2011-09-19: Updated translating rules.
The translation rules for our Sierra program were updated; for a more detailed list of changes to the program and/or report please follow this link.
2011-07-12: Updated the rules for Agence Nationale de Recherches sur le SIDA (ANRS V20).
The algorithm rules used in the HIValg Program for Comparison of Genotypic Resistance Algorithms were updated to reflect the latest 2011 version of Agence Nationale de Recherches sur le SIDA (ANRS rules). To view the underlying files used in the HIValg program follow this link.
2011-03-29: Updated our classification into Major and Minor mutations; a few scores and comments were also changed.
Our classification of mutations into PI Major, PI Minor, NRTI, NNRTI, INI Major, and INI Minor was updated; a discussion of mutation categories and links to the files with the latest versions can be found here. The changes are detailed here
2011-03-29: Will update our classification into Major and Minor mutations; a few scores and comments will also change.
Our classification of mutations into PI Major, PI Minor, NRTI, NNRTI, INI Major, and INI Minor will be updated; a discussion of mutation categories and links to the files with the latest versions can be found here. The changes are detailed here
2011-01-20: Corrected trigger for comment on unusual mutations at integrase position 72.
Comment on unusual mutations at integrase position 72 is no longer triggered by I72V.
Causing an update on the HIVDB algorithm to version 6.0.10; for more details follow this link
2011-01-12: Updated the rules for Agence Nationale de Recherches sur le SIDA (ANRS V19).
The algorithm rules used in the HIValg Program for Comparison of Genotypic Resistance Algorithms were updated to reflect the latest 2010 version of Agence Nationale de Recherches sur le SIDA (ANRS rules). To view the underlying files used in the HIValg program follow this link.
2011-01-10: Updated lists of typical protease and RT mutations.
We have updated our lists of protease typical mutations and RT typical mutations used to determine the Unusual Residues QA Problem section of our Sequence Quality Assessment in our HTML report. We are currently working to update the list of IN typical mutations.
2011-01-10: Updated criteria for identifying sequences with evidence of Apobec 3G/3F hypermutation.
Our recently revised method a) uses an updated list of mutations which can compared to the previous under section APOBEC3G-mediated defective (A3GD) mutation list, b) looks at one gene at a time to determine hypermutation, and c) requires just 2 positions with evidence of hypermutation for a sequence to be considered hypermutated.
The XML 2009 report (discussed in detail here) has also been updated to show the mutations with evidence of Apobec 3G/3F hypermutation instead of just the positions. Consequently, its schema (sierra.xsd) was updated to version 1.2 since the element <GAHypermutatedPositions> under the complexType <QualityAnalysis> was renamed to <GAHypermutatedMutations>.
2009-10-15: Updated the rules from Rega Institute and ANRS
The two algorithm rules used in the HIValg Program for Comparison of Genotypic Resistance Algorithms were updated to reflect their latest 2009 versions: i. Rega Institute (rules), and ii. Agence Nationale de Recherches sur le SIDA (ANRS rules). To view the underlying files used in the HIValg program follow this link.
2009-10-15: Added Protease Resistance Combination Scores
For more details follow this link
2009-09-01: Added integrase Resistance Scores
For more details follow this link
2009-06-17: Crystallographic Structures of RT, Protease & Integrase
A sample set of RT, protease, & integrase structures were chosen from PDB to give a 3D visual/structural context to mutations associated with drug resistance; Crystallographic Structures of RT, Protease & Integrase
2009-05-06: HIVdb: Updated handling of sequence QA problems
We have further standardized our approach to handling sequences with quality control problems. For more details follow this link
2009-05-06: HIVdb: adopted new ASI rules compiler
We have adopted a new compiler for the Algorithm Specification Interface (ASI). For more details follow this link
2009-03-09: HIVDB Users Guide updated
The HIVDB User Guide was vastly updated. You can find it in this page
2009-03-06: Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update
A new article updating the mutation list for Surveillance of Transmitted Drug Resistant HIV Strains was published on PLoS ONE, 2009;4(3):e4724. Here is the PDF file for the article. You can find this and other information on surveillance mutations in our Surveillange page. And finally, you can find this and our other publications in our Publications page
2009-02-10: HIVdb Comments: minor updates
A few comment rules were updated.
Regarding the QA table, the rule for defining atypical mutations was revisited and updated: any mutation absent in the typical files including those at positions missing from the file (those with no typical mutations) are now included. For more details follow this link
2009-01-21: HIVdb Comments updated extensively
For more details follow this link
2008-12-03: New Program MARVEL & HIVdb Updates
(1) Mutation ARV Evidence Listing (MARVEL 0.8) - provides the underlying data and references that show which mutations cause resistance to which drugs by bringing together the evidence from genotype-treatment, genotype-phenotype, and genotype-virological outcome correlations. MARVEL 0.8 can be accessed from the home page or by linking on the mutations in the scoring table of the HIVdb report. MARVEL 0.9 and 1.0 will have tailored links to additional references containing data that is not in the HIVDB database. (2) HIVdb program - genotypic resistance interpretations for HIV-1 integrase, expanded release notes, and updated Mutation Scores and Comments. (3) Updated drug summaries.
