TABLE 2.

Amino acid signature patterns of viruses of patients 1 through 3 with reference to unrelated HIV-1 subtype B local controls

Signature pattern and virus	Amino acid frequency or reference amino acida
	C2-V3														V4-C4-V5
Patient 1 signature patternb	A	V	N	V	G	P	M	A	A	S	H	I	N		Y	W	V	K
Patient 3 viruses	1.0	0.96	1.0	1.0	1.0	1.0	1.0	1.0	1.0	0.0	0.56	0.0	0.0		1.0	1.0	1.0	1.0
Patient 2 viruses	1.0	0.96	1.0	1.0	1.0	1.0	1.0	1.0	1.0	0.0	1.0	0.0	0.0		1.0	0.62	1.0	1.0
Unrelated local field isolatesc	0.13	0.02	0.04	0.22	0.04	0.07	0.07	0.44	0.05	0.05	0.00	0.08	0.0		0.00	0.13	0.00	0.07
Unrelated local field isolates	E	T	E	E	N	H	I	T	E	A	Q	K	K		—	—	—	R
Patient 1 viruses	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	1.0					0.0
Patient 3 viruses	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	1.0					0.0
Patient 2 viruses	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	1.0					0.0
Common signature patterns of patients 1–3	A	—	N	V	G	P	M	A	A	—	H	I	—		Y	W	V	K
Unrelated local field isolates	0.13		0.04	0.22	0.04	0.07	0.07	0.44	0.05		0.00	0.08			0.0	0.0	0.0	0.0
Reference 34d	A	—	A	—	—	—	—	A	—	—	—	—	—		M	W	E	R
Reference 14e	E	—	—	—	W	—	—	—	—	—	—	—	—		NA	NA	NA	NA

^aNumbers depict the frequency at which the same amino acid is found at a given position within the signature pattern. —, absence of amino acid signature at that position. NA, not available. Top panel: frequencies of the amino acids defining the signature pattern of patient 1 in viruses of patients 2 and 3, as well as in the reference set of unrelated local field isolates of HIV-1 subtype B; middle panel: frequencies of the amino acids of the reference set of unrelated local field isolates of HIV-1 subtype B at the homologous positions of the signature pattern of patient 1, in viruses of patients 2 and 3; bottom panel: frequencies of the amino acids of the reference set of unrelated local field isolates of HIV-1 subtype B at positions of the common amino acid signature pattern of viruses of patients 1 to 3, and signature patterns previously reported by Ou et al. (34) and Fitzgibbon et al. (14). 

^bThe signature pattern corresponds to amino acids which differ by more than 50% of those present in the same positions in the reference set of C2-V3 and V4-C4 sequences of local HIV-1 subtype B isolates from Europe or Paris. 

^cForty-eight distinct sequences in the C2-V3 domain and nine sequences in the V4-C4-V5 domain of field isolates from Europe and Paris. 

^dAmino acid signature pattern of the viruses of the dentist reported by Ou et al. (34). 

^eCommon amino acid signature pattern of the viruses of the children reported by Fitzgibbon et al. (14).