Annotation Definitions

The HIV RT and Protease Sequence Database (HIVRT&PrDB) catalogs data linking sequence changes in the molecular targets of HIV therapy to other forms of data including (1) treatment history, (2) phenotypic(drug susceptibility) data on laboratory isolates, (3) phenotypic(drug susceptibility) data on clinical isolates, and (4) clinical outcome (plasma HIV RNA levels and CD4+ cell counts) data. These data are necessary to create the four major correlations that provide the basis for interpreting genotypic tests in clinical settings: Major Correlations Linking Mutations to HIV Drug Resistance

In addition to obtaining sequences from GenBank, HIVRT&PrDB solicits data from those publishing important papers on drug resistance. Conversely, data in GenBank are not entered into HIVRT&PrDB if they don't contribute to one of the four correlations described above. Examples of sequences that are not entered into HIVRT&PrDB are: (1) Sequences of recently transmitted viruses: Ascertaining the frequency of transmitted resistance requires the capture of additional information that is not in our database such as whether a patient is undergoing seroconversion, has had a positive detuned serological assay (indicating recent infection), or knows the year in which HIV was acquired; (2) Sequences of latent viruses obtained from persons with complete virus suppression. In these persons, the sequence does not reflect the selective pressure of the person's drug treatment; (3) In vitro and in vivo studies of HIV-1 quasispecies; and (4) Laboratory isolates other those designed specifically for drug-resistance experiments (i.e. having specific drug-resistance mutations inserted by site-directed mutagenesis).

In the following table, we have annotated each set of GenBank entries according to whether its sequences are in the database ("HIVDB"), or being prepared for entering into the database ("Pending"), whether key correlative data is missing from the entry ("ARV Rx and/or other data are N/A"), whether the study describes sequences that are not suitable for entry into the database ("Evolution/quasispecies data", "Laboratory/experimental isolate"), and whether the study requires further evaluation ("Unpublished", "New")