TABLE 2.
Primers used in the second 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 | FluARe-F1 | AAGACCAATCCTGTCACCTCTGA | 0.103 | 104 | Matrix | 30 |
| FluARe-R1 | CAAAGCGTCTACGCTGCAGTCC | 0.103 | ||||
| Influenza A virus H1 | H1-IF2 | TCGCCGACTATGAGGAACTGAGGGA | 0.021 | 431 | Hemagglutinin | This study |
| H1-IR2 | TTGTATCCCCGGGTTCCAGCAGAGT | 0.021 | ||||
| Influenza A virus H3 | H3-IF2 | CCCTTATGATGTGCCGGATTATGCC | 0.205 | 259 | Hemagglutinin | This study |
| H3-IR2 | GGTGGTGAACCCCCCAAATGTACAA | 0.205 | ||||
| Influenza A virus H5 | H5N1-VIET-1A | TGCGACTGGRCTCAGAAATA | 0.512 | 172 | Hemagglutinin | This study |
| H5N1-VIET-4B | GGATTCTTTGTCTGCAGCGT | 0.512 | ||||
| Influenza B virus | FLUB-IF3 | AAAACAARTGCTCTGCRCCYCAAC | 0.41 | 516 | Nucleoprotein | This study |
| FLUB-IR3 | CRTCTCCACCTACTTCRTTYCCCCC | 0.41 | ||||
| Group 2 | ||||||
| PIV-1 | PIV-1-IF1 | AATTGGTGATGCAATATATGCKTATTC | 0.61 | 600 | Hemagglutinin-neuraminidase | This study |
| PIV-1-IR1 | TCGACAACAATYTTTGGCCTATC | 0.61 | ||||
| PIV-2 | PIV2-F2 | AGGACAGCAGAGGACCTCGGCATG | 0.0305 | 343 | Hemagglutinin-neuraminidase | This study |
| PIV2-R2 | ACCTGATGTTCTTTGCGGTATGGGG | 0.0305 | ||||
| PIV-3 | PIV-3-IF1 | CAACTGTGTTCRACTCCCAAAG | 0.457 | 717 | Hemagglutinin-neuraminidase | This study |
| PIV-3-IR1 | TGGGTTYACTCTCGATTTTTGY | 0.457 | ||||
| PIV-4 | PIV-4AB-IF2 | GACGGATGYYTRCKGWATTGTGT | 0.153 | 231 | Hemagglutinin-neuraminidase | This study |
| PIV-4AB-IR2 | CCRTRAGRCCYCCATACAARGGAA | 0.153 | ||||
| Group 3 | ||||||
| hRSV A | RSVA-IF2 | TGACCCATTAGTGTTCCCCTCTGATGAAT | 0.278 | 228 | Fusion protein | This study |
| RSVA-IR2 | CTTCTGGCCTTRCAGTATARGAGCAGT | 0.278 | ||||
| hRSV B | RSV-B-IF1 | GTCGCATCTCCAACATTGRAAC | 0.069 | 336 | Fusion protein | This study |
| RSV-B-IR1 | TGGTGCATAGAGGTGATGTGTG | 0.069 | ||||
| hRV | RV-OF2 | CACTTCTGTTTCCCCGGAGCGAGG | 0.139 | 283 | 5′ UTR | 14 |
| JWA-1B-MOD-RV | CCGCATTCAGGGGCCGGAG | 0.139 | ||||
| hEV | EV-IF3 | CCTCCGGCCCCTGAATGCG | 0.139 | 106 | 5′ UTR | 3, 14 |
| EV-IR3 | CCAAAGTAGTCGGTTCCGCYRCRGA | 0.139 | ||||
| Group 4 | ||||||
| HCoV-OC43 | HCoVOC43-IF2 | CKGTGCCCTCTCCATTAAATTGGG | 0.25 | 635 | Spike protein | This study |
| HCoVOC43-IR2 | GACCCGAACAGTGCTCACCTATGCC | 0.25 | ||||
| SARS-CoV | COR3 | AGTGAGATGGTCATGTGTGG | 0.5 | 210 | Polymerase | 32 |
| COR4 | CACTCATAGAGCCTGTGTTG | 0.5 | ||||
| HCoV-229E | COR229E-IF3 | TTGGGATTCTAATTGGGCCTTTGTTGC | 0.25 | 361 | Matrix | This study |
| COR229E-IR3 | GCTCGGCACGGCAACTGTCATGTAT | 0.25 | ||||
| hMPV | Meta-M-IF2 | CCCTTTGTTTCAGGCCAAYACACCACC | 0.25 | 431 | Matrix protein | 2 |
| Meta-M-IR2 | GCAGCTTCAACAGTRGCTGATTCACTCTC | 0.25 | ||||
| Group 5 | ||||||
| M. pneumoniae | Mpneumoniae-OF1 | AGGGGGTTCTTCAGGCTCAGGTCAA | 0.094 | 160 | Cytadhesin P1 gene | 17 |
| Mpnuemoniae-OR1 | CCCCACCACATCATTCCCCGTATTA | 0.094 | ||||
| C. pneumoniae | Chlamy-pneum-IF6 | RCCTACWGGATCCGCTRCTGCRAA | 0.313 | 317 | Outer membrane protein A | 17 |
| Chlamy-pneum-IR6 | GCRCCTACGCTCCAAGMRAAAGWRG | 0.313 | ||||
| L. pneumophila | Legionella-IF1 | TGAAAACAAAAACAAGCCAGGCGTTG | 0.063 | 232 | Macrophage infectivity potentiator (“mip”) | This study |
| Legionella-IR1 | TGGCATCAATTGYAAAGCYTCTGTCC | 0.063 | ||||
| ADV | ADVAtoF-IF3 | TGGCYWSCACNTWCTTTGACATYMG | 0.782 | 463 | Hexogene | This study |
| ADVAtoF-IR3 | GCRWAWGAHCCRTARCAKGGYTDCAT | 0.782 |
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.