Table 1 Primer and PCRs used in this study
Method | Target region | Primer ID | Sequence (5′–3′) | Product length (bp) | Primer position (5′–3′)* |
|---|---|---|---|---|---|
Method A | ORF1 | 1679 | CCAYCAGTTYATHAAGGCTCC | 348 | 36-56 |
1680 | TACCAVCGCTGRACRTC | 383-367 | |||
1681 | CTCCTGGCRTYACWACTGC | 172 | 53-71 | ||
1682 | GGRTGRTTCCAIARVACYTC | 224-205 | |||
Method B | ORF1 | 1829 | ACATTTGAATTATCTGACATTGTGCA | 1076 | 3880-3905 |
1828 | ACACACATCTGAGCTACATTCGTGAG | 4955-4930 | |||
1830 | GACGTGTCCAGGATCACCTTCTTC | 559 | 4147-4170 | ||
1831 | ACTCACTGCAAAGCACTATCGAAT | 4705-4682 | |||
Method C | ORF2 | 1722 | CAAGGHTGGCGYTCKGTTGAGAC | 506 | 5912-5934 |
1723 | CCCTTRTCCTGCTGAGCRTTCTC | 6417-6395 | |||
1724 | GYTCKGTTGAGACCWCBGGBGT | 457 | 5922-5943 | ||
1725 | TTMACWGTCRGCTCGCCATTGGC | 6378-6356 | |||
Method D | ORF2 | 1837 | AATTATGCYCAGTAYCGRGTTG | 731 | 5687-5708 |
1838 | CCCTTRTCYTGCTGMGCATTCTC | 6417-6395 | |||
1839 | GTWATGCTYTGCATWCATGGCT | 348 | 5972-5993 | ||
1840 | AGCCGACGAAATCAATTCTGTC | 6319-6298 | |||
Method E | ORF2/ORF3 | 1847 | GCRGTGGTTTCTGGGGTGAC | 164 | 5259-5278 |
1848 | CTGGGMYTGGTCDCGCCAAG | 5422-5403 | |||
1849 | GYTGATTCTCAGCCCTTCGC | 137 | 5282-5301 | ||
1850 | GMYTGGTCDCGCCAAGHGGA | 5418-5399 | |||