TABLE 2.
HRV genotype sequence groups and RT-PCR genotype-specific primer and probe sequences
| Sequence group (No. of genotypes) | HRV genotypesa | Genotype-specific sequences (forward primer/reverse primer/probe)b |
|---|---|---|
| A (27) | 3, 4, 6, 13, 14, 17–19, 27, 37, 41, 48, 49, 53, 61, 73, 79, 82–84, 90, 92, 93, 96, 97, C12, C13 | CTAGCCTGCGTGGC/GAAACACGGACACCCAAAGTA/TCCTCCGGCCCCTGAATGYGGC |
| B (41) | 2, 8–11, 15, 16, 20, 21, 23–25, 29, 30, 32, 34, 38, 40, 44, 46, 50, 54–57, 60, 62, 66–68, 74, 76, 80, 81, 85, 95, 98, 100, C3, C6, C22 | |
| C (12) | 1A, 1B, 22, 43, 51, 64, 71, 75, 86, 94, C16, C17 | CCAGCCTGCGTGGC/GAAACACGGACACCCAAAGTA/TCCTCCGGCCCCTGAATGYGGC |
| D (13) | 7, 12, 31, 36, 39, 45, 47, 58, 89, C4, C10, C39, C49 | |
| E (8) | 5, 35, 42, 52, 65, 69, 91, C43 | TCAGCCTGCGTGGC/GAAACACGGACACCCAAAGTA/TCCTCCGGCCCCTGAATGYGGC |
| F (2) | 26, 99 | TTAGCCTGCGTGGC/GAAACACGGACACCCAAAGTA/TCCTCCGGCCCCTGAATGYGGC |
| H (1) | 28 | |
| G (2) | 59, 63 | CTAGCCTGCGTGGC/GAAACACGGACATCCAAAGTA/TCCTCCGGCTCCTGAATGTGGC |
| I (1) | 33 | CTAGCCTGCGCGGC/GAAACACGGACACCCAAAGTA/TCCTCCGGCCCCTGAATGYGGC |
| J (1) | 70 | TCAGCCTGCGTGGC/GAAACACGGACACCCAAAGTA/TCCTCCGGCCCCCGAATGCGGC |
| K (1) | 72 | CCAGCCTGCGTGGC/GAAACACGGACACCCAAAGTA/TCCGCCGGCCCCTGAATGCGGC |
| L (4) | 77, C15, C23, C30 | CTTGCCTGCGTGGC/TACTTTGGGTGTCCGTGTTTC/TCCTCCGGCCCCTGAATGYGGC |
| M (5) | 78, C7, C21, C31, C42 | CTAGCCCGCGTGGC/GAAACACGGACACCCAAAGTA/TCCTCCGGCCCCTGAATGYGGC |
| N (1) | 88 | CCAGCTTGCGTGGC/GAAACACGGACACCCAAAGTA/TCCTCCGGCCCCTGAATGYGGC |
| O (6) | C2, C5, C11, C24, C25, C27 | NDc |
| P (3) | C8, C18, C28 | ND |
| Q (2) | C29, C45 | ND |
| R (3) | C19, C26, C55 | GTAGCCTGCGTGGT/GAAACACGGACACCCAAAGTA/TCCTCCGGCCCCTGAATGYGGC |
| S (1) | C20 | ND |
| T (2) | C37, C51 | ND |
| U (6) | C9, C14, C33, C36, C38, C46 | GTAGCCCGCGTGGT/GAAACACGGACACCCAAAGTA/TCCTCCGGCCCCTGAATGYGGC |
| V (1) | C35 | ND |
a
The representative HRV genotype used to generate the RNA transcript for each group is in bold.
b
Probes were 5′-labeled with 6-carboxyfluorescein (6FAM) and 3′-labeled with black hole quencher 1 (BHQ1).
c
ND, not tested.