Table 2.

Polyvalent PCR assays for the detection of plant viruses and/or viroids at the genus level.

Genus	Primers	Region	Amplicon (bp)	Species identification	Reference
Ilarvirus	Degenerated	RNA2/RdRp gene	381	Amplicon sequencing/RFLP	Maliogka et al., 2007
Pospiviroid	Degenerated		270	Luminex	van Brunschot et al., 2014b
Pospiviroid	Specific/several primers	Terminal conserved region (TCR) and terminal right domain (TR)	170–180	TaqMan probe only for genus	Botermans et al., 2013
Bromovirus/cucumovirus	Degenerated with adaptor sequences	RNA1	337	Amplicon sequencing	Seo et al., 2014
Pospiviroid	Degenerated		200	Amplicon sequencing	Olivier et al., 2014
Pospiviroid	Degenerated	The terminal left and the pathogenesis domains	300	Amplicon sequencing/RFLP	Luigi et al., 2014
Begomovirus	Degenerated	C3 ORF	290	Luminex	van Brunschot et al., 2014a
Potyvirus	Degenerated	NIb	350	Amplicon sequencing	Zheng et al., 2010
Trichoviruses, capilloviruses, foveaviruses	Degenerated	RdRp	362	Amplicon sequencing	Foissac et al., 2005
Phytoplasmas	Specific	16S rDNA	200	TaqMan only for phytoplasmas	Christensen et al., 2013; Malandraki et al., 2015
Allexivirus	Degenerated	3′-end of ORF6	183–192	Amplicon sequencing	Kumar et al., 2010; Majumder and Baranwal, 2014