After the first wave of new patient sequences arrived, it becomes clear that there are at least two major lineages that are distinguishable by only few mutations. Most notably, N248 has mutated to Aspartate (D248) in the New York infection cluster. All intra-strain mutations available before May 8 th 2009 are indicated in Figures 4B and 5. As expected, they are predominantly found on the surface and in regions that are known to be variable from the conservation analysis. While the drug binding pocket remains unaffected by these most recent mutations, the N248D substitution changes a central part of an antibody recognition site. This has important consequences for vaccine development, forcing to either avoid this epitope or produce combined vaccines to account for the epitope in the first annotation line) is displayed as the respective mutated residue in capital letters if found in multiple patients (e.g. D for the N248D substitution) or lower-case (e.g. "i" for V241I) for single occurrences. In the second annotation row, antigenic regions are labelled as "*". Residues with < 3 Å contact to antibodies are labelled "A" for interactions derived from PDB:1ncb, "B" from both PDB:1ncb and PDB:1nmb, "C" from PDB:1nmb and "D" from PDB:2aep. variation observed in different patient groups. Although the mutation pattern will become less transparent over time it may still serve to delineate chains of transmission, retrospectively.