Prevalence of Helicobacter pylori vacA, cagA, and iceA Genotypes in Cuban Patients with Upper Gastrointestinal Diseases

Table 1

Primers used in PCR for amplification of cagA, vacA, and iceA sequences and s1 region sequencing.

DNA amplified region	Primer	Primer sequence	PCR product	PCR program	Reference
		(5′-3′)	(bp)
cagA	CAG-L	TGCTAAATTAGACAACTTGAGCGA	289	30 cycles (1 min at 95°C, 1 min at 50°C, and 1 min at 72°C)	[13]
	CAG-R	AATAATCAACAAACATCACGCCAT
vacAs1a	SS1-F	GTCAGCATCACACCGCAAC	190	35 cycles (1 min at 95°C, 1 min at 56°C, and 1 min at 72°C)	[5]
vacAs1b	SS3-F	AGCGCCATACCGCAAGAG	187
vacAs1c	SS1C-F	CTAGCTTTAGTGGGGATA	213		[14]
vacAs2	SS2-F	GCTAACACGCCAAATGATCC	199		[5]
	VA1-R^*	CTGCTTGAATGCGCCAAAC
vacA m1/m2	VAG-F	CAATCTGTCCAATCAAGCGAG	567/645^±		[5]
	VAG-R	GCGTCAAAATAATTCCAAGG
VacAs1	SIG-F	ATGGAAATACAACAAACACACCG	338		[8]
	SIG-R	CAACCTCCATCAATCTTACTGGA
	VA1-F	ATGGAAATACAACAAACACAC	259		[5]
iceA1	iceA1-F	GTGTTTTTAACCAAAGTATC	246	30 cycles (1 min at 95°C, 1 min at 50°C, and 1 min at 72°C)	[8]
	iceA1-R	CTATAGCCATTATCTTTGCA
iceA2	iceA2-F	GTTGGGTATATCACAATTTAT	229/334^¥
	iceA2-R	TTTCCCTATTTTCTAGTAGGT

Used as reverse primer with SS1-F, SS3-F, SS1C-F, SS2-F, and VA1-F. ^±The size of the product is variable depending on the present subtype 567 bp for m1 and 645 pb for m2. ^¥The primers yield a fragment of 229 or 334 bp depending on the presence of a repetitive sequence of 105 nucleotides codifying for 35 amino acids in some iceA2 alleles.