| S8A forward | 5'-ggagcctgcacccgcccgaGctccgaggccccagc-3' |
| S8E forward | 5'-ggagcctgcacccgcTcgaGAAccgaggccccagcag-3' |
| S8 reverse | 5'-atggcgttgtcatcgtcatccttg-3' |
| T28;S36/38/40A forward | 5'-atgcctccccccgagGcGccctctgaaggccgccagcccGCTcccG-CGccGGCccctacagagcgagc-3' |
| T28;S36/38/40E forward | 5'-atgcctccccccgagGAAccctctgaaggccgGcagcccGAAccc-GAAcccGAAcctacagagcgagcc-3' |
| T28;S36/38/40 reverse | 5'-ggtgggctcctggggccgggcggg-3' |
| S117A | 5'-agtctgcagcggcgcTtAGcggtgtaccggcaga-3' |
| S117E forward | 5'-tctgcagcggcgcctCGAggtgtaccggcagat-3' |
| S117E reverse | 5'-ctctcgaaaaagacgttatccagggcggg-3' |
| S399/403;T409A forward | 5'-aaGgaCgcGgcGgtGGCTaaAaaGgccGCcccagaggctgcca-gcGctcccagggacccta-3' |
| S399/403;T409E forward | 5'-aaGgaCgcGgcGgtGGAGaaAaaGgccGAAccTgaggctgcc-agcGAAcccagggaccctatt-3' |
| S399/403;T409 reverse | 5'-cccctgggtgatgcaagagctgag-3' |
| S480;T482;S493A forward | 5'-cagaagaggaagtgcGCGcagGcccagtgccccaggaaggtcatca-agatggagGctgaggaggggaagg-3' |
| S480;T482;S493E forward | 5'-cagaagaggaagtgcGAGcagGAAcagtgcccTaggaaggtcatc-aagatggagGAAgaggaggggaaggag-3' |
| S480;T482;S493 | 5'-ggctgtcgttgtattggagacatc-3' |
| S504/505A forward | 5'-ggcaaggttggctcgAGCcGccccggagcagccca-3' |
| S504/505A reverse | 5'-tccttcccctcctcagactccatc-3' |
| S504/505E forward | 5'-gcaaggttggctcggGAAGAGccggagcagcccagg-3' |
| S505/505E reverse | 5'-ctccttcccctcctcagactccat-3' |
| S518A forward | 5'-cagcacctccaaggcagtcGcaccTccTcacctggatggaccg-3' |
| S518E forward | 5'-cagcacctccaaggcCgtGGAaccaccccacctgga-3' |
| S518 reverse | 5'-ggcctgggctgctccgg-3' |
| S527/530A | 5'-ctggatggaccgcctGCccccaggGCccccgtcataggaag-3' |
| S527/530E forward | 5'-ctggatggaccgcctGAAccTaggGAAcccgtcataggaagt-3' |
| S527/530E reverse | 5'-gtggggtggtgagactgccttggag-3' |
| S560/561/562/565A forward | 5′-cgcgttgtggtgatcGCGGCcGcggaagacGcagatgccgaaaact-3′ |
| S560/561/562/565A reverse | 5'-ttcctctgcctccccggcgccact-3' |
| S560/561/562/565E forward | 5'-ggaggcagaggaacgTgttgtggtgatcGAAGAAGAggaagacGA-Agatgccgaaaactcg-3' |
| S560/561/562/565E reverse | 5'-ccggcgccactggccacgtggttg-3' |
| S565A forward | 5'-agcagctcggaagacGcagatgccgaaaact-3' |
| S565A reverse | 5'-gatcaccacaacgcgttcctctgc-3' |
| S565E forward | 5'-gttgtggtgatcagcTCTtcggaagacGAagatgccgaaaactc-3' |
| S565E reverse | 5'-gcgttcctctgcctccccggcgcc-3' |
| V556/557/558A;I559S forward | 5'-aggcagaggaacgcgCtgCggCTaGcagcagctcggaaga-3' |
| Δ476–490 forward | 5'-gaggcaaggttggctcgga-3' |
| Δ476–490 reverse | 5'-ctgggctgtcgttgtattggaga-3' |
| K65R | 5'-atgccaggcggaagcGCGCtgcccgaagctgctg-3' |
| K160R forward | 5'-acaccagtggttcctACGTcaTgaAgcccggcccctagca-3' |
| K160R reverse | 5'-gcctcgaagcacttggcgcag-3' |
| K490R | 5'-cccaggaaggtcatcCGgatggagtctgagga-3' |
| K616R forward | 5'-gttttctttgacctcCGgattgacaatgaaa-3' |
| K616R reverse | 5'-cagaggtctgtcttctgcttggg-3' |