Persistence of attenuated HIV-1 rev alleles in an epidemiologically linked cohort of long-term survivors infected with nef-deleted virus

Table 2 rev alleles with rare Pro-74, Leu-104 and/or Pro-106 mutations^a

Clade B HIV-1 strain or Rev clone	Residue at position: (Clade B consensus residue; frequency^b)			Frequency of residue combination^b	Status of HIV-1 progression^d	GenBank accession no.	Reference
	74 (Gln; 0.90)	104 (Val; 0.94)	106 (Ser; 0.97)
C64	Pro	Leu	Pro	unique	LTNP	EF634155	This report
D36	Pro	Leu	Pro	unique	LTS	EF634154	This report
MA^c	Gln	Val	Ser	0.884	LTS	N/A	Iversen et al., [10]
C42	Pro	Val	Ser	0.049	N/A	AF538305	Unpublished
D31	Pro	Val	Ser	0.049	N/A	U43096	Kreutz et al., [48]
UKR1216	Pro	Val	Ser	0.049	N/A	AF193278	Liitsola et al., [49]
NY5CG	Gln	Leu	Ser	0.018	AIDS	M38431	Willey et al., [50]
89.6	Pro	Val	Ser	0.049	AIDS	U39362	Collman et al., [51]
WEAU160	Pro	Leu	Ser	0.006	N/A	U21135	Unpublished
1299_d22	His	Val	Pro	0.018	N/A	AY308761	Bernardin et al., [52]
1006_08	Pro	Val	Ser	0.049	Acute infection	AY331284	Bernardin et al., [53]
1058_08	Pro	Val	Ser	0.049	Acute infection	AY331294	Bernardin et al., [53]
PRB959_03	Gln	Val	Pro	0.018	Acute infection	AY331296	Bernardin et al., [53]
RU128005	Gln	Val	Pro	0.018	N/A	AY682547	Unpublished
98USHVTN3605c9	Pro	Val	Ser	0.049	N/A	AY560108	Unpublished
PCM013	Glu	Leu	Ser	0.018	N/A	AY561237	Unpublished
50333-03	Gln	Leu	Ser	0.018	LTS	U30750	Iversen et al., [10]
931395-04	Pro	Val	Ser	0.049	AIDS	U30775	Iversen et al., [10]
LA-09	Gln	Leu	Pro	0.006	AIDS	U30785	Iversen et al., [10]

a; Sixteen of 164 Clade B HIV-1 rev sequences screened from the Los Alamos National Laboratory HIV Database and other published studies [10] contained Pro-74, Leu-104 and/or Pro-106 mutations. Underlined boldface indicates the presence of one or more of these rare amino acid changes.
b; Amino acid frequency was calculated by dividing the number of sequences with the amino acid, or the particular amino acid combination, by the total number of sequences analyzed (n = 164).
c; Patient MA, identified as a LTS with attenuated rev alleles in a previous study by Iversen et al., [10] was included for comparison.
d; LTNP, long-term nonprogressor; LTS, long-term survivor; AIDS, acquired immune deficiency syndrome; N/A, not available.

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