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. 1998 May;36(5):1271–1276. doi: 10.1128/jcm.36.5.1271-1276.1998

TABLE 2.

LiPA probes for the vacA and cagA gene

Gene and probe Sequencea Position Specificity
vacA s region
 P1S1a GGAGCRTTRGTCAGCATCAC 61–80b s1a
 P22S1a GCTTTAGTAGGAGCRTTRGTC 52–72b s1a
 P1S1b (S1b) GGAGCGTTGATTAGYKCCAT 61–80b s1b
 P2S1b GTTTTAGCAGGAGCGTTGA 52–72b s1b
 P1S2 (VAS2) GCTAAYACGCCAAAYGATCC 88–107c s2
 P2S2 GATCCCATACACAGCGAGAG 103–122c s2
vacA m region
 P1M1 TTGATACGGGTAATGGTGG 1526–1544b m1
 P2M1 GGGTAATGGTGGTTTCAACA 1533–1552b m1
 P1M2 ACGAATTTAAGAGTGAATGGC 1522–1542c m2
 P2M2 AGAGCGATAACGGGCTAAACA 1577–1597c m2
cagA
 cagApro1 GTTGATAACGCTGTCGCTTC 94–113d cagA
 cagApro2 TAATCTTCARGTRGCTTTTCTT 68–89d cagA
a

R is A or G, W is A or T, Y is C or T, and K is G or T. 

b

Nucleotide position numbers are according to the start codon of the vacA open reading frame in strain 60190 (GenBank accession no. U05676) for s1 and m1. 

c

Nucleotide position numbers are according to the start codon of the vacA open reading frame in strain Tx30a (GenBank accession no. U29401) for s2 and m2. 

d

For cagA the positions are according to the start codon of the cagA open reading frame in the sequence of the strain with GenBank accession no. L11714