Table 3. Early escape in the VNC child... | Rockefeller University Press

Table 3.

Early escape in the VNC child 517-C develops in non-Gag epitopes

Subject	Child's age	*C03 Gag ²⁹⁶YL9³⁰⁴**	Frequencey	*B42 Nef ⁷¹RM9⁷⁹**	Frequency	*A30 Pol ³²⁸AY9³⁶⁶**	Frequency	*A30 Env ⁷⁰⁴IY9⁷¹²**	Frequency	*A30 Env ⁷⁹⁴KY9⁸⁰²**	Frequency	*B42 Env ²⁹⁸RI10³⁰⁷**	Frequency	*B42 Env ⁸⁴³IF9⁸⁵¹**	Frequency	*B15:10 Rev ⁵²IL9⁶⁰**	Frequency	*B15:10 Vif ⁷⁸WI9⁸⁷**^{^a}	Frequency
Subject	Child's age	YVDRFFKTL	Frequencey	RPQVPLRPM	Frequency	AQNPEIVIY	Frequency	IVNRVRQGY	Frequency	KYLGSLVQY	Frequency	RPNNNTRKSI	Frequency	IPRRIRQGF	Frequency	IHSISERIL	Frequency	DWHLGHGVSI	Frequency
	yr
517-M	0.25	·········	100%	·········	100%	·········	100%	V·R······	68%	·········	100%	··········	85%	L········	86%	·········	100%	··········	100%
								V·S······	22%			·······R··	15%	L···V····	13%
								V········	4%
								I·S······	3%
	6	·········	100%	·········	100%	·········	93%	V·R······	97%	·········	100%	·········T	55%	L········	36%	·········	100%	··········	100%
						·R·······	4%	V·RK·····	2%			·········V	29%	L···L····	29%
						·K·······	2%					··S······V	13%	L···F····	29%
												··S······I	1.6%	L···V····	5%
517-C	0.2	·········	100%	·········	100%	·········	53%	··K······	100%	····N··L·	100%	·TG····R··	100%	········L	100%	·RA······	94%	··········	40%
						········C	47%									·RA·····I	6%	·······A··	36%
																		E·········	18%
																		··Q·······	2%
																		··L·······	2%
																		·······I··	1.1%
	2.5	·········	98%	·········	100%	·········	88%	V·R······	98.6%	·········	91%	··G····R··	51%	L········	100%	·N·······	76%	E·········	61%
		······R··	2%			·····L···	12%	V·RK·····	1.2%	····N····	9%	··G·······	40%			·RA······	12%	·······A··	30%
												··S·······	9%			·H·······	10%	E······A··	5%
																LN·······	1.3%	··········	4%
	5	·········	58%	·········	100%	·····L···	82%	V·R······	86%	·········	91%	··G····R··	82%	L········	96%	·N·······	59%	E·········	70%
		·······V·	39%			·········	16%	··R······	13%	····N····	9%	··G····R·M	14%	L···V····	3%	·N·L·····	17%	·······A··	25%
		·······A·	3%			T····L···	2%					··S····R··	2%			LN·······	11%	E······A··	5%
																·H·······	7%
																·RA······	4%
																VN·······	2%
	8.5	·······V·	75%	·········	100%	·····L···	55%	V·R······	97%	·········	98%	··G····R·T	69%	L········	49%	LN·······	71%	E·········	61%
		·········	22%			·········	41%	V·RK·····	1.5%	····N····	2%	··G····R··	31%	L·T······	21%	·N·L·····	21%	E······A··	22%
		······R··	1.6%			T····L···	2%	··R······	1.2%					L···L····	17%	·N·······	7%	·······A··	17%
		·······A·	1.5%											L···F····	14%
HLA association		HLA-C*03		HLA-B*42
Escape variant		Y303X		R71X
q value		4 × 10-18

