Among env sequences present in Los Alamos Database, 255 and 101 sequences predicted as CCR5 and CXCR4 were selected, respectively. The classical V3 signatures at positions 11 and 25, and other specific V3 and gp41 amino acid changes were found statistically associated with different co-receptor usage. Furthermore, several statistically significant associations between V3 and gp41 signatures were also observed. The dendrogram topology showed a cluster associated with CCR5-usage composed by five gp41 mutated positions, A22V, R133M, E136G, N140L, and N166Q that clustered with T2VV3 and G24TV3 (bootstrap = 1). Conversely, a heterogeneous cluster with CXCR4-usage, involving S11GRV3, 13-14insIG/LGV3, P16RQV3, Q18KRV3, F20ILVV3, D25KRQV3, Q32KRV3 along with A30Tgp41, S107Ngp41, D148Egp41, A189Sgp41 was identified (bootstrap = 0.86).
Our results show that as observed for HIV-1 subtype-B, also in subtype-C specific and different gp41 and gp120V3 amino acid changes are associated individually or together with CXCR4 and/or CCR5 usage. These findings strengthen previous observations that determinants of tropism may also reside in the gp41 protein.