How does HIVDB indicate mutations?
Mutations are indicated by a shorthand consisting of the consensus B amino acid followed by the amino acid position followed by the amino acid detected in a sequence. For example, the RT mutation T215Y indicates that the consensus amino acid is T (Thr; threonine) but that the mutation found in the sequence of interest is Y (Tyr; tyrosine). The expression T215TY indicates that there is a mixture of viruses with the wildtype T and the mutation Y in the same sequence. Mixtures consisting of two amino acids at the same position in a sequence are common and generally represent true mixtures rather than sequence artifact (Shafer et al. 2001; Wang et al. 2007). Rarely, a sequence will contain a mixture of three or four amino acids at the same position. For example, the change from T to Y at position 215 requires two nucleotide changes (e.g. ACC => TAC). Rarely, a sequence will detect WMC (where W indicates the IUB ambiguity code for A and T and M indicates the ambiguity code for A and C). WMC