Subject	Child's age	*C03 Gag ²⁹⁶YL9³⁰⁴**	Frequencey	*B42 Nef ⁷¹RM9⁷⁹**	Frequency	*A30 Pol ³²⁸AY9³⁶⁶**	Frequency	*A30 Env ⁷⁰⁴IY9⁷¹²**	Frequency	*A30 Env ⁷⁹⁴KY9⁸⁰²**	Frequency	*B42 Env ²⁹⁸RI10³⁰⁷**	Frequency	*B42 Env ⁸⁴³IF9⁸⁵¹**	Frequency	*B15:10 Rev ⁵²IL9⁶⁰**	Frequency	*B15:10 Vif ⁷⁸WI9⁸⁷**^{^a}	Frequency
Subject	Child's age	YVDRFFKTL	Frequencey	RPQVPLRPM	Frequency	AQNPEIVIY	Frequency	IVNRVRQGY	Frequency	KYLGSLVQY	Frequency	RPNNNTRKSI	Frequency	IPRRIRQGF	Frequency	IHSISERIL	Frequency	DWHLGHGVSI	Frequency
	yr
517-M	0.25	·········	100%	·········	100%	·········	100%	V·R······	68%	·········	100%	··········	85%	L········	86%	·········	100%	··········	100%
								V·S······	22%			·······R··	15%	L···V····	13%
								V········	4%
								I·S······	3%
	6	·········	100%	·········	100%	·········	93%	V·R······	97%	·········	100%	·········T	55%	L········	36%	·········	100%	··········	100%
						·R·······	4%	V·RK·····	2%			·········V	29%	L···L····	29%
						·K·······	2%					··S······V	13%	L···F····	29%
												··S······I	1.6%	L···V····	5%
517-C	0.2	·········	100%	·········	100%	·········	53%	··K······	100%	····N··L·	100%	·TG····R··	100%	········L	100%	·RA······	94%	··········	40%
						········C	47%									·RA·····I	6%	·······A··	36%
																		E·········	18%
																		··Q·······	2%
																		··L·······	2%
																		·······I··	1.1%
	2.5	·········	98%	·········	100%	·········	88%	V·R······	98.6%	·········	91%	··G····R··	51%	L········	100%	·N·······	76%	E·········	61%
		······R··	2%			·····L···	12%	V·RK·····	1.2%	····N····	9%	··G·······	40%			·RA······	12%	·······A··	30%
												··S·······	9%			·H·······	10%	E······A··	5%
																LN·······	1.3%	··········	4%
	5	·········	58%	·········	100%	·····L···	82%	V·R······	86%	·········	91%	··G····R··	82%	L········	96%	·N·······	59%	E·········	70%
		·······V·	39%			·········	16%	··R······	13%	····N····	9%	··G····R·M	14%	L···V····	3%	·N·L·····	17%	·······A··	25%
		·······A·	3%			T····L···	2%					··S····R··	2%			LN·······	11%	E······A··	5%
																·H·······	7%
																·RA······	4%
																VN·······	2%
	8.5	·······V·	75%	·········	100%	·····L···	55%	V·R······	97%	·········	98%	··G····R·T	69%	L········	49%	LN·······	71%	E·········	61%
		·········	22%			·········	41%	V·RK·····	1.5%	····N····	2%	··G····R··	31%	L·T······	21%	·N·L·····	21%	E······A··	22%
		······R··	1.6%			T····L···	2%	··R······	1.2%					L···L····	17%	·N·······	7%	·······A··	17%
		·······A·	1.5%											L···F····	14%
HLA association		HLA-C*03		HLA-B*42
Escape variant		Y303X		R71X
q value		4 × 10-18

Mother 517-M: A*30:02+ B*42+/B*15:10− C*03-ve. Child 517-C: A*30:02+ B*42+/B*15:10+ C*03+. Footprints associated with the HLA class I allele are indicated below the table; known escape variants and q values indicating significance of an HLA-polymorphism association are shown (Carlson et al., 2014). 517-M indicates mother of the child 517-C. Frequency represents percentage at which a particular haplotype is present at the indicated time point.

HLA-B*15:10–restricted Vif epitope is WI9 (WHLGHGVSI, residues 79–87; in bold), but HLA-B*15:10–associated polymorphisms are at the residue 85 (V85A) within the epitope and at the residue 78 (D78E) upstream of the epitope.

[ViewLarge]