A curated public database designed to represent, store, and analyze the divergent forms of data underlying HIV drug resistance.

Shafer RW, Schapiro JM (2008). HIV-1 Drug Resistance Mutations: an Updated Framework for the Second Decade of HAART. AIDS, Rev. 2008;10:67-84

Gifford RJ, Rhee SY, Eriksson N, Liu TF, Kiuchi M, Das AK, Shafer RW (2008). Sequence Editing by Apolipoprotein B RNA-editing Catalytic Component-B and Epidemiological Surveillance of Transmitted HIV-1 Drug Resistance. AIDS, 2008 Mar 30;22(6):717-25

Shafer RW, Rhee SY, Bennett DE (2008). Consensus Drug Resistance Mutations for Epidemiological Surveillance: Basic Principles and Potential Controversies. Antiviral Therapy, Vol. 13 (2008) Suppl 2:59-68

Mitsuya Y, Liu TF, Rhee SY, Fessel WJ, Shafer RW (2007). Prevalence of Darunavir Resistance-Associated Mutations: Patterns of Occurrence and Association with Past Treatment. Journal of Infectious Diseases, Oct 15, 2007 196:1177-9

Petersen ML, Wang Y, van der Laan MJ, Rhee SY, Shafer RW, Fessel WJ (2007). Virologic Efficacy of Boosted Double Versus Boosted Single Protease Inhibitor Therapy. AIDS July 31, 2007 ISSN 0269-9370

Wang C, Mitsuya Y, Gharizadeh B, Ronaghi M, Shafer RW (2007). Characterization of Mutation Spectra with Ultra-Deep Pyrosequencing: Application to HIV-1 Drug Resistance. Genome Research June 28, 2007 ISSN 1088-9051/07

Rhee SY, Liu TF, Holmes SP, Shafer RW (2007). HIV-1 Subtype B Protease and Reverse Transcriptase Amino Acid Covariation. PLoS Computational Biology May 2007 3:5(e87)

Shafer RW, Rhee SY, Pillay D, Miller V, Sandstrom P, Schaprio JM, Kuritzkes DR, Bennett D.(2006). HIV-1 protease and reverse transcriptase mutations for drug resistance surveillance. AIDS Jan 11, 2007

Mitsuya Y, Winters MA, Fessel WJ, Rhee SY, Hurley L, Horberg M, Schiffer CA, Zolopa AR, Shafer RW.(2006). N88D Facilitates the Co-occurrence of D30N and L90M and the Development of Multidrug Resistance in HIV Type 1 Protease following Nelfinavir Treatment Failure. AIDS Res Hum Retroviruses 22(12):1300-5

Rhee SY, Taylor J, Wadhera G, Ben-Hur A, Brutlag DL, Shafer RW(2006). Genotypic predictors of human immunodeficiency virus type 1 drug resistance. Proceedings of National Academy of Sciences of the United States of America Oct 25, 2006

Click here to access the data sets and the results.

Mitsuya Y, Winters MA, Fessel WJ, Rhee SY, Slome S, Flamm J, Horberg M, Hurley L, Klein D, Shafer RW(2006). HIV-1 Drug Resistance Genotype Results in Patients With Plasma Samples With HIV-1 RNA Levels Less than 75 Copies/mL. JAIDS 43(1):56-9

Rhee SY, Kantor R, Katzenstein DA, Camacho R, Morris L,Sirivichayakul S,Jorgensen L, Brigido LF, Schapiro JM,and Shafer RW for the international Non Subtype B HIV-1 Working Group(2006). HIV-1 pol mutation frequency by subtype and treatment experience: extension of the HIVseq program to seven non-B subtypes. AIDS 20(5):643-651, March 21, 2006

Click here to access the HIVseq program

Rhee SY, Fessel WJ, Zolopa AR, Hurley L, Liu T, Taylor J, Nguyen DP, Slome S, Klein D, Horberg M, Flamm J, Follansbee S, Schapiro JM, Shafer RW (2005). HIV-1 Protease and Reverse-Transcriptase Mutations: Correlations with Antiretroviral Therapy in Subtype B Isolates and Implications for Drug-Resistance Surveillance. Journal of Infectious Diseases, Aug 1;192(3):456-65. Epub 2005 Jul 5.

