Table 2. Coreceptor prediction for NL-952.1, NL-952.2 and NL-952.3 V3 loop mutants.

Virus	NL-952.1					NL-952.2 and NL-952.3
	CC	G2P	PSSM		HcP	CC	G2P	PSSM		HcP
			SINSI	R5X4				SINSI	R5X4
RRR*	X4	X4	X4	X4	X4	X4	X4	X4	X4	X4
RRK	X4R5	X4	X4	X4	X4	X4	X4	X4	X4	X4
RKR	X4R5	X4	X4	X4	X4	X4	X4	X4	X4	X4
RKK	X4R5	X4	X4	X4	X4	X4	X4	X4	X4	X4
KRR	X4R5	X4	X4	X4	X4	X4	X4	X4	X4	X4
KRK	X4R5	X4	X4	X4	X4	X4	X4	X4	X4	X4
KKR	X4R5	X4	X4	X4	X4	X4	X4	X4	X4	X4
KKK	X4R5	X4	X4	X4	X4	X4	X4	X4	X4	X4
RRQ	R5	X4	R5	R5	X4	R5	X4	X4	X4	X4
RKS	R5	R5	R5	R5	R5	R5	X4	X4	X4	X4
RTR	R5	X4	X4	X4	X4	R5	X4	X4	X4	X4
KKN	R5	R5	R5	X4	X4	R5	X4	X4	X4	X4
KKQ	R5	R5	R5	X4	X4	R5	X4	X4	X4	X4
KTK	R5	X4	X4	X4	X4	R5	X4	X4	X4	X4
SRR	R5	X4	X4	X4	X4	R5	X4	X4	X4	X4
SKR	R5	X4	X4	X4	X4	R5	X4	X4	X4	X4
SKK	R5	X4	X4	X4	X4	R5	X4	X4	X4	X4
Predicted correctly		4	5	3	2		8	8	8	8

* amino acid sequence at V3 loop positions 9-to-11.

CC = cell culture tested coreceptor usage using GHOST-CXCR4 and GHOST-CCR5 indicator cell lines.

G2P = prediction algorithm geno2pheno (http://www.geno2pheno.org).

PSSM = position-specific scoring matrices (indra.mullins.microbiol.washington.edu/webpssm).

HcP = prediction algorithm HIVcoPred (http://www.imtech.res.in/raghava/hivcopred).

R5X4 = prediction algorithm developed using V3 sequences were CCR5 and CXCR4 coreceptor usage was assayed [14].

SINSI = prediction algorithm developed using V3 sequences were MT2 cell tropism was assayed [14].