HIV integrase variability and genetic barrier in antiretroviral naïve and experienced patients

Table 1 Conserved and variable amino acid distribution in Integrase sequences and amino acid divergence among RT, PR and IN sequences in HIV-1

Category (strain no.)	Mean nucleotide divergence ± SD			Mean amino acid divergence ± SD			IN conserved amino acid (%)	IN variable amino acid (%)		IN conserved amino acid in three functional domains (%)
	RT gene	PR gene	IN gene	RT gene	PR gene	IN gene		Singleton^a	Parsimony^b	NTD (1-50)	CCD (51-212)	CTD (213-277)
HAART-naïve (41)	9.2 ± 2.3	10.5 ± 2.9	8.8 ± 2.5	6.3 ± 1.8	11.3 ± 3.5	7.0 ± 1.8	180 (65.9)	36 (13.2)	57 (20.9)	26 (52.0)	114 (70.4)	40 (62.5)
RT/PI-experienced (54)	9.8 ± 2.5	12.2 ± 3.6	8.3 ± 2.5	9.8 ± 2.6	18.8 ± 7.8	6.5 ± 1.9	170 (62.3)	39 (14.3)	64 (23.4)	26 (52.0)	103 (63.6)	41 (64.1)
HAART-naïve vs RT/PI-experienced	p < 0.001	p < 0.001	p < 0.001	p < 0.001	p < 0.001	p < 0.001	ns	ns	ns	ns	ns	ns
HIV-2 (4)	ND	ND	13.0 ± 1.1	ND	ND	7.9 ± 1.4	241(88.3)	9(3.3)	23 (8.4)	39 (78.0)	149 (91.9)	53 (82.8)
HIV-2 vs HIV-1			p < 0.001			p < 0.001	p < 0.001	p < 0.001	p < 0.001	p < 0.001	p < 0.001	p < 0.001

SD: standard deviation; ND: not done; ns: not significant; NTD: N-terminal domain; CCD: catalytic core domain; CTD: C-terminal domain; RT: reverse trancriptase; PR: protease; IN: integrase.
^a A singleton site contains at least two types of amino acid with, at most, one occurring multiple times.
^b Parsimony-informative if it contains at least two types of amino acid, and at least two of these occur with a minimum frequency of two.
^c Significant p-values are reported.

ISSN: 1743-422X