Stanford HIV Drug Resistance Database

Names
More detailed information about this field from each metasource.

Stanford HIV Drug Resistance Database
metasource: Fairsharing.org
version: None

HIVDB
metasource: Fairsharing.org
version: None

HIV RT and Protease Sequence Database
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

HIV-DRLink
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:43.648520

metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:43.648520

Other names: HIVDB, HIV RT and Protease Sequence Database, HIV-DRLink

The Stanford HIV Drug Resistance Database (HIVDB) is an essential resource for public health officials monitoring ADR and TDR, for scientists developing new ARV drugs, and for HIV care providers managing patients with HIVDR.

Webpage:

https://hivdb.stanford.edu/

Licence:

Name: HIV Drug Resistance Database Terms of Use
URL: https://hivdb.stanford.edu/pages/FAQ/FAQ.html

Publications:

Publications
More detailed information about this field from each metasource.

Human immunodeficiency virus reverse transcriptase and protease sequence database
PMID: 12520007
metasource: Fairsharing.org
version: None

Rationale and uses of a public HIV drug-resistance database
PMID: 16921473
metasource: Fairsharing.org
version: None

http://dx.doi.org/10.1101/866715
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:43.648520

Human immunodeficiency virus reverse transcriptase and protease sequence database PubMed citations: 372.

372 articles citing: Human immunodeficiency virus reverse transcriptase and protease sequence database

