Volume 17, Number 4—April 2011
Dispatch
Rapid Genotyping of Swine Influenza Viruses
Polly W.Y. Mak, Chloe K.S. Wong, Olive T.W. Li, Kwok Hung Chan, Chung Lam Cheung, Edward S. Ma, Richard J. Webby, Yi Guan, Joseph S. Malik Peiris, and Leo L.M. Poon
Table 1
Primer–probe sets selective for pandemic (H1N1) 2009 virus gene segments*
| Segment | Primer and probe† | Sequence, 5′ → 3′‡ |
|---|---|---|
| PB2 | PB2-1877F§ | AACTTCTCCCCTTTGCTGCT |
| PB2-2062R§ | GATCTTCAGTCAATGCACCTG | |
| PB2-2028RP |
Cy5-AACTGTAAGTCGTTTGGT-BHQ2 |
|
| PB1 | PB1-825F§ | ACAGTCTGGGCTCCCAGTA |
| PB1-1023R | GAACCACTCGGGTTGATTTCTG | |
| PB1-863FP |
Cy5-CCAAACTGGCAAATG-BHQ2 |
|
| PA | PA-821F§ | GCCCCCTCAGATTGCCTG |
| PA-1239R§ | GCTTGCTAGAGATCTGGGC | |
| PA-844FP |
Cy5-CCTCTTTGCCATCAGC-BHQ2 |
|
| HA | HA-398F§ | GAGCTCAGTGTCATCATTTGAA |
| HA-570R§ | TGCTGAGCTTTGGGTATGAA | |
| HA-470FP |
Cy5-CAAAGGTGTAACGGCA-BHQ2 |
|
| NP | NP-593F§ | TGAAAGGAGTTGGAACAATAGCAA |
| NP-942R§ | GACCAGTGAGTACCCTTCCC | |
| NP-872RP |
Cy5-AGGCAGGATTTATGTG-BHQ2 |
|
| NA | NA-163F§ | CATGCAATCAAAGCGTCATT |
| NA-268R§ | ACGGAAACCACTGACTGTCC | |
| NA-248RP |
Cy5-AGCAGCAAAGTTGGTG-BHQ2 |
|
| M | M-504F§ | GGTCTCACAGACAGATGGCT |
| M-818R§ | GATCCCAATGATATTTGCTGCAATG | |
| M-530FP |
Cy5-ACCAATCCACTAATCAGG-BHQ2 |
|
| NS | NS-252F§ | ACACTTAGAATGACAATTGCATCTGT |
| NS-345R | GCATGAGCATGAACCAGTCTCG | |
| NS-288FP | Cy5-CGCTACCTTTCTGACAT/BHQ2/ |
*PB, polymerase basic protein; PA, polymerase acidic protein; HA, hemagglutinin; NP, nucleocapsid protein; NA, neuraminidase; M, matrix protein; NS, nonstructural protein; Cy5, cyanine 5; BHQ2, Black Hole Quencher 2.
†Number represents nucleotide position of the first base in the target sequence (cRNA sense).
‡Locked nucleic acid–modified bases are underlined.
§Primers adapted from the assays as previously described (5,6).
