda; CBSIs – cassava brown streak ipomoviruses; CBSV – Cassava brown streak virus; UCBSV – Ugandan Cassava brown streak virus.