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)