How does HIVDB indicate insertions and deletions (indels)?
Insertions and deletions in the enzymatic targets of HIV therapy are not common. Yet they do occur and some are associated with decreased susceptibility. In the HIVdb program the presence of one or more amino acid insertions is indicated by the lower case letters “ins” whereas amino acids are always indicated by single upper-case letters; the presence of one or more deletions are indicated by the lower case letters “del”. In amino acid alignments, we have chosen to indicate insertions using the symbol “#” and deletions using the symbol “~”. Because these are not standard representations, an explanation for these symbols are provided wherever they are used. Although they are not common, we have been asked many questions about indels such as how is their location determined, does the size of the insertion or deletion influence drug susceptibility, does the particular amino acid or amino acids inserted influence drug susceptibility. These questions will be addressed as the FAQs fo
