Applicability of duplex real time and lateral flow strip reverse-transcription recombinase aided amplification assays for the detection of Enterovirus 71 and Coxsackievirus A16

Table 1 List of primers used in the study for rapid detection of EV71 and CA16

Assay	Primer/probe	Sequence 5′- 3′	Genomic Position ^a	Product size
Real time RAA	EV71-exo-F	CCTGCGAGTGCTTACCAATGGTTTTATGACGG	3026–3057	199 bp
	EV71-exo-R	GTATCCACGCCCTGACGTGCTTCATTCTCAT	3194–3224
	EV71-exo-P	AACATGATGGGCACGTTCTCAGTGCGGAC-[FAM-dT]-[THF] -[BHQ-dT]-GGGGACCTCCAAGTC-C3-spacer	3119–3165
	CA16-exo-F	GCAAGTAGTCACAGATTAGGCACTGGTGTTGT	2557–2588	161 bp
	CA16-exo-R	GCACGGCTAAAGAAATTCCCAATGGCTGTC	2688–2717
	CA16-exo-P	GTGACAAGAATCTCATTGAGACKAGATG-[FAM-dT]-[THF] [BHQ-dT]-GTTGAACCATCACTCCA-C3-spacer	2633–2680
	IAC-P	GTAAGGTGCTAGACTAAAATTGTTGGGACTT- [HEXdT]-G [THF]-A-[BHQ-dT]-CTCTGAAGTAAAAGG-C3-spacer
LFS RAA	EV71-LF-F	CCTGCGAGTGCTTACCAATGGTTTTATGACGG	3026–3057	199 bp
	EV 71-LF-R	Biotin-GTATCCACGCCCTGACGTGCTTCATTCTCAT	3194–3224
	EV71-LF-P	FAM-AACATGATGGGCACGTTCTCAGTGCGGAC -[THF]-TGGGGACCTCCAAGTC-C3-spacer	3119–3165
	CA16-LF-F	GCAAGTAGTCACAGATTAGGCACTGGTGTTGT	2557–2588	161 bp
	CA16-LF-R	Biotin-GCACGGCTAAAGAAATTCCCAATGGCTGTC	2688–2717
	CA16-LF-P	FAM -GTGACAAGAATCTCATTGAGACKAGATG-[THF] -TGTTGAACCATCACTCCA-C3-spacer	2633–2680

^aGenome position depending on Enterovirus A71 strain HP (GenBank accession no.KY074643.1) and Coxsackievirus A16 isolate ZJ10–48 (GenBank accession no. KC755235.1)

ISSN: 1743-422X