Table 2

Nucleotide variations in HPV16As LCRs from HSIL and SCC samples compared with the HPV16 LCR reference sequence [GenBank:AY686584]
HPV16 LCR Number of samples (%) (n=43)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38
Binding site TEF-1 GRE-1 GRE-1 YY-1 YY-1 YY-1, SP-1, OCT-1 E2BS-3 SP-1 SP-1, E2BS-2 E2BS-1
% of samples 100 100 7 2.3 100 100 2.3 2.3 4.7 95.3 100 95.3 4.7 2.3 2.3 41.9 4.7 2.3 2.3 100 2.3 2.3 100 9.3 2.3 2.3 2.3 2.3 100 2.3 2.3 39.5 2.3 100 4.7 4.7 4.7 100
Changed position 7175 7177 7179 7186 7193 7201 7213 7217 *7218 7270 7287 7289 *7384 7405 7418 *7429 *7430 7485 7489 7521 *7617 7623 7730 7781 7791 7792 7802 7813 7842 *7844 7868 *7874 7886 24 *28 *46 *61 81
HPV16 pt. A T G T G T G G T C A A T T T G C A G G C G A T T C C T G A G C C C G T T G
HPV16 As C C - - T C - - - - C - - - - - - - - A - - C - - - - - A/T - - - - T - - - -
SCC
As C C - - T C - - - T C C - - - - - - - A - - C - - - - - A - - - - T - - - T 8 (18.6%)
As-sv1 C C - - T C - - - T C C - - - A - - - A - - C - - - - - A - - G - T - - - T 4 (9.3%)
As-sv2 C C - G T C - - - T C C - - - - - - - A - - C C - T - - T - - - - T - - - T 1 (2.3%)
As-sv3 C C - - T C - A - T C C - - - - - - - A - C^ C - - - - - A - - - - T - - - T 1 (2.3%)
As-sv4 C C - - T C - - A T C - - - - - - - - A - - C - - - - - A - - - - T - - - T 1 (2.3%)
As-sv5 C C - - T C - - - T C T G - - - T - - A - - C - - - - - A - - - - T - - - T 1 (2.3%)
As-sv6 C C - - T C - - - T C T G - - - T - - A - - C - - - A - A - - - - T - - - T 1 (2.3%)
As-sv7 C C - - T C - - - T C - - G - - - - - A - - C - - - - - A - - - - T - - - T 1 (2.3%)
As-sv8 C C - - T C - - - T C C - - A A - - - A A^ - C - - - - - A - - G - T - - - T 1 (2.3%)
As-sv9 C C - - T C - - - T C C - - - - - - - A - - C C - - - - A - - - - T - - - T 1 (2.3%)
As-sv10 C C - - T C - - - T C C - - - - - - - A - - C C - - - - T C - - - T - - - T 1 (2.3%)
As-sv11 C C - - T C - - - T C C - - - - - - - A - - C C - - - - A - - G - T - - - T 1 (2.3%)
As-sv12 C C - - T C - - - - C C - - - - - C A A - - C - - - - - A - - - - T - - - T 1 (2.3%)
As-sv13 C C - - T C - - - T C C - - - A - - - A - - C - - - - - A - - G - T - G^ - T 1 (2.3%)
As-sv14 C C - - T C - - - T C C - - - - - - - A - - C - - - - - A - - G - T A^ G^ G^ T 1 (2.3%)
As-sv15 C C - - T C - - - T C C - - - - - - - A - - C - - - - - A - - - - T A^ - G^ T 1 (2.3%)
As-sv16 C C - - T C - - - T C C - - - A - - - A - - C - del - - G^ A - - - - T - - - T 1 (2.3%)
HSIL
As-sv1 C C - - T C - - - T C C - - - A - - - A - - C - - - - - A - - G - T - - - T 8 (18.6%)
As-sv17 C C T - T C - - - T C C - - - A - - - A - - C - - - - - A - - - - T - - - T 2 (4.7%)
As-sv18 C C - - T C - - - T C C - - - A - - - A - - C - - - - - A - - - - T - - - T 2 (4.7%)
As-sv19 C C T - T C C^ - - T C C - - - - - - - A - - C - - - - - A - - G - T - - - T 1 (2.3%)
As-sv20 C C - - T C - - A - C C - - - A - - - A - - C - - - - - A - - - - T - - - T 1 (2.3%)
As-sv21 C C - - T C - - - T C C - - - A - - - A - - C - - - - - A - A G - T - - - T 1 (2.3%)
As-sv22 C C - - T C - - - T C C - - - A - - - A - - C - - - - - A - - G A T - - - T 1 (2.3%)

*Novel nucleotide sequence variation found in this study, HPV16pt. = HPV16 prototype [GenBank:AY686584], As = HPV16As, As-sv = HPV16As sub-variant, TEF-1 = transcription factor binding site, GRE-1 = glucocorticoid response element, YY-1 = yin yang factor, SP-1 = trans-acting transcription factor, Oct-1 = octamer binding transcription factor, E2BS = E2 binding site.

Pientong et al.

Pientong et al. Virology Journal 2013 10:30   doi:10.1186/1743-422X-10-30

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