Genetic Diversity and Low Therapeutic Impact of Variant-Specific Markers in HIV-1 Pol Proteins. PMID:35910645
Prevalence and Evolution of Transmitted Human Immunodeficiency Virus Drug Resistance in Belgium Between 2013 and 2019. PMID:35794938
HIV-1 Drug Resistance Assay Using Ion Torrent Next Generation Sequencing and On-Instrument End-to-End Analysis Software. PMID:35699434
Viruses Previously Identified in Brazil as Belonging to HIV-1 CRF72_BF1 Represent Two Closely Related Circulating Recombinant Forms, One of Which, Designated CRF122_BF1, Is Also Circulating in Spain. PMID:35694315
Spectrum of Atazanavir-Selected Protease Inhibitor-Resistance Mutations. PMID:35631067
Islatravir Has a High Barrier to Resistance and Exhibits a Differentiated Resistance Profile from Approved Nucleoside Reverse Transcriptase Inhibitors (NRTIs). PMID:35546110
Public availability of HIV-1 drug resistance sequence and treatment data: a systematic review. PMID:35544100
HIV-1 non-B resistance mutations and natural polymorphisms to integrase strand transfer inhibitors in recently diagnosed patients in Gabon, Central Africa. PMID:35474382
Consistent Quantification of Complex Dynamics via a Novel Statistical Complexity Measure. PMID:35455168
Pretreatment Human Immunodeficiency Virus (HIV) Drug Resistance Among Treatment-Naive Infants Newly Diagnosed With HIV in 2016 in Namibia: Results of a Nationally Representative Study. PMID:35434174
Potential Resistance of SARS-CoV-2 Main Protease (Mpro) against Protease Inhibitors: Lessons Learned from HIV-1 Protease. PMID:35408866
First report of computational protein-ligand docking to evaluate susceptibility to HIV integrase inhibitors in HIV-infected Iranian patients. PMID:35368742
Analyses of HIV proteases variants at the threshold of viability reveals relationships between processing efficiency and fitness. PMID:35299788
Coronavirus Resistance Database (CoV-RDB): SARS-CoV-2 susceptibility to monoclonal antibodies, convalescent plasma, and plasma from vaccinated persons. PMID:35263335
Achieving virological control in pan-resistant HIV-1 infection: A case series. PMID:35255457
Antiretroviral Imprints and Genomic Plasticity of HIV-1 pol in Non-clade B: Implications for Treatment. PMID:35222310
Management of a human immunodeficiency virus case with discordant antiviral drug resistance profiles in cerebrospinal fluid compared with plasma: a case report. PMID:35164871
An Android-Based Mobile App (ARVPredictor) for the Detection of HIV Drug-Resistance Mutations and Treatment at the Point of Care: Development Study. PMID:35107425
Limits to detecting epistasis in the fitness landscape of HIV. PMID:35041711
Statewide Longitudinal Trends in Transmitted HIV-1 Drug Resistance in Rhode Island, USA. PMID:34988256
Why the HIV Reservoir Never Runs Dry: Clonal Expansion and the Characteristics of HIV-Infected Cells Challenge Strategies to Cure and Control HIV Infection. PMID:34960781
Adherence, resistance, and viral suppression on dolutegravir in sub-Saharan Africa: implications for the TLD era. PMID:34848579
Genetic Diversity and Acquired Drug Resistance Mutations Detected by Deep Sequencing in Virologic Failures among Antiretroviral Treatment Experienced Human Immunodeficiency Virus-1 Patients in a Pastoralist Region of Ethiopia. PMID:34819737
Who's slipping through the cracks? A comprehensive individual, clinical and health system characterization of people with virological failure on first-line HIV treatment in Uganda and South Africa. PMID:34755438
Deep sequencing of HIV-1 reveals extensive subtype variation and drug resistance after failure of first-line antiretroviral regimens in Nigeria. PMID:34741609
High prevalence of HIV-1 transmitted drug resistance and factors associated with time to virological failure and viral suppression in Taiwan. PMID:34648632
MDM-TASK-web: MD-TASK and MODE-TASK web server for analyzing protein dynamics. PMID:34589183
Revealing the Mutation Patterns of Drug-Resistant Reverse Transcriptase Variants of Human Immunodeficiency Virus through Proteochemometric Modeling. PMID:34572515
Development of Human Immunodeficiency Virus Type 1 Resistance to 4'-Ethynyl-2-Fluoro-2'-Deoxyadenosine Starting with Wild-Type or Nucleoside Reverse Transcriptase Inhibitor-Resistant Strains. PMID:34516245
Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C. PMID:34491984
Phylogenetic and Drug-Resistance Analysis of HIV-1 Sequences From an Extensive Paediatric HIV-1 Outbreak in Larkana, Pakistan. PMID:34484134
Revertant mutation V48G alters conformational dynamics of highly drug resistant HIV protease PRS17. PMID:34419931
Molecular epidemiology and HIV-1 variant evolution in Poland between 2015 and 2019. PMID:34400726
