Table 1

Oligonucleotides used to detect the cagA gene, the iceA variants iceA1 and iceA2, and the signal regions s1 and s2 and mid regions m1 and m2 of the vacA gene

Gene	Region	Primer	Primer sequence	Size (bp) PCR product
vacA	s1/ s2	vacA1F	5′-CTG-GT(C/T)-TAA-AGT-CGC-ACC-CTT-TGT-GC-3′	s1: 120
				s2: 150
		vacA1R	5′-CAA-TGG-CTG-GAA-TGA-TCA-CGG-TTG-T(A/G)-3′
		vacA2F	5′-CAA-ACA-CAC-CGC-AAA-ATC-AAT-CGC-CC-3′

	m1	m1F1	5′-CAA-CAA-TCA-AGG-CAC-TAT-CAA-(C/T)TA-3′	301
		m1R1	5′-CCG-CAT-GCT-TTA-ATG-TCA-TCA-G-3′
		m1F2	5′-TGG-TCC-GAG-GCG-GG(A/C)-AAG-T-3′
		m1R2	5′-TCA-TCA-GTA-TTT-CGC-ACC-ACA-C-3′

	m2	m2F1	5′-TTT-GGA-GC(C/T)-CCA-GGA-AAC-ATT-G-3′	102
		m2R1	5′-C(C/T)A-CAC-GCC-CAT-CTT-GGA-CAA-3′
		m2F2	5′-ACC-CTA-AA(C/T)-AGC-AAC-GCA-AGC-3′
		m2R2	5′-GAC-AAA-AAG-ATT-CAT-CGT-GCC-TT-3′

cagA		cagA1F	5′-CGT-TGA-TAA-GAA-(C/T)GA-TAG-GGA-TAA-C-3′	181
		cagA1R	5′-GAT-CCC-CAA-ATT-TCT-GAA-AGC-TCT-T-3′
		cagA2F	5′-(C/T)GA-TAG-GGA-TAA-CAG-GCA-AGC-TT-3′
		cagA2R	5′-CTG-AAA-GCT-CTT-TGT-GGA-AGA-TTC-3′

iceA	iceA1	ice1.1F	5′-ATC-ATA-AAG-ACG-GCC-GCA-AAG-AT-3′	218
		ice1.1R	5′-AT(A/G)-GGG-TCA-TAT-TGA-TAA-CA(A/G)-CC-3′
		ice1.2F	5′-CCG-CAA-GGA-TGA-TT(C/T)-AAG-AGT-TTC-3′
		ice1.2R	5′-GTC-ATA-TTG-ATA-ACA-(A/G)CC-CAC-ACA-3′

	iceA2	ice2.1F	5′-CGC-TGT-TTT-TCT-AGC-GGT-GTT-TTA-3′	247
		ice2.1R	5′-CAT-TGA-TCT-(A/G)TG-TTT-GTA-TGC-TTC-3′
		ice2.2F	5′-CGG-TGT-TTT-AAT-GAG-(C/T)(A/G)G-TTG-CG-3′
		ice2.2R	5′-ATG-CTT-CTT-TGA-AAA-TGG-TAT-GGC-3′