TABLE 2.

Features of viral clones from ES

Genetic feature and gene	ES with feature	Residue(s)a (nucleotide or amino acid)	Position(s)b (nucleotide or amino acid)	Frequency of feature among ES clones	Frequency of feature in clade Bc	Comment(s)
Deletion
LTR	ES8	C	368	0.33	0.00	Novel single nucleotide deletion in NF-κB site I
	ES10	T	541	0.17	0.00	Novel single nucleotide deletion in R region
Gag	ES10	T	371	0.17	0.05	Single-codon deletion in region of length polymorphism in p2
Nef	ES10	RS	8, 9	0.17	0.03, 0.12	Two-codon deletion in region of length polymorphism
		D	28	0.17	0.01	Single-codon deletion at position of rare length polymorphism
Insertion
LTR	ES8, ES10	G	374	0.50	0.33	Common insertion between NF-κB and Sp1 sites
	ES8	T	541	0.33	0.00	Single-nucleotide insertion in R region
Gag	ES10	AAAN	117	0.17	0.14	Located in region of length polymorphism between matrix and capsid, 14 amino acids upstream of protease cleavage site
	ES8	PSA	457	0.33	0.09	Located at site of length polymorphism in p6 between PTAP motif and first helical region
	ES8	LID	478	0.33	0.05	Located in a region of length polymorphism in p6 between the helical regions
Vif	ES1	DN	61	0.33	<0.01	Located in region of rare length polymorphism; reported polymorphisms are in LTNP
Vpu	ES1	DRL	4	0.33	0.02	Located in region of length polymorphism upstream of the beginning of the transmembrane α-helix
	ES1, ES8	V	64	0.67	0.03	Located in region of length polymorphism near C terminus
	ES10	GQLEM	67	0.17	0.03	Located in region of length polymorphism near C terminus
Env	ES1, ES8	W	10	0.67	0.03	Located in region of length polymorphism in signal peptide
	ES10	SWRWG	14	0.17	0.09	Located in region of length polymorphism in signal peptide
Nef	ES10	RAEPRMR	21	0.17	0.37	Located in a region of common length polymorphism
		E	64	0.17	0.17	Located in a region of common length polymorphism in acid cluster
Recurrent polymorphismd
LTR	ES1, ES10	A→C	24	0.50	0.043	Located in U3; results in rare K‡Q mutation in Nef
	ES8, ES10	A→C	119	0.50	0.021	Located in U3; silent in Nef
	ES1, ES8	T→C	252	0.67	0.064	Located in U3; silent in Nef
Gag	ES1, ES4, ES10	D→N	121	0.67	0.016	Located in flexible region between matrix and capsid, 12 amino acids upstream of protease cleavage site
Pol	ES8, ES10	K→R	535	0.50	0.027	Located in RT, residue 281
Vif	ES1, ES8	T→I	67	0.67	0.047
Vpr	ES1, ES8	I→T	37	0.50	0.093	Polymorphism at position of substantial variability
Tat	ES8, ES10	F→Y	32	0.50	0.056	Conserved hydrophobic residue
	ES1, ES10	D→N	80	0.50	0.028	Located in second exon
Tat	ES1, ES10	R→T	93	0.50	0.028	Located in second exon
	ES1, ES10	D→A	101	0.50	0.062	Located in second exon
Env	ES8, ES10	K→M	4	0.50	0.065	Located in signal peptide
	ES1, ES8	L→W	10	0.67	0.100	Located in signal peptide
Nef	ES1, ES10	K→Q	105	0.50	0.09

^aResidue(s) in clade B consensus sequence affected.

^bPosition of the feature in HXB2 coordinates. Insertions occur after the indicated nucleotide or amino acid position in the reference HXB2 sequence. Gag numbering is from the first Met of Gag open reading frame. Env numbering is from the first Met in the Env open reading frame.

^cFor insertions and deletions, this value reflects the frequency of any insertion or deletion at this position in all clade B sequences in the Los Alamos HIV Database.

^dOnly polymorphisms found in at least two of four ES studied but in <10% of clade B isolates in the Los Alamos database are listed.