CoRSeqV3-C: a novel HIV-1 subtype C specific V3 sequence based coreceptor usage prediction algorithm

Retrovirology

Table 1 V3 amino acid alterations associated with C-HIV coreceptor usage

Mutation ^a	Phenotype		Fisher’s exact test (p value)	Mutation	Phenotype		Fisher’s exact test (p value)
	CCR5 usage	CXCR4 usage			CCR5 usage	CXCR4 usage
Asn6Tyr	0	4.3	ns	Gln18Arg	1.1	20.3	<0.0001
Asn7Lys	0	4.3	ns	Gln18His	0.4	13	0.0002
Thr8Ile	0.2	7.2	0.014	Gln18Lys	0	2.9	ns
Arg9Ile	0	5.8	0.0289	Phe20Val	0	7.2	0.0068
Lys10Glu	4.4	0	ns	Phe20Trp	0	2.9	ns
Ser11Arg	0.2	15.9	<0.0001	Thr23-	2.3	0	ns
Ser11Asn	0	4.3	ns	Thr23Arg	0	5.8	0.0289
Ser11His	0	2.9	ns	Gly24Lys	1.3	13	0.0013
Ser11Ile	0	2.9	ns	Asp25Arg	0.2	10.1	0.0015
Ser11Lys	0	1.4	ns	Asp25Lys	0.6	17.4	<0.0001
Ile12Lys	0	2.9	ns	Asp25Thr	0	7.2	0.0068
Arg13Asn	0	2.9	ns	Asp25His	0	1.4	ns
Arg13-	0.4	8.7	0.0067	Asp25-	2.5	4.3	ns
Ile14Leu	0.6	10.1	0.0015	Ile27Arg	0	7.2	0.0068
Ile14Thr	0	4.3	ns	Ile27Asn	0	2.9	ns
13-14 insertion	0	40.4	<0.0001	Gly28Lys	0	2.9	ns
Pro16Arg	0	37.7	<0.0001	Ile30Val	0	4.3	ns
Pro16Gln	0	4.3	ns	Gln32Glu	8	0	0.0068
Gly17Arg	0.4	8.7	0.0067	His34Phe	0	7.2	0.0068

^a Amino acid numbering is based on the consensus C-HIV V3 sequence.
Values are percentages of R5 or CXCR4-using C-HIV V3 sequences.
For these analyses, 69 unique CXCR4-using and 473 unique R5 C-HIV V3 sequences were included.
ns, not significant; -, deleted sequence.

ISSN: 1742-4690