<!--#set var="title" value="Genbank References" --> <!--#if expr="$title" --> <!--#echo var="title" --> <!--#else --> HIV Drug Resistance Database <!--#endif -->
Stanford University HIV Drug Resistance Database - A curated public database designed to represent, store, and analyze the divergent forms of data underlying HIV drug resistance.

Genbank References

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")

HIVDB The sequences are in the HIV Drug Resistance Database (HIVDB).
Pending The sequences should be added within the next three months or are being evaluated further for inclusion in HIVDB.
Unpublished The paper describing the sequences has not yet been published. There is currently insufficient information to add the sequences and associated data to HIVDB. The sequences from these studies will be re-examined every three months.
ARV Rx and/or other data are N/A There is insufficient information about the sequences to add them to HIVDB. Either the treatment history or the provenance of the virus isolates are missing. In most cases, the authors of the paper in which the sequences were published have been contacted and this information has been requested.
Laboratory/experimental isolate Sequences submitted to GenBank more than once or derived from a previously submitted sequence through experimental manipulation are not routinely added to HIVDB. For example, site-directed mutants or viruses modified via in vitro passage in the presence of drugs are added if phenotypic data are available. However, virus isolates resulting from manipulations not relevant to drug resistance are not added.
Case report(s) / study subset Case reports of complete genomic sequences that were submitted to GenBank because of some unusual characteristics unrelated to drug resistance or sequence diversity. A subset of sequences obtained from a large study is not added, if the subset is highly unrepresentative of the larger study.
Gene fragment(s) Sequences containing only a small proportion of the protease, RT, or integrase are not added.
Sequence quality Sequences with many stop codons, reading frame shifts, or highly ambiguous nucleotides are not added to HIVDB.
Quasispecies Studies that contain many clones and/or sequences from a few individuals that address questions about HIV evolution and tissue reservoirs. Population genetic studies lacking treatment information.
New The sequences have been newly submitted to GenBank.
Consensus sequences HIVDB contains a single consensus amino acid sequence for each set of clones for each virus isolate.
NGS The GenBank sequences in this study appear to represent the consensus nucleotide sequence generated from next-generation sequencing reads.
NHPL/SIV Sequences of non-human primate lentiviruses or simian immunodeficiency viruses are not added.
Proviral DNA Reservoir Sequences obtained from the HIV DNA in viral reservoirs are not added.
SGS Single genome sequences (SGS) generated from limiting dilution PCR are in a separate database: https://hivdb.stanford.edu/project/sgs/