ERVW-1 and HIV-1 infection: In this study we found that i) there is evidence of positive selection in early HIV-1 infection, which appears to be driven in many cases by escape from early cytotoxic T lymphocyte (CTL) responses; ii) in several cases CTL escape occurred via mutations in the APOBEC sequence context, suggesting a role for APOBEC in determining the pathway of immune escape; and iii) frameshifting insertions and deletions are evenly spread throughout env but are preferentially fixed in the variable regions.