Conserved positive selection signals in gp41 across multiple subtypes and difference in selection signals detectable in gp41 sequences sampled during acute and chronic HIV-1 subtype C infection

Table 2 Codons evolving under different selection pressures in the AI and CI datasets.

Codon position (relative to HXB2 gp160)	Normalised dN/dS (SLAC, FEL, IFEL)^a		Gp41 domain	nAb/CTL epitope
	AI	CI
43 (554)	-1.62, -0.36, -0.37	0.50, 0.1, 0	N-heptad repeat
48 (559)	-3.43, -0.71, -0.7	0.43, 0.1, 0	N-heptad repeat	RAIEAQQH- B, C & Cw
105 (616)^b	-1.62, -0.36, -0.37	0.49, 0.03, 0	Loop region (glyc site)
163 (674)^b	-0.07, -0.04, 0.48	2.88, 0.19, 0.44	MPER	NWFNIT (4E10 nAb)
300 (804)^b	0.22, 0.01, -0.04	-1.62, -0.16, -0.18	LLP3	LLQYWSQEL A*0201
309 (813)^b	-0.24, -0.05, -0.04	2.14, 0.19, 0.24	LLP3	QELKNSAVSL B60 & B*4001

^aSignificant (P < 0.05) values marked in bold typeface.
^bsites at which selection signals were inferred to be significantly different between the AI and CI datasets using the PARRIS based test described in the methods.

ISSN: 1743-422X