2008-11-04: Most PI and NNRTI Resistance Scores and Comments Updated; integrase added; PI drugs renamed
Most PI and NNRTI resistance scores and comments were updated. The report now accepts sequences with integrase and provides a partial report on the integrase portion. PI drugs were renamed to include '/r' - FPV/r, IDV/r, SQV/r, LPV/r, ATV/r, TPV/r, DRV/r - to explicitly indicate ritonavir boosting. For more details follow this link
2008-05-02: A few DRV Resistance Scores and Comments Updated
A few DRV scores and comments were updated. For more details follow this link
2008-04-29: Resistance Scores and Comments Updated
A few scores and comments were updated. For more details follow this link
2007-07-12: NNRTI Resistance Scores and Comments Updated: added drug TMC125
Scores and comments for TMC125, a new NNRTI drug, were added. For more details follow this link
2007-01-30: Three new programs launched: ART-AiDE, eCARE, and CPR
Antiretroviral Therapy - Acquisition and Display Engine (ART-AiDE) makes it
possible to generate a permanent electronic and graphical record of a
patient's antiretroviral treatment (ARV) history, plasma HIV-1 RNA levels,
CD4 counts, and genotypic resistance data. The electronic Clinical
Antiretroviral Resistance Estimator (eCARE) matches submitted ARVs with
sequences in the Stanford HIV Drug Resistance Database obtained from
persons with matching ARV histories. eCARE, which is an early stage of
development, is available through ART-AiDE. The link to ART-AiDE is provided on the right in the home page.
Calibrated Population Resistance (CPR) analysis tool determines the
prevalence of NRTI, NNRTI, and PI resistance in a set of protease and/or RT
sequences using a standardized analysis that enables users to compare their
results to those of other published studies. Although designed primarily
for studies of primary HIV drug resistance, CPR can be applied to any HIV
protease and/or RT sequence set. The link to CPR is provided under the section "ANALYSIS TOOLS" in the home page.
2006-12-04: Few PI Resistance Scores Updated
A few scores for PI drugs were updated. For more details follow this link
2006-11-21: Resistance Scores and Comments Updated
A few scores for PI drugs and comments were updated, especially TPV. fAPV was renamed FPV and TMC114 was renamed DRV. For more details follow this link
2006-10-11: PI Resistance Scores Updated
A few scores for PI drugs were updated, especially TMC 114. For more details follow this link
2006-09-18: ANRS Resistance Algorithm Updated
Scores for ANRS resistance algorithm were updated to 2006 July version. For more details follow this link to their site
2006-09-18: PI Resistance Scores Updated
Scores and comments for PI drugs were updated, especially TMC 114. For more details follow this link
2006-08-22: PI Resistance Summaries Updated
PI resistance summary pages have been updated to reflect recently reported data relevant to atazanavir (ATV), tipranavir (TPV), and darunavir (DRV, TMC114). Most of the changes reflect data from salvage therapy trials. Sequences from TPV and DRV treated persons have not yet been submitted to the database. TPV and DRV drug susceptibility data have also not yet been submitted to the database. Researchers who would like to submit such data should contact us at HIVDB.
2006-05-30: Positions available
We are seeking two post-doctoral fellows to perform studies of HIV sequence variation, molecular evolution, population genetics, and antiviral drug resistance; to develop software to assist other researchers performing similar analyses; and to further the development of the Stanford HIV Drug Resistance Database (http://hivdb.stanford.edu).
Candidates should have degrees in biology, biomedical informatics, or statistics and be motivated to innovate and publish. Candidates will have to become highly knowledgeable about the biological and clinical aspects of HIV drug resistance and how the data representing this knowledge is organized in the Stanford database. Candidates will need to be able to write their own programs for querying the Stanford database and for performing statistical and machine learning analyses of data within the Stanford database as well as of data from additional ongoing collaborations. Ideally, one candidate will have a stronger computer programming background and will contribute to improving the database and its tools and another will have a stronger analytic background with statistical skills and an understanding of molecular evolution and population genetics analyses.
Please e-mail your CV, a brief statement, and the names, telephone numbers, and e-mail addresses of three references to HIVDB.
2005-05-25: Letter Written to the FDA
Show us the data! To better meet their responsibility, the FDA should encourage pharmaceutical companies to release the data supporting the activity of new HIV drugs against drug-resistant viruses. The full text of the letter »