Single genome analysis reveals genetic characteristics of Neuroadaptation across HIV-1 envelope

Retrovirology

Table 4 CCR5-tropic virus predominates in the CSF and plasma in the majority of HIV-1+ individuals with varying degrees of neurocognitive impairment

Participant	Compartment	G2P CCR5	G2P CXCR4	PSSM CCR5	PSSM CXCR4	No Prediction
NCN1	CSF	7	0	7	0	0
	Plasma	20	0	20	0	0
NCN2	CSF	29	0	29	0	0
	Plasma	23	0	23	0	0
NCN3	CSF	26	0	26	0	0
	Plasma	29	0	29	0	0
NCN4	CSF	35	0	35	0	0
	Plasma	22	0	22	0	0
NCN5	CSF	28	0	28	0	0
	Plasma	21	0	21	0	0
NCN6	CSF	18	0	18	0	0
	Plasma	17	0	17	0	1 G2P + PSSM (Ins)
ANI1*	CSF	28	0	28	0	0
	Plasma	23	2	23	2	0
ANI2*	CSF	20	0	20	0	0
	Plasma	20	1	20	1	0
ANI3*	CSF	0	12	0	12	0
	Plasma	1	16	1	16	0
ANI4	CSF	24	0	24	0	0
	Plasma	40	0	41	0	1 G2P (Del)
ANI5	CSF	22	0	22	0	0
	Plasma	19	0	19	0	0
ANI6	CSF	30	0	30	0	0
	Plasma	27	0	28	0	1 G2P (Del)
ANI7*	CSF	31	0	29	2	0
	Plasma	23	0	22	1	0
MND1	CSF	20	0	20	0	0
	Plasma	26	0	26	0	0
MND2	CSF	26	0	26	0	0
	Plasma	29	0	29	0	0

The number of translated V3 loop sequences predicted to be CCR5 and CXCR4-tropic using both the Geno2Pheno (G2P) and the SINSI position-specific scoring matrix (PSSM) for all sequenced viral variants are shown. Three sequences yielded invalid predictions on co-receptor usage as a result of insertions (Ins) or deletions (Del) in the translated V3 loop sequence. Individuals for whom CXCR4-tropic variants are predicted in the CSF or plasma compartments are starred (*).

ISSN: 1742-4690