TABLE 1.

Oligonucleotide primers used in this study

Primer pairSanger's strain no./ GenBank accession no.bPrimer sequence (5′→3′)Nucleotide positioncProduct size (bp)
1-fZ83335CTC TAT AGA ATG GAG TAT ATA AAC TAT GGT TA10469280
1-rCCA AAG AAA ATA CTA ACA TTA TCA CAA TAT TGG C10715
3-fZ47210ATG GTG TGA TTT CTC CTA GAT TGG AAA GTA G9179371
3-rCTT CTC CAA TTG CTT ACC AAG TGC AAT AAC G9519
4-faAF316639CTG TTA CTT GTT CTG GAC TCT CGA TAA TTG G9558430
4-rGCC CAC TCC TGT TAA AAT CCT ACC CGC ATT G9957
5-fAY336008ATA CCT ACA CAA CTT CTG ATT ATG CCT TTG TG6123362
5-rGCT CGA TAA ACA TAA TCA ATA TTT GAA AAA GTA TG6450
6A/B-f (biotin)dAF316640AAT TTG TAT TTT ATT CAT GCC TAT ATC TGG8656250
6A/B-rTTA GCG GAG ATA ATT TAA AAT GAT GAC TA8877
7F-f554/62CCT ACG GGA GGA TAT AAA ATT ATT TTT GAG13356826
7F-rCAA ATA CAC CAC TAT AGG CTG TTG AGA CTA AC14150
7C-fSutcliffCTA TCT CAG TCA TCT ATT GTT AAA GTT TAC GAC GGG A9438260
7C-rGAA CAT AGA TGT TGA GAC ATC TTT TGT AAT TTC9665
8-f573/62GAT GCC ATG AAT CAA GCA GTG GCT ATA AAT C8084294
8-rATC CTC GTG TAT AAT TTC AGG TAT GCC ACC8348
9V-f980/68CTT CGT TAG TTA AAA TTC TAA ATT TTT CTA AG12345753
9V-rGTC CCA ATA CCA GTC CTT GCA ACA CAA G13070
10A-f1006/38GGT GTA GAT TTA CCA TTA GTG TCG GCA GAC12423628
10A-rGAA TTT CTT CTT TAA GAT TCG GAT ATT TCT C13021
11A-f1813/39GGA CAT GTT CAG GTG ATT TCC CAA TAT AGT G11640463
11A-rGAT TAT GAG TGT AAT TTA TTC CAA CTT CTC CC12071
12F-f6312GCA ACA AAC GGC GTG AAA GTA GTT G14407376
12F-rCAA GAT GAA TAT CAC TAC CAA TAA CAA AAC14753
14-f34359CTT GGC GCA GGT GTC AGA ATT CCC TCT AC7968208
14-rGCC AAA ATA CTG ACA AAG CTA GAA TAT AGC C8145
15A-f389/39ATT AGT ACA GCT GCT GGA ATA TCT CTT C7114436
15A-rGAT CTA GTG AAC GTA CTA TTC CAA AC8313
15B/C-f7904/39TTG GAA TTT TTT AAT TAG TGG CTT ACC TA7314496
15B/C-rCAT CCG CTT ATT AAT TGA AGT AAT CTG AAC C7779
16F-fNr.34361CTG TTC AGA TAG GCC ATT TAC AGC TTT AAA TC11521988
16F-rCAT TCC TTT TGT ATA TAG TGC TAG TTC ATC C12478
17F-fRose (am)TTC GTG ATG ATA ATT CCA ATG ATC AAA CAA GAG10484693
17F-rvac.GAT GTA ACA AAT TTG TAG CGA CTA AGG TCT GC11145
Sg18-f4593/40CTT AAT AGC TCT CAT TAT TCT TTT TTT AAG CC12687573
Sg18-rTTA TCT GTA AAC CAT ATC AGC ATC TGA AAC13230
19A-faAF094575GTT AGT CCT GTT TTA GAT TTA TTT GGT GAT GT12118478
19A-rGAG CAG TCA ATA AGA TGA GAC GAT AGT TAG12566
19F-fU09239GTT AAG ATT GCT GAT CGA TTA ATT GAT ATC C7828304
19F-rGTA ATA TGT CTT TAG GGC GTT TAT GGC GAT AG8100
20-f34365 (am)GAG CAA GAG TTT TTC ACC TGA CAG CGA GAA G9567514
20-rCTA AAT TCC TGT AAT TTA GCT AAA ACT CTT ATC10048
22F-f1772/40 (da)GAG TAT AGC CAG ATT ATG GCA GTT TTA TTG TC11055643
22F-rCTC CAG CAC TTG CGC TGG AAA CAA CAG ACA AC11666
23F-faAF057294GTA ACA GTT GCT GTA GAG GGA ATT GGC TTT TC12118384
23F-rCAC AAC ACC TAA CAC ACG ATG GCT ATA TGA TTC12566
31-fNr.34374 (am)GGA AGT TTT CAA GGA TAT GAT AGT GGT GGT GC9144701
31-rCCG AAT AAT ATA TTC AAT ATA TTC CTA CTC9815
33F-fAY163221GAA GGC AAT CAA TGT GAT TGT GTC GCG181338
33F-rCTT CAA AAT GAA GAT TAT AGT ACC CTT CTA C488
34-f676/74GCT TTT GTA AGA GGA GAT TAT TTT CAC CCA AC7350408
34-rCAA TCC GAC TAA GTC TTC AGT AAA AAA CTT TAC7725
35B-f4356/39 (da)GAT AAG TCT GTT GTG GAG ACT TAA AAA GAA TG10556677
35B-rCTT TCC AGA TAA TTA CAG GTA TTC CTG AAG CAA G11199
35F-f361/39 (da)GAA CAT AGT CGC TAT TGT ATT TTA TTT AAA GCA A7374517
35F-rGAC TAG GAG CAT TAT TCC TAG AGC GAG TAA ACC7858
38-f9687/39CGT TCT TTT ATC TCA CTG TAT AGT ATC TTT ATG13848574
38-rATG TTT GAA TTA AAG CTA ACG TAA CAA TCC14392
cpsA-fAF057294GCA GTA CAG CAG TTT GTT GGA CTG ACC2314160
cpsA-rGAA TAT TTT CAT TAT CAG TCC CAG TC2473
  • a Primers previously published as in reference 3.

  • b Primers were designed using the sequence either from the GenBank (accession numbers provided) or from www.sangers.ac.uk (strain numbers provided).

  • c Start position of each primer.

  • d The biotinylated forward primer is required for subsequent resolution of serotypes 6A and 6B by pyrosequencing.