TABLE 2.

Comparison of 97cn54-derived coding sequences with the corresponding genes of reference strains and clade-specific consensus sequences^a

Coding sequence	% Identity to 97cn54b in:
	gag	pol	vif	vpr	tat	rev	vpu	env	nef
A	87.68	91.80	86.81	83.66	84.90	83.97	79.82	85.75	84.19
B	90.43	91.93	88.04	90.31	86.56	82.08	94.24	84.52	88.13
B-mn	89.38	90.82	86.01	89.31	87.44	79.48	88.21	82.33	85.41
B′-rl42	91.53	90.76	86.01	88.97	91.163	80.23	96.74	82.70	85.99
C	94.65	94.29	95.06	91.39	89.01	91.99	78.23	93.93	88.82
C-92br025	92.19	92.91	88.51	90.03	87.91	89.70	76.13	88.51	86.20
C-eth2220	91.4	92.06	87.15	90.77	85.57	88.08	80.09	87.15	87.08
D	89.80	91.08	87.74	87.94	83.93	84.39	87.30	85.26	86.88
E/A	86.324	89.07	86.59	83.39	81.44	81.74	77.31	82.09	84.18
F	88.02	88.99	86.36	86.25	80.65	86.25	82.33	84.02	—
G	88.08	—c	—	—	—	—	—	84.55	—
H	87.69	89.45	86.01	85.22	—	—	—	83.74	—
O	73.42	78.02	72.12	76.604	72.31	76.60	59.54	67.01	80.35
CPZ	74.14	78.80	93.75	75.44	76.00	75.44	64.41	72.42	—

^aNucleotide sequence comparison of all coding sequences between 97cn54 and DNA sequences, representing either consensus sequences of distinct HIV-1 clades (obtained from the Las Alamos HIV database) or standard subtype C (92br025 and eth2220) and B (mn and rl42) isolates. 

^bThe data show the percent identity of a given sequence to 97cn54. Ambiguous nucleotide positions within consensus sequences were scored as a match. The highest degrees of homology are highlighted in boldface. 

^c—, no consensus sequence was available from the Los Alamos database.