TABLE 1.
Primers used in the first round of multiplex nested PCR
| Organism | Primer | Sequence (5′→3′)a | Primer concn (μM) | Product length (bp) | Target geneb | Source or reference |
|---|---|---|---|---|---|---|
| Group 1 | ||||||
| Influenza A virus | FluA-OF3 | TYGAGGCTCTCATGGARTGGCTAAAG | 0.052 | 412 | Matrix | This study |
| FluA-OR3 | GCTGGCCARMACCATTCTGTTYTCAT | 0.052 | ||||
| Influenza A virus H1 | H1-OF1 | CCCAGGRTATTTCKCCGAYTATGAGG | 0.104 | 760 | Hemagglutinin | This study |
| H1-OR1 | TACCATTCCAGTCCACCCCCCTTCA | 0.104 | ||||
| Influenza A virus H3 | H3-OF1 | ATGGGACCTTTTTRTYGAACGCAGCA | 0.052 | 519 | Hemagglutinin | This study |
| H3-OR1 | CCCCKAGGAGCAATTAGATTCCCTGT | 0.052 | ||||
| Influenza A virus H5 | H5N1-VIET-1B | ATCAAACAGATTAGTCCTTGCG | 0.208 | 265 | Hemagglutinin | This study |
| H5N1-VIET-2B | GGCCTCAAACTGAGTGTTCATT | 0.208 | ||||
| Influenza B virus | FluB-OF3 | AGGAAGRGCAATGGCAGAYAGAGG | 0.834 | 883 | Nucleoprotein | This study |
| FluB-OR2 | TGCTGTGTCCCTCCCAAAGAAGAAA | 0.834 | ||||
| Group 2 | ||||||
| PIV-1 | PIV-1-OF1 | TCTGGATCCACCACAATTTCAG | 0.933 | 848 | Hemagglutinin-neuraminidase | This study |
| PIV-1-OR1 | WACCAGTTGCAGTCTKGGTTTC | 0.933 | ||||
| PIV-2 | PIV2-F1 | CTTGCAGCATTTTCTGGGGAACTCC | 0.0373 | 716 | Hemagglutinin-neuraminidase | This study |
| PIV2-OR1 | GCATCATCATCCTGGGAGCCTCTGT | 0.0373 | ||||
| PIV-3 | PIV-3-OF1 | GATTTTTGGAGATGCACGTCTG | 0.187 | 1,118 | Hemagglutinin-neuraminidase | This study |
| PIV-3-OR1 | GAGAGTGTTYTGTTTCGGATGG | 0.187 | ||||
| PIV-4 | PIV-4AB-IF1 | AYGGATGCATTCGAATTCCATCATTC | 0.093 | 432 | Hemagglutinin-neuraminidase | This study |
| PIV-4AB-OR1 | TCCRTRAGRCCYCCATACAARGG | 0.093 | ||||
| Group 3 | ||||||
| hRSV A | RSV-A-OF2 | CAGCTCCGTTATCACATCTCTAGGAGCC | 0.278 | 576 | Fusion protein | This study |
| RSV-A-OR2 | TGGGTTGTCTATGAGCAGATAKKAAACCA | 0.278 | ||||
| hRSV B | RSV-B-OF2 | CGGGCCAGAAGAGAAGCACCACAGTA | 0.069 | 673 | Fusion protein | This study |
| RSV-B-OR2 | TGATCCTTCTTTGATGTTGGTGGTGC | 0.069 | ||||
| hRV | OL26-MOD-RV | CACTTCTGTTTCCCCGGAGCGAG | 0.139 | 388 | 5′ UTR | 14 |
| RV-OR2 | GAAACACGGACACCCAAAGTAGTCGGT | 0.139 | ||||
| hEV | EV-OF3 | CTGCGYTGGCGGCCYMCC | 0.139 | 481 | 5′ UTR | 14 |
| EV-OR2 | CCGGATGGCCAATCCAATAACTATATGGT | 0.139 | ||||
| Group 4 | ||||||
| HCoV-OC43 | HCoVOC43-OF3 | CGGTTACACTGTTCAGCCAATYGCA | 0.313 | 793 | Spike protein | This study |
| HCoVOC43-OR3 | CCAACCCAAAAATGCTTGTGGTYG | 0.313 | ||||
| SARS-CoV | COR1 | CACCGTTTCTACAGGTTAGCTAACGA | 0.313 | 310 | Polymerase | 32 |
| COR2 | AAATGTTTACGCAGGTAAGCGTAAAA | 0.313 | ||||
| HCoV-229E | COR229E-IF2 | TCACCCATTTGAAGAATTGGAATTTTGG | 0.313 | 566 | Matrix | This study |
| COR229E-IR2 | TCGTACGTAGAAAACCCAGCCTGTGC | 0.313 | ||||
| hMPV | Meta-M-OF2 | CAATATGGTTCCCTTTGTTTCAGGCCA | 0.313 | 462 | Matrix | This study |
| Meta-M-OR2 | TGGTCTGCTTCACTGCTTATWGCAGCTT | 0.313 | ||||
| Group5 | ||||||
| M. pneumoniae | Mpneumoniae-OF2 | GACCATTCCACCCAGCCCCAGC | 0.089 | 343 | Cytadhesin P1 gene | 17 |
| Mpneumoniae-OR2 | GTTCAGCGAGTGGGGTGCGTACAATA | 0.089 | ||||
| C. pneumoniae | Chlamy-pneum-OF4 | TGCGCTACTTGGTGCGACGCTA | 0.179 | 571 | Outer membrane protein A | 17 |
| Chlamy-penum-OR4 | CGCCTTTATAGCCCTTGGGTTTRTTT | 0.179 | ||||
| L. pneumophila | Legionella-OF1 | CGCTCAATTGGCTTTAACCGAACAG | 0.054 | 425 | Macrophage infectivity potentiator (“mip”) | This study |
| Legionella-OR1 | CGCTRCGTGGRCCATATGCARGAC | 0.054 | ||||
| ADV | ADVAtoF-OF3 | TACATGCACATCKCSGGVCAGGA | 0.179 | 983 | Hexogene | This study |
| ADVAtoF-OR3 | CCRGCCARHACHCCCATRTTDCCHGT | 0.179 |
a
Degenerate primer abbreviations are as follows: M, A/C; R, A/G; W, A/T; S, C/G; Y, C/T; K, G/T; V, A/C/G; H, A/C/T; D, A/G/T; N, A/C/G/T.
b
UTR, untranslated region.