Appendix 3—table 2. Which HLA subtype alleles are responsible for the allele group associations in HIV-1 infection?

Predictors of Log₁₀(early viral load set point) were determined by linear regression. Other significant covariates (gender) were included in the model. A negative coefficient (Coeff) indicates a protective effect (decrease in log viral load associated with possession of the allele); a positive coefficient indicates a detrimental effect. Predictors of the rate of progression to CD4 cell count <350 cells/mm³ was determined by Cox regression; hazard ratio = exp(Coeff). Other significant covariates (age at infection, and HIV-1 clinic site which is essentially collinear with viral subtype but available for more subjects) were included in the model. A hazard ratio (HR) less than 1 indicates a protective effect (reduced risk of progression to low CD4 count associated with possession of the allele); a HR greater than 1 indicates a detrimental effect. N is the number of individuals with early viral load information (numbers with time to low CD4 cell count are slightly higher, total cohort size=568). Significance codes: p<0.001 ***; p<0.01 **; p<0.05 *; p<0.1. ; P values are two tailed.

	Early viral load set point			Time to low CD4 cell count			N
	Coeff	P val		HR		P val	HLA+	HLA-
B*57	−0.51	0.00005 ***		0.48		0.01 *	50	474
B*57:01	Insufficient numbers for analysis						1	523
B*57:02	−0.63	0.005 **		0.40		0.07	15	509
B*57:03	−0.46	0.002 **		0.50		0.04 *	36	488
B*35Px	+0.23	0.02 *		1.0		1.0	98	426
B*35:02	Insufficient numbers for analysis						3	521
B*53:01	+0.23	0.02 *		+0.93		0.7	95	429