Table 1.

Potential sites of HLA-mediated selection pressure and codon evolution in HIV-2 p26 as predicted by a phylogenetic dependency network analysis.

HIV-2 Gag codon	Amino acid	HLA association	Directionb	P value	q valuec	Predicted epitope around codon associated with relevant HLA typed	Prediction probability (%)
245	D	B58_STa	Adapted	0.0002	0.0684	STVDEQIQWe	94
245	E	B58_ST	Nonadapted	6.73E-05	0.0309	STVEEQIQWe	92
254	A	B35	Nonadapted	0.0002	0.1030	FRAQNPVPVGNIYRRWf	71
254	P	B35	Adapted	0.0001	0.0336	FRPQNPVPVGNIYRRWf	71
254	P	C08	Adapted	8.89E-05	0.0336	WMFRPQNPVPV	53
256	V	A03_STa	Adapted	0.000749	0.1721	NPVPVGNIYRR	51
256	I	A03_ST	Nonadapted	0.000749	0.1721	NPIPVGNIYRR	57
294	S	C0401	Nonadapted	2.79E-07	0.0002	ESFQSYVDRFYKSLRA	60
294	P	C0401	Adapted	1.10E-07	8.32E-05	EPFQSYVDRFYKSLRA	60
313	A	B5801	Adapted	4.93E-08	5.66E-05	QTDAAVKNW	66
313	P	B5801	Nonadapted	1.79E-10	4.11E-07	QTDPAVKNW	65

^aST, SuperType (15).

^bAdapted indicates that reported amino acid is the putative adaption at that site (i.e. ‘escaped’ variant). Nonadapted indicates that reported amino acid is putatively susceptible to escape (i.e. ‘reversion’).

^cEstimation of false-discovery rate for each association, that is, q value of 0.05 = 5% false discovery rate.

^dWherever codon is in flanking region, epitope is underlined. Codon is shown in bold. Epitope predictions are made by scanning the candidate sequence for peptide lengths of 8–11 amino acids. Only peptides within three amino acids of the associated codon are considered.

^eThe 10-mer TSTVEEQIQW has been previously identified as a B58_ST-restricted epitope via functional assays. The prediction algorithm used identifies the 9-mer STVDEQIQW as an optimal B58_ST-restricted epitope.

^fNPVPVGNIY is a known B^*35-restricted epitope.