HIV-1 Drug Resistance and Genetic Transmission Networks Among MSM Failing Antiretroviral Therapy in South China 2014-2019. PMID:34377002
Prediction of HIV drug resistance based on the 3D protein structure: Proposal of molecular field mapping. PMID:34347839
Identifying and Characterizing Trans Women in the Swiss HIV Cohort Study as an Epidemiologically Distinct Risk Group. PMID:34282827
RHIVDB: A Freely Accessible Database of HIV Amino Acid Sequences and Clinical Data of Infected Patients. PMID:34178036
HIV Protease: Historical Perspective and Current Research. PMID:34066370
Systematic screening of viral and human genetic variation identifies antiretroviral resistance and immune escape link. PMID:34061023
Emergence of Human Immunodeficiency Virus-1 Drug Resistance During the 3-Month World Health Organization-Recommended Enhanced Adherence Counseling Period in the CART-1 Cohort Study. PMID:34046513
Longitudinal typing of molecular HIV clusters in a statewide epidemic. PMID:34033589
HIV Drug Resistance and Transmission Networks Among a Justice-Involved Population at the Time of Community Reentry in Washington, D.C. PMID:33896212
Guidelines are needed for studies of pre-treatment HIV drug resistance: a methodological study. PMID:33874897
Hepatitis B virus resistance to tenofovir: fact or fiction? A systematic literature review and structural analysis of drug resistance mechanisms. PMID:33869791
Priority Intervention Targets Identified Using an In-Depth Sampling HIV Molecular Network in a Non-Subtype B Epidemics Area. PMID:33854982
Short Communication: Integrase Strand Transfer Inhibitors Drug Resistance Mutations in Puerto Rico HIV-Positive Individuals. PMID:33800269
Drug Design Strategies to Avoid Resistance in Direct-Acting Antivirals and Beyond. PMID:33410674
Evolution of drug resistance in HIV protease. PMID:33375936
Absence of Integrase Inhibitor-Associated Resistance Among Antiretroviral Therapy-Naïve HIV-1-Infected Adults in Guangdong Province, China, in 2018. PMID:33324078
Identification of an Antiretroviral Small Molecule That Appears To Be a Host-Targeting Inhibitor of HIV-1 Assembly. PMID:33148797
Predictors of Virological Failure and Time to Viral Suppression of First-Line Integrase Inhibitor-Based Antiretroviral Treatment. PMID:33095848
Contrast-FEL-A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches. PMID:33064823
Differences in human immunodeficiency virus-1C viral load and drug resistance mutation between plasma and cerebrospinal fluid in patients with human immunodeficiency virus-associated cryptococcal meningitis in Botswana. PMID:33031315
Virologic suppression in patients with a documented M184V/I mutation based on the number of active agents in the antiretroviral regimen. PMID:33014372
Few amino acid signatures distinguish HIV-1 subtype B pandemic and non-pandemic strains. PMID:32960906
High nonnucleoside reverse transcriptase inhibitor resistance levels in HIV-1-infected Zambian mother-infant pairs. PMID:32889853
Raltegravir use and outcomes among children and adolescents living with HIV in the IeDEA global consortium. PMID:32722897
Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses. PMID:32674515
Targeting HIV-1 RNase H: N'-(2-Hydroxy-benzylidene)-3,4,5-Trihydroxybenzoylhydrazone as Selective Inhibitor Active against NNRTIs-Resistant Variants. PMID:32640577
A de novo approach to inferring within-host fitness effects during untreated HIV-1 infection. PMID:32492061
Drug Resistance Prediction Using Deep Learning Techniques on HIV-1 Sequence Data. PMID:32438586
A near full-length HIV-1 genome from 1966 recovered from formalin-fixed paraffin-embedded tissue. PMID:32430331
An Innovative Sequence-to-Structure-Based Approach to Drug Resistance Interpretation and Prediction: The Use of Molecular Interaction Fields to Detect HIV-1 Protease Binding-Site Dissimilarities. PMID:32411655
HIV-1 molecular epidemiology and drug resistance-associated mutations among treatment-naïve blood donors in China. PMID:32371875
Diverse HCV Strains And HIV URFS Identified Amongst People Who Inject Drugs In India. PMID:32350342
Massively multiplexed nucleic acid detection with Cas13. PMID:32349121
Prevalence of acquired drug resistance mutations in antiretroviral- experiencing subjects from 2012 to 2017 in Hunan Province of central South China. PMID:32183889
Discordance between Etravirine Phenotype and Genotype-Based Predicted Phenotype for Subtype C HIV-1 from First-Line Antiretroviral Therapy Failures in South Africa. PMID:32071061
Multi-state design of flexible proteins predicts sequences optimal for conformational change. PMID:32032348
A cross-sectional study to characterize local HIV-1 dynamics in Washington, DC using next-generation sequencing. PMID:32029767
A Computational Approach for the Prediction of Treatment History and the Effectiveness or Failure of Antiretroviral Therapy. PMID:31979356
Pre-treatment HIV-drug resistance associated with virologic outcome of first-line NNRTI-antiretroviral therapy: A cohort study in Kenya. PMID:31956856
HIV-1 Unique Recombinant Forms Identified in Slovenia and Their Characterization by Near Full-Length Genome Sequencing. PMID:31947872
Highly drug-resistant HIV-1 protease reveals decreased intra-subunit interactions due to clusters of mutations. PMID:31920003
The ability of single genes vs full genomes to resolve time and space in outbreak analysis. PMID:31878875
Characterizing Protein-Ligand Binding Using Atomistic Simulation and Machine Learning: Application to Drug Resistance in HIV-1 Protease. PMID:31877249
Elucidating molecular interactions of L-nucleotides with HIV-1 reverse transcriptase and mechanism of M184V-caused drug resistance. PMID:31872074
High levels of pretreatment and acquired HIV drug resistance in Nicaragua: results from the first nationally representative survey, 2016. PMID:31860167
Moderately High Tenofovir Diphosphate in Dried Blood Spots Indicates Drug Resistance in Viremic Persons Living with HIV. PMID:31750768
Epistasis and entrenchment of drug resistance in HIV-1 subtype B. PMID:31591964
Prevalence and Correlates of Pre-Treatment HIV Drug Resistance among HIV-Infected Children in Ethiopia. PMID:31546824
MiDRMpol: A High-Throughput Multiplexed Amplicon Sequencing Workflow to Quantify HIV-1 Drug Resistance Mutations against Protease, Reverse Transcriptase, and Integrase Inhibitors. PMID:31480341
Transmission Dynamics of HIV Subtype A in Tel Aviv, Israel: Implications for HIV Spread and Eradication. PMID:31363777
Picomolar to Micromolar: Elucidating the Role of Distal Mutations in HIV-1 Protease in Conferring Drug Resistance. PMID:31361460
NNRTI-induced HIV-1 protease-mediated cytotoxicity induces rapid death of CD4 T cells during productive infection and latency reversal. PMID:31242909
A MiSeq-HyDRA platform for enhanced HIV drug resistance genotyping and surveillance. PMID:31222149
Nonnucleoside Reverse Transcriptase Inhibitor Hypersusceptibility and Resistance by Mutation of Residue 181 in HIV-1 Reverse Transcriptase. PMID:31160281
An Evolutionary Model-Based Approach To Quantify the Genetic Barrier to Drug Resistance in Fast-Evolving Viruses and Its Application to HIV-1 Subtypes and Integrase Inhibitors. PMID:31109980
Avirulins, a Novel Class of HIV-1 Reverse Transcriptase Inhibitors Effective in the Female Reproductive Tract Mucosa. PMID:31052477
Role of co-expressed APOBEC3F and APOBEC3G in inducing HIV-1 drug resistance. PMID:31025011
Mutations in the HIV-1 envelope glycoprotein can broadly rescue blocks at multiple steps in the virus replication cycle. PMID:30975760
Low rates of nucleoside reverse transcriptase inhibitor and nonnucleoside reverse transcriptase inhibitor drug resistance in Botswana. PMID:30946161
PERSIA for Direct Fluorescence Measurements of Transcription, Translation, and Enzyme Activity in Cell-Free Systems. PMID:30920800
The Utility of Efavirenz-based Prophylaxis Against HIV Infection. A Systems Pharmacological Analysis. PMID:30918485
High predictive efficacy of integrase strand transfer inhibitors in perinatally HIV-1-infected African children in therapeutic failure of first- and second-line antiretroviral drug regimens recommended by the WHO. PMID:30891603
Resistance Analysis of Bictegravir-Emtricitabine-Tenofovir Alafenamide in HIV-1 Treatment-Naive Patients through 48 Weeks. PMID:30803969
Maintenance of Viral Suppression after Optimization Therapy from Etravirine Plus Raltegravir to Rilpivirine Plus Dolutegravir in HIV-1-Infected Patients. PMID:30798670
Constrained Mutational Sampling of Amino Acids in HIV-1 Protease Evolution. PMID:30721995
Increased predominance of HIV-1 CRF01_AE and its recombinants in the Philippines. PMID:30676308
First-line HIV treatment failures in non-B subtypes and recombinants: a cross-sectional analysis of multiple populations in Uganda. PMID:30670037
Prevalence and persistence of transmitted drug resistance mutations in the German HIV-1 Seroconverter Study Cohort. PMID:30650082
Structural Adaptation of Darunavir Analogues against Primary Mutations in HIV-1 Protease. PMID:30543749
Characterisation of HIV-1 transmission clusters and drug-resistant mutations in Denmark, 2004 to 2016. PMID:30401010
Genetic divergence of HIV-1 B subtype in Italy over the years 2003-2016 and impact on CTL escape prevalence. PMID:30356083
A Computational Approach for the Prediction of HIV Resistance Based on Amino Acid and Nucleotide Descriptors. PMID:30355996