TABLE 1.

Characteristics of SHIV-89.6P-infected Macaca nemestrina

Group	Animal no.	Vaccine group	Viral load (RNA copies/ml plasma at 32 wpi)	CD4+ T cells (cells/μl at 32 wpi)	Ratio of dN/dSa	% Divergence at wk 32b	% Diversity at wk 32	Avg no. of PNGsc
Minimally divergent	K97107	Control	2.8 × 102	1,155	0.3	0.3	0.6	22.0
	K98099	DNA-vaccinia virus	1.2 × 103	601	0.2	0.3*	0.5	21.9
	L97191	DNA-vaccinia virus	2.5 × 105	73	0.5	0.3*	0.5	21.3
	J97168	Vaccinia virus-DNA	5 × 101	1,372	0.3	0.4	0.7	21.7
Divergent	T98098	DNA-protein	1.6 × 105	40	0.8	0.9*	1.2	20.2d
	A98069	DNA-DNA	1.2 × 104	141	1.3	1.2*	1.6	22.2
	J98071	Control	1.4 × 105	29	1.8	1.4**	1.3	23.7
	J97156	DNA-protein	5.6 × 104	56	2.2	1.8**	1.6	24.9
	K97246	DNA-DNA	1.6 × 105	11	2.4	1.9	1.5	24.1
	T98108	DNA-protein	5.9 × 104	5	2.0	1.9**	1.0	24.3
	L98152	Vaccinia virus-DNA	5 × 101	1,820	2.9	1.9**	1.4	21.1

^aAverage ratio within the proviral clones of nonsynonymous change to synonymous change, calculated using PAML codeml.

^bAverage percent divergence of each animal's cloned quasispecies away from the inoculum. *, Mann-Whitney P value of <0.05; **, P value of <0.001.

^cAverage number of PNGs per env region from V1 to gp41. Note that N88 is not included in this region and therefore not represented in the average but is likely well conserved.

^dT98098 sequence reads did not cover the N130 and N136 motifs, which were well conserved in the other macaques. Therefore, the average is likely a low estimate.