Kantor R, Katzenstein DA, Efron B, Carvalho AP, Wynhoven B, Cane P, Clarke J, Sirivichayakul S, Soares MA, Snoeck J, Pillay C, Rudich H, Rodrigues R, Holguin A, Ariyoshi K, Bouzas MB, Cahn P, Sugiura W, Soriano V, Brigido LF, Grossman Z, Morris L, Vandamme AM, Tanuri A, Phanuphak P, Weber JN, Pillay D, Harrigan PR, Camacho R, Schapiro JM and Shafer RW (2005). Impact of HIV-1 Subtype and Antiretroviral Therapy on Protease and Reverse Transcriptase Genotype: Results of a Global Collaboration. PLoS Med. Apr;2(4):e112.

Johnston E, Dupnik KM, Gonzales MJ, Winters MA, Rhee SY, Imamichi T and Shafer RW (2005). Panel of prototypical infectious molecular HIV-1 clones containing multiple nucleoside reverse transcriptase inhibitor resistance mutations. AIDS 19(7):731-3.

Click here to access sequences.

Jie Zhang, Soo-Yon Rhee, Jonathan Taylor and Robert W. Shafer (2005). Comparison of the Precision and Sensitivity of the Antivirogram and PhenoSense HIV Drug Susceptibility Assays. JAIDS 38(4):439-444.

Click here to access data sets and statistical analyses used.

Johnston E, Winters MA, Rhee SY, Merigan TC, Schiffer CA and Shafer RW. (2004). Association of a novel human immunodeficiency virus type 1 protease substrate cleft mutation, L23I, with protease inhibitor therapy and in vitro drug resistance. Antimicrobial Agents and Chemotherapy 48(12):4864-8.

Soo-Yon Rhee, Tommy Liu, Jaideep Ravela, Matthew J. Gonzales and Robert W. Shafer (2004). Distribution of Human Immunodeficiency Virus Type 1 Protease and Reverse Transcriptase Mutation Patterns in 4,183 Persons Undergoing Genotypic Resistance Testing. Antimicrobial Agents and Chemotherapy 48(8):3122-3126.

Rami Kantor, Robert W. Shafer, Stephen Follansbee, Jonathan Taylor, David Shilane, Leo Hurley, Dong-Phuong Nguyen, David Katzenstein, and W. Jeffrey Fessel (2004). Evolution of resistance to drugs in HIV-1-infected patients failing antiretroviral therapy. AIDS 18(11):1503-1511.

Amit Kapoor, Morris Jones, Robert W. Shafer, Soo-Yon Rhee, Powel Kazanjian, and Eric L. Delwart (2004). Sequencing-based detection of low-frequency human immunodeficiency virus type 1 drug-resistant mutants by an RNA/DNA heteroduplex generator-tracking assay.

Gonzales MJ, Johnson E, Dupnik KM, Imamichi T, Shafer RW.(2003) Colinearity of reverse transcriptase inhibitor resistance mutations detected by population-based sequencing. JAIDS,1;34(4):398-402

Matthew J. Gonzales, Ilana Belitskaya, Kathryn M. Dupnik, Soo-Yon Rhee and Robert W. Shafer. (2003) Protease and Reverse Transcriptase Mutation Patterns in HIV Type 1 Isolates from Heavily Treated Persons: Comparison of Isolates from Northern California with Isolates from Other Regions. AIDS Res Hum Retroviruses, 19:909-915

Matthew J. Gonzales, Eric Delwart, Soo-Yon Rhee, Rose Tsui, Andrew R. Zolopa, Jonathan Taylor, and Robert W. Shafer. (2003) Lack of Detectable Human Immunodeficiency Virus Type 1 Superinfection during 1072 Person-Years of Observation. Journal of Infectious Diseases, 188(3):397-405

