Table 1 Primers and probes
From: Molecular subtyping of European swine influenza viruses and scaling to high-throughput analysis
Target Gene | Primer/Probe | Sequence, labeling | Locationa | Reference Sequence (accession number) |
|---|---|---|---|---|
H1av | H1av_Fo | gaaggrggatggacaggaatga | 1063–1084 | A/Sw/Cotes d’Armor/0388/2009 (KC881265) |
H1av_Re | caattahtgarttcactttgttgc | 1178–1201 | ||
H1av_Pr | (HEX)-tctggttacgcagcwgatcagaaaa-(BHQ1) | 1126–1150 | ||
H1hu | H1hu_Fo_1 | gagggggrtggaccggaatgatagatgga[i]5tggttatcatca | 1090–1109 | A/Sw/Cotes d’Armor/0113/2006 (AM503902) |
H1hu_Fo_2 | ggatggtacggttatcatca | 1064–1109 | ||
H1hu_Re_1 | acctacagctgtgaattgagtgttcatyttntcg[i]5agagttcacct | 1184–1204 | ||
H1hu_Re_2 | tttcgatcacagaattcacct | 1184–1233 | ||
H1hu_Pr | (FAM)-cagggatctggctatgctgcagayc-(BHQ1) | 1120–1144 | ||
H1huΔ146–147 | H1hu_dif_Fw | agttcagtatcatcattcgagagattcgaaat | 367–398 | A/Sw/France/22-130212/2013 (KJ128323) |
H1hu_dif_Rv | actgcatcatgctcccataagggga | 468–492 | ||
H1hu_var_FAM | (FAM)-cagcataggagca-(MGB) | 454–466 | ||
H1pdm | H1pdm_Fo | gggcattcaccatccatctact | 582–603 | A/California/04/2009 (FJ966082) |
H1pdm_Re | cctcactttgggtcttattgctattt | 689–714 | ||
H1pdm_Pr | (FAM)-atacagcaagaagttcaagc-(MGB) | 666–685 | ||
H3 | H3_Swine_Fw | cttgatggrgmaaaytgcaca | 223–243 | A/Sw//France/59–120031/2012 (KC345622) |
H3_Swine_Rv | ggcacatcatawgggtaaca | 337–356 | ||
H3_Swine_CY5 (or HEX) | (CY5 or HEX)-ctctattgggrgaccctcaytgtga-(BHQ1) | 254–278 | ||
N1 | N1.3_F | agrccttgyttctgggttga | 1255–1274 | A/Sw/Germany/SIV04/2008 (FN429079) [20] |
N1.3_R | accgtctggccaagacca | 1363–1380 | ||
AIV N1.3 FAM | (FAM)-atytggacyagtgggagcagcat-(BHQ1) | 1306–13,028 | ||
N1pdm | N1pdm_Fo | gggacagacaataacttctcaataaagc | 1144–1171 | A/California/04/2009 (FJ966082) |
N1pdm_Re | ttcagcatccagaactaacagggt | 1220–1243 | ||
N1pdm_Pr | (FAM)-aaatgagtggtcaggatat-(MGB) | 1188–1206 | ||
N2 | N2_1367F | agtctggtggacytcaaayag | 1305–1325 | A/Sw/Bakum/8602/1999 (EF409258) [20] |
N2_1468R | ttgcgaaagcttatatagvcatga | 1397–1420 | ||
AIV N2 1444 HEX | (HEX)-ccatcaggccatgagcctgwwccata-(BHQ1) | 1357–1382 | ||
M | SIV-Forw | agatgagtcytctaaccgaggtcg | 24–47 | A/Sw/France/22–130212/2013 (KM267912) [30] |
SIV-Rev | tgcaaaracayyttcmagtctctg | 101–124 | ||
M64_FAM | (FAM)-tcaggccccctcaaagccga-(BHQ1) | 74–93 | ||
β-actin | Sw_actine_Forw | ctcgatcatgaagtgcgacgt | [31] | |
Sw_actine_Rev | gtgatctccttctgcatcctgtc | |||
β-actine_sus_scrofa_HEX | (HEX)-atcaggaaggacctctacgccaacacgg-(BHQ1) |