Table 2.

Amino acid substitutions accumulated during three passages of SIV_B670 in hu-mice.

Protein	Position	Stock Residuea	Variant Residueb	Stock Frequencyc	P3 Endpoint Frequencyd	P3 Endpoint Frequencye
Gag	150	S	T	0.00f	1.00	1.00
Gag	216	L	V	0.00f	0.70	0.96
Gag	224	I	M	0.00f	0..88	0.91
Gag	465	D	E	0.11	0.99	0.99
Gag	469	N	D	0.34	1.00	1.00
Gag	472	E	K	0.30	0.95	0.91
Pol	382	M	I	0.43	0.80	0.54
Pol	477	K	R	0.48	1.00	1.00
Pol	655	L	V	0.00f	0.55	0.59
Env	128	P	T	0.37	0.74	0.64
Env	135	S	A	0.09	0.72	0.65
Env	162	P	Q	0.44	1.00	1.00
Env	166	V	I	0.00f	0.71	0.82
Env	200	G	E	0.49	0.69	0.91
Env	201	N	S	0.49	0.78	0.94
Env	202	E	D	0.00f	0.66	0.91
Env	473	N	D	0.29	0.50	1.00
Env	479	G	S	0.37	0.50	1.00
Env	479	G	D	0.37	0.50	1.00
Env	481	R	Q	0.30	1.00	1.00
Env	575	V	L	0.00f	0.89	0.95
Env	714	V	I	0.34	1.00	1.00
Rev	105	C	R	0.50	1.00	0.99
Rev	105	C	Y	0.49	1.00	1.00
Nef	13	H	R	0.42	1.00	1.00
Nef	22	R	Q	0.46	1.00	1.00
Nef	28	Y	H	0.39	1.00	1.00
Nef	33	G	E	0.43	1.00	1.00
Nef	93	E	K	0.24	0.93	0.15
Nef	93	E	D	0.20	0.91	0.14
Nef	140	R	K	0.00	0.93	0.09
Nef	144	I	M	0.00f	0.87	0.43

^aConsensus amino acid residue from sequenced stock virus.

^bVariant amino acid residue from passaged virus.

^cFrequency of variant residue in the stock virus population.

^dReplicate 1 frequency of variant residue at the end of the third passage.

^eReplicate 2 frequency of variant residue at the end of the third passage.

^fThe 0.00 indicates that the variant frequency was below the limit of detection of the variant identification pipeline.