Sequences and alignment

Publicly available V3 loop sequences (relative to HXB2 positions 7,110–7,217) for HIV-1 subtype B were downloaded from the HIV sequence database at the Los Alamos National Laboratory (www.hiv.lanl.gov/content/index) and translated into amino-acid sequences. The search criteria for each tropism were limited to “only CCR5,” “only CXCR4,” or “only R5X4.” The tropism fields at the Los Alamos HIV database are annotated based on only biological experiments and are not presumed using inferred genetic sequences. Identical sequences were removed from each category. The amino-acid sequences were aligned using the ClustalW algorithm that was implemented within the MEGA5 sequence analysis package¹⁶ and then manually edited to correct for any obvious alignment errors. Diversity in each data set was calculated using the Poisson substitution model and 1,000 bootstrap replicates in MEGA5.