Unique features of HLA-mediated HIV evolution in a Mexican cohort: a comparative study

Avila-Rios, Santiago; Ormsby, Christopher E; Carlson, Jonathan M; Valenzuela-Ponce, Humberto; Blanco-Heredia, Juan; Garrido-Rodriguez, Daniela; Garcia-Morales, Claudia; Heckerman, David; Brumme, Zabrina L; Mallal, Simon; John, Mina; Espinosa, Enrique; Reyes-Teran, Gustavo

doi:10.1186/1742-4690-6-72

Retrovirology

Table 4 Protease and Reverse Transcriptase HLA-HIV codon associations in free plasma virus RNA and PBMC proviral DNA for the Mexican cohort.

From: Unique features of HLA-mediated HIV evolution in a Mexican cohort: a comparative study

Free plasma virus pol sequences†						PBMC proviral pol sequences†
HLA	Associated HIV Codon		Conditioning variables	p-value	q-value	HLA	Associated HIV codon		Conditioning variables	p-value	q-value
						A*02^c	PR	15I	PR 77V^c, PR 36M^d, PR 13I^a	0,0010442	0,1522376
A*03^b	RT	277R		1,14E-08	1,10E-05	A*03^b	RT	277R		1,74E-09	1,48E-05
A*03^a	RT	277K		1,14E-08	1,10E-05	A*03^a	RT	277K		1,74E-09	1,48E-05
A*11^b	RT	333E	PR 35E^c, RT 293I^a, RT 207Q^d, PR 62I^d	0,00113806	0,1336789
A*30^c	RT	281K	RT 278Q^d	0,00109204	0,1336789
A*68^a	RT	326V		0,00035689	0,1048983
B*07^b	RT	165I		0,00067347	0,1191747
B*07^a	RT	165T		0,00067347	0,1191747
B*18^b	RT	138A		0,00012948	0,0494756
B*18^a	RT	138E		0,00012948	0,0494756
B*18^b	RT	245E	PR 45K^c	0,00068267	0,1191747
B*18^b	RT	177D		0,00094587	0,1312293	B*18^b	RT	177D	RT 123D^d, RT 121D ^d	0,0017257	0,19555
B*18^a	RT	177E		0,00094513	0,1312293	B*18^a	RT	177E		0,0006388	0,1183628
B*18^a	RT	245V		0,00115452	0,1336789
B*27^a	RT	135I	B*51^a, PR 12T^d, RT 202I^d	0,00096164	0,1312293
B*39^a	RT	102R	B*48^b, RT 64K^a	0,00016533	0,0539628
B*39^c	PR	71V	PR 93L^d, PR 39P^a, PR 57K^d, Cw*15^b	0,00193116	0,1994313	B*39^c	PR	71V	PR 57R^a, PR 93I^c, Cw*15^d, RT 178M^b, PR 39P^a	0,0003592	0,0888581
						B*39^a	PR	60E	PR 39Q^b, PR 37D^b, PR 37E^b	0,0019258	0,199068
B*44^b	PR	35D		1,16E-08	1,10E-05	B*44^b	PR	35D		5,77E-08	0,0002091
B*44^a	PR	35E		1,16E-08	1,10E-05	B*44^a	PR	35E		5,77E-08	0,0002091
B*44^a	RT	211R		0,00112279	0,1336789
B*44^a	RT	329I	RT 334L^b	0,00120957	0,1359348
B*48^b	RT	102R		2,47E-08	1,89E-05	B*48^b	RT	102R		1,53E-11	3,88E-07
B*48^a	RT	102K		0,00016947	0,0539628	B*48^a	RT	102K		1,90E-05	0,0120849
						B*48^a	RT	276V	RT 272P^c, Cw*07^c	0,0005419	0,1049938
						B*49^a	RT	48S		0,0004979	0,1035941
						B*49^b	RT	48T		0,0004979	0,1035941
B*51 ^a	RT	135I		4,03E-07	0,0002198
B*51^b	PR	12S		0,00038855	0,1060476
B*51^b	PR	14R	RT 135I^a, RT 200A ^a	0,00144043	0,1528856	B*51^b	PR	14R		7,41E-06	0,005226
B*51 ^a	PR	14K	RT 135I^b, RT 200A^b	0,00138006	0,1506635	B*51^a	PR	14K		7,41E-06	0,005226
B*52^b	PR	12A		5,59E-07	0,0002671	B*52^b	PR	12A	RT 135T^d	0,0005416	0,1049938
B*52 ^a	PR	12T		3,73E-08	2,38E-05	B*52^a	PR	12T		1,60E-06	0,0016939
B*57^b	RT	297A		0,00060553	0,1191747	B*57^b	RT	297A		0,0004121	0,0941468
						Cw*03^b	RT	283I		0,0017747	0,1964929
						Cw*03^a	RT	283L		0,0017747	0,1964929
Cw*03^b	PR	12P	PR 14R^d, PR 67C^c	0,00070538	0,1191747
Cw*05^b	RT	214L	RT 118I^b	0,00065426	0,1191747	Cw*05^b	RT	214L	RT 118V^c	0,0002149	0,0665192
Cw*05 ^a	RT	214F	RT 118I^a	0,00065426	0,1191747	Cw*05^a	RT	214F	RT 118V^d	0,0002149	0,0665192
Cw*07^c	RT	276V	RT 272P^c	0,00054742	0,1191747	Cw*07^c	RT	276V	RT 272P^c	0,0004154	0,0941468
Cw*07 ^a	RT	179D		0,00072749	0,1191747
Cw*12^b	RT	162S	PR 64L^b, RT 165T^c, PR 91T^c, RT 135V^a	0,00106536	0,1336789
Cw*15^a	PR	18Q		0,00074855	0,1191747
Cw*15^b	PR	71V	PR 93L^d, PR 39P^a, PR 57K^d	0,0009574	0,1312293

†Associations for 250 plasma virus sequences and the corresponding PBMC proviral sequences with q < 0.2 are shown. ^a escape (having the predictor makes it less likely to have the target), ^b attraction (having the predictor makes it more likely to have the target), ^c reversion (not having the predictor makes it more likely to have the target), ^d repulsion (not having the predictor makes it less likely to have the target.

Back to article page

ISSN: 1742-4690

Contact us

Submission enquiries: journalsubmissions@springernature.com