Jaideep Ravela, Bradley J. Betts, Francoise Brun-Vézinet, Anne-Mieke Vandamme, Diane Descamps, Kristel Van Laethem, Kate Smith, Jonathan M. Schapiro, Dean Winslow, Caroline Reid, Robert W. Shafer (2003). HIV-1 Protease and Reverse Transcriptase Mutation Patterns Responsible for Discordances Between Genotypic Drug Resistance Interpretation Algorithms JAIDS 33(1):8-14

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Thomas D. Wu, Celia A. Schiffer, Matthew J. Gonzales, Jonathan Taylor, Rami Kantor, Sunwen Chou, Dennis Israelski, Andrew R. Zolopa, W. Jeffrey Fessel, and Robert W. Shafer (2003). Mutation Patterns and Structural Correlates in HIV-1 Protease Following Varying Degrees of Protease Inhibitor Treatment J. Virol. 77(8): 4836-4847.

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Matthew J. Gonzales, Thomas D. Wu, Jonathan Taylor, Ilana Belitskaya, Rami Kantor, Dennis Israelski, Sunwen Chou, Andrew R. Zolopa, W. Jeffrey Fessel, and Robert W. Shafer (2003). Extended spectrum of HIV-1 reverse transcriptase mutations in patients receiving multiple nucleoside analog inhibitors AIDS 17(6):791-799.

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Rami Kantor, Lynn S. Zijenah, Robert W. Shafer, Solomon Mutetwa, Elizabeth Johnston, Robert Lloyd, Andrea Von Lieven, Dennis Israelski, and David A. Katzenstein (2002). HIV-1 subtype C reverse transcriptase and protease genotypes in Zimbabwean patients failing antiretroviral therapy AIDS Res Hum Retroviruses, 18(18):1407-13.

Sarah Palmer, Dominique Vuitton, Matthew J. Gonzales, Agnés Bassignot, and Robert W. Shafer (2002) Reverse Transcriptase and Protease Sequence Evolution in Two HIV-1-Infected Couples JAIDS, 31(3):285-290.

Susan H. Eshleman, Matthew J. Gonzales, Graziella Becker-Pergola, Shawn C. Cunningham, Laura A. Guay, G. Brooks Jackson, and Robert W. Shafer (2002) Identification of Ugandan HIV Type 1 Variants with Unique Patterns of Recombination in pol Involving Subtypes A and D AIDS Research and Human Retroviruses, 18:507-511.

Rami Kantor, W. Jeffrey Fessel, Andrew R. Zolopa, Dennis Israelski, Nancy Shulman, Jose G. Montoya Michael Harbour, Jonathan M. Schapiro and Robert W. Shafer. (2002) Evolution of primary protease inhibitor resistance mutations during protease inhibitor salvage therapy Antimicrobial Agents and Chemotherapy, 46:1086-1092.

Matthew J. Gonzales, Rhoderick N. Machekano, and Robert W. Shafer. (2001) Human immunodeficiency virus type 1 reverse-transcriptase and protease subtypes: classification, amino acid mutation patterns, and prevalence in a northern california clinic-based population. Journal of Infectious Diseases, 184:998-1006.

Shafer RW, Hertogs K, Zolopa AR, Warford A, Bloor S, Betts BJ, Merigan TC, Harrigan R, Larder BA(2001). High Degree of Interlaboratory Reproducibility of Human Immunodeficiency Virus Type 1 Protease and Reverse Transcriptase Sequencing of Plasma Samples from Heavily Treated Patients. Journal of Clinical Microbiology 39(4):1522-9

Robert W. Shafer, Phillip Hsu, Amy K. Patick, Charles Craig, and Volker Brendel. (1999) Identification of biased amino acid substitution patterns in human immunodeficiency virus type 1 isolates from patients treated with protease inhibitors. Journal of Virology, 73:6197-6202.

Andrew R. Zolopa, MD; Robert W. Shafer, MD; Ann Warford, PhD; Jose G. Montoya, MD; Philip Hsu, BA; David Katzentein, MD; Thomas C. Merigan, MD; and Brad Efron, PhD. (1999) HIV-1 Genotypic Resistance Patterns Predict Response to Saquinavir-Ritonavir Therapy in Patients in Whom Previous Protease Inhibitor Therapy Had Failed. Annals of Internal Medicine, 131(11):813-21

Bradley J. Betts and Robert W. Shafer, (2003) Algorithm Specification Interface for Human Immunodeficiency Virus Type 1 Genotypic Interpretation. Journal of Clinical Microbiology, 41(6), 2792-4.

Soo-Yon Rhee, Matthew J. Gonzales, Rami Kantor, Bradley J. Betts, Jaideep Ravela, and Robert W. Shafer (2003) Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Research, 31(1), 298-303.

Matthew J. Gonzales, Jonathan M. Dugan, and Robert W. Shafer (2002) Synonymous-non-synonymous mutation rates between sequences containing ambiguous nucleotides (Syn-SCAN) Bioinformatics, 18(6), 886-887.

Rami Kantor, Rhoderick Machekano, Matthew J. Gonzales, Kathryn Dupnik, Jonathan M. Shapiro, and Robert W. Shafer. (2001) Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database: an expanded data model integrating natural language text and sequence analysis programs Nucleic Acids Research, 29(1), 296-299.

Robert W. Shafer, Duane R. Jung, and Bradley J. Betts. (2000) Human immunodeficiency virus type 1 reverse transcriptase and protease mutation search engine for queries. Nature Medicine, 6(11), 1290-1292.

Robert W. Shafer, Duane R. Jung, Bradley J. Betts, Yinong Xi, and Matthew J. Gonzales. (2000) Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Research, 28(1), 346-348.

Robert W. Shafer, Derek Stevenson, and Bryan Chan. (1999) Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Research, 27(1), 348-352.

Shafer RW(2006). Rationale and Uses of a Public HIV Drug-Resistance Database. Journal of Infectious Diseases 194 Suppl 1:S51-8

Liu TF, Shafer RW(2006). Web Resources for HIV type 1 Genotypic-Resistance Test Interpretation. Clin Infect Dis 42(11):1608-18. Epub 2006 Apr 28

Shafer RW and Schapiro JM. (2005) Drug resistance and antiretroviral drug development. J Antimicrob Chemother

Robert W. Shafer (2002) Genotypic testing for human immunodeficiency virus type 1 drug resistance Clinical Microbiology Reviews 15:247-277

Robert W. Shafer, Kathryn M. Dupnik, Mark A. Winters, and Susan H. Eshleman. (2001) A guide to HIV-1 reverse transcriptase and protease sequencing for drug resistance studies. Human Retroviruses and AIDS, Theoretical Biology and Biophysics. Los Alamos National Laboratories.

Robert W. Shafer, Rami Kantor, and Matthew J. Gonzales. (2000) The genetic basis of HIV-1 resistance to reverse transcriptase and protease inhibitors AIDS Reviews, 2, 211-228.

Robert W. Shafer, Stanley C. Deresinski (2000) Human immunodeficiency virus information on the web: A guided tour. Clin Infect Dis, 31(2):568-77.

Nancy Shulman, Robert W. Shafer (2007) Case files from Stanford University Medical Center: Ten Years of HAART: A Long Wait for Full HIV Suppression   Medscape General Medicine 2007;9(1):10.

Robert W. Shafer, Dong Phuong Nguyen, Jeffrey Fessel (2006) Case files from Stanford University Medical Center: Drug Resistance Testing in Previously Untreated Patients with HIV -- Knowing What to Look for and Choosing Appropriate Therapy   Medscape General Medicine 2006;8(3):32.

Minghsun Liu, Mark Holodniy, Andrew R. Zolopa, Robert W. Shafer (2006) Case files from Stanford University Medical Center: The Initial Presentation of HIV-1 Infection -- Where Public and Personal Health Meet   Medscape General Medicine 2006;8(1):24.