Primate immunodeficiency viruses have similar physical, morphological, and biochemical characteristics but differ in their behavior. Many African primates have coevolved with these virus, allowing for disease-free productive infection. Molecular variations may explain these variations in outcomes. To characterize these differences, we analyzed viral and host binding partners (gp41 and CXCR4). FASTA protein sequences were gathered for human and non-human primate proteins (CXCR4) and viral glycoproteins (gp41). Protein sequences were aligned using Clustal Omega and these alignments were used to generate phylogenetic trees. A sequence logo generator clearly displayed amino acid. Notable sequence differences were observed that mapped well with the apparent evolutionary pattern and disease susceptibility. To further characterize these evolutionary patterns, we wrote code in Anaconda Python to generate outputs for the number of nonsynonymous changes, compare the DNA sequences and recognize the site differences and report the dN/dS score/ratio. The data suggest that the differences in the protein sequences were caused by negative purifying or stabilizing selection. Taken together, we report protein sequences that align with virus-host disease appear to be the result of some level of selective pressure.
