Table 1.

PCR primer sequences for amplification of cag PAI and vacA genes

Gene	Primer name	Sequence	Reference
cagA*,†	CAGTF	5’ACCCTAGTCGGTAATGGG	[69]
	CAGTR	5’GCTTTAGCTTCTGAYACYGC	[69]
	A2530S	5’GTTAARAATRGTGTRAAYGG	[70]
	3000AS	5’TTTAGCTTCTGATACCGC	[70]
cagE †	cagEAF	5’TTGAAAACTTCAAGGATAGGATAGAGC	[13]
	cagEAR	5’GCCTAGCGTAATATCACCATTACCC	[13]
	cagEBF	5’AGTGATGCTTTGAGTCGCAAGTC	[71]
	cagEBR	5’TGGGGCAATAGTGTGATGACG	[71]
cagT †	cagTAF	5’CCATGTTTATACGCCTGTGT	[54]
	cagTAR	5’CATCACCACACCCTTTTGAT	[54]
	cagTBF	5’TCTAAAAAGATTACGCTCATAGGCG	[72]
	cagTBR	5’CTTTGGCTTGCATGTTCAAGTTGCC	[72]
virD4 †	virD4BF	5’TTTCATAGGTTCTATGGCAAGCGGG	[73]
	virD4BR	5’TTAGCGCCATTCCTACCATAACC	[73]
	virD4AF	5’TTTATGATGATAATCGATCGCC	[73]
	virD4AR	5’GAACGCCTGCCCTGCGTAAGCG	[73]
Right end cagPAI†	3’F	5’GGCTCAAGCTCGGAATGAT
	emptyR	5’CTCTTTTTGTGCCTTTGATTGAA
Left end cagPAI†	emptyF	5’CCAAATACATTTTGGCTAAATAAAC
	5’R	5’GCTTATCAGTCAAATTGTTTTTG
vacA s1a	SS1F	5’GTCAGCATCACACCGCAAC	[29]
	VAIR	5’CTGCTTGAATGCGCCAAAC	[29]
vacA s1b	SS3F	5’AGCGCCATACCGCAAGAG	[29]
	VAIR	5’CTGCTTGAATGCGCCAAAC	[29]
vacA s1c	S1cF	5’CTYGCTTTAGTRGGGYTA	[74]
	VAIR	5’CTGCTTGAATGCGCCAAAC	[29]
vacA s2	SS2F	5’GCTAACACGCCAAATGATCC	[29]
	VAIR	5’CTGCTTGAATGCGCCAAAC	[29]
vacA m1a	VA3F	5’GGTCAAAATGCGGTCATGG	[29]
	VA3R	5’CTAATGCCATTGGTACCTGTAGAAAC	[29]
vacA m1b	VAMF	5’CCCCAATGCAGTCATGGAT	[75]
	VAMR	5’GCTGTTAGTGCCTAAAGAAGCAT	[75]
vacA m2	VA4F	5’GGAGCCCCAGGAAACATTG	[29]
	VA4R	5’TGTCATAACTAGCGCCTTGCAC	[29]
vacA i1	F1	5’GTTGGGATTGGGGGAATGCCG	[63]
	c1R	5’TTAATTTAACGCTGTTTGAAG	[63]
vacA i2	F1	5’GTTGGGATTGGGGGAATGCCG	[63]
	c2R	5’GATCAACGCTCTGATTTGA	[63]

^*Also used to determine the EPIYA sequence for cagA-positive samples.

^†Sample is considered to have an intact cagPAI if all of these genes are present.