we provide direct and unequivocal evidence that the usage of CCR8 and the switch from R8 to R5 or R5X4 phenotype is determined by amino acids located in the base and tip of V1 and V2 loops of HIV-2 Env surface glycoprotein.

I think that the amino acid covariation previously reported is explained by differences in amino acid frequencies among virus subpopulations in different patients and by nonsystematic disequilibrium among patients. Disequilibrium within patients appears to be entirely due to differences in amino acid frequencies among sampling time points and among chemokine coreceptor usage phenotypes of virus particles, but not source tissues. Positive selection explains differences in allele frequencies among time points and phenotypes, indicating that these differences are adaptive rather than due to genetic drift.

Hi Jessica,

I suggest this following paper for you, in which you can get the clear-cut view of your basic doubt in finding about amino-acid diferences. :) Good luck !! http://www.ncbi.nlm.nih.gov/pubmed/10563013

SRI

Thank you both for your helpful responses.