Population-associated differences between the phase variable LPS biosynthetic genes of Helicobacter pylori

Table 1 Presence and absence of the 8 LPS genes studied among 23 H. pylori strains

Strain name	Population	HP0651	HP0379	HP0093	HP0619	jhp0562*	HP0208	jhp0820	HP0217
JP9	hpEastAsia	○	●	●	●	+	●	absent	●
GU17	hpEastAsia	●	○	●	missing	missing	●	EMPTY	●
GU5	hpEastAsia	●	○	●	absent	+	●	EMPTY	●
RE12001	hpEastAsia	●	○	●	●	+	●	EMPTY	●
L133	hpEastAsia	●	○	●	●	+	●	⊙	●
L7	hpLadakh	○	○	●	missing	missing	absent	EMPTY	●
L72	hpLadakh	●	○	●	●	+	absent	EMPTY	●
L67	hpLadakh	○	○	●	absent	+	absent	EMPTY	●
B225	hpEurope	●	●	●	●	+	●	absent	●
26695	hpEurope	●	●	●	●	absent	●	absent	●
SS1	hpEurope	○	●	●	●	+	●	●	●
H1413	hpEurope	●	●	●	●	+	●	EMPTY	○
NQ367	hpEurope	○	●	●	●	+	●	●	EMPTY
111UK	hpEurope	●	●	●	●	+	●	EMPTY	●
VZ21	hpEurope	●	○	●	absent	+	●	●	●
105UK	hpEurope	○	●	●	●	+	●	●	●
LSU2003-1	hpAfrica1	○	●	●	●	+	●	●	●
J99	hpAfrica1	○	●	●	●	+	●	●	●
C164	hpAfrica1	○	●	●	●	+	●	⊙	●
CC31C	hpAfrica1	○	missing	●	●	+	●	●	●
CC42C	hpAfrica1	○	●	●	missing	missing	●	○	EMPTY
129	hpAfrica2	○	●	●	●	+	●	●	●
162	hpAfrica2	○	●	●	●	+	●	absent	●

Status of the genes is coded as followed:
●, gene present and harbouring the repeat
○, phase variable gene present but repeat absent or stabilized (i.e. repeat interrupted by one or more bases or a homopolymeric tract < 7 bp or dinucleotide tracts with < 5 repeats)
⊙, phase variable gene harbouring a repeat, whereas a stabilized repeat was found previously [12]
EMPTY, empty site, i.e. the phase variable gene was found using primers designed within the coding sequence in regions immediately adjacent to the phase variable tract [12], but the site is found to be empty in this study
missing, missing data, i.e. the PCR product was obtained but could not be sequenced absent, gene absent
* jhp0562 is a non phase variable homologue of HP0619 (+: jhp0562 present)