1. Department of Experimental Medicine and Biochemistry, University of Rome &ldquo Tor Vergata&rdquo , Rome, Italy 2. Slemani Polytechnic University, Iraqi Kurdistan Region 3. Faculty of Pharmacy, University of Calabria, Cosenza, Italy 4. National Institute for Infectious Diseases &ldquo L. Spallanzani,&rdquo Rome, Italy.
After infection and integration steps, HIV-1 transcriptions increase sharply and singly-spliced mRNAs are produced. These encode Env (gp120 and gp41) and auxiliary proteins Vif, Vpr and VpU. The same localization within the unique structure of the mRNAs suggests that the VpU sequence prior to the Env could affect the Env polyprotein expression. The HIV-1 infection process begins when the gp120 subunit of the envelope glycoprotein complex interacts with its receptor(s) on the target cell. The V3 domain of gp120 is the major determinant of cellular co-receptor binding. According to phenotypic information of HIV-1 isolates, sequences from the VpU to V3 regions (119 in R5- and 120 X4-tropic viruses; one per patient) were analysed. The binomial correlation phi coefficient was used to assess covariation among VpU and gp120V3 signatures. Subsequently, average linkage hierarchical agglomerative clustering was performed. Beyond the classical V3 signatures (R5-viruses: S11, E25D; X4-viruses: S11KR, E25KRQ), other specific V3 and novel VpU signatures were found to be statistically associated with co-receptor usage. Several statistically significant associations between V3 and VpU mutations were also observed. The dendrogram showed two distinct large clusters: one associated with R5-tropic sequences (bootstrap=0.94), involving: (a) H13NPV3, E25DV3, S11V3, T22AV3 and Q61HVpU, (b) E25AV3 and L12FVpU, (c) D44EVpU, R18QV3 and D80NVpU; and another associated with X4-tropic sequences (bootstrap=0.97), involving: (i) E25IV3 and V10AVpU, (ii) 0-1insVVpU, H13RV3, I46LVpU, I30MV3 and 60-62delVpU, (iii) S11KRV3 and E25KRQV3. Some of these pairs of mutations were encoded always by one specific codon. These data indicate the possible VpU mutational patterns contributing to regulation of HIV-1 tropism.