The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus

Table 4 Nucleotide composition of the HIV-1 RNA genome over time (1983–2009)

HIV-1 group/subtype	Number of genomes analysed^a	Average nucleotide composition % 1983-1997^b	Range	Number of full-length genomes analysed	Average nucleotide composition % 1998-2009^b	Range
M, subtype A^c	24	A 36.5	35.8-36.9	38	A 36.6	36.3-36.9
		C 17.5	17.3-17.8		C 17.5	17.0-17.7
		G 23.8	23.3-24.4		G 23.8	23.4-24.2
		U 22.3	21.8-22.6		U 22.1	21.8-22.5
M, subtype B^d	16	A 36.7	36.5-37.0	25	A 36.7	36.3-37.0
		C 17.4	17.1-17.7		C 17.4	17.1-17.7
		G 23.7	23.5-24.0		G 23.7	23.4-24.1
		U 22.2	22.0-22.4		U 22.3	22.1-22.5
N ^e	2	A 35.7	35.6-35.8	6	A 36.1	36.0-36.4
		C 17.7	17.6-17.9		C 17.5	17.2-17.9
		G 24.2	24.1-24.3		G 23.9	23.9-24.1
		U 22.3	22.2-22.3		U 22.2	22.0-22,4
O ^d	4	A 35.4	35.0-35.8	3	A 35.3	34.8-36.1
		C 18.7	18.6-18.8		C 18.8	18.3-19.1
		G 23.7	23.5-24.2		G 23.8	23.3-24.1
		U 22.2	21.9-22.4		U 22.1	21.9-22.3
P ^f	0	NA	NA	2	A 34.1	33.9-34.4
					C 18.4	18.3-18.5
					G 24.5	24.4-24.6
					U 22.4	22.2-22.6

^a Gag-pol-env only.
^b No significant differences in nucleotide composition were scored between groups over time (p>0.05, Student’s t-test).
^c A shorter sequence of HIV-1 subtype A was analysed (approx. 8600 nt), as not many full-length genomes were available.
^d Only genomes with ≤ 10 ambiguous nucleotides were used for the analysis.
^e Seven of eighth group N genomes contain ambiguous nucleotides (range 5–38).
^f Only two full-length genomes of group P viruses are available from the Los Alamos Database, which contain 54 and 66 ambiguous nucleotides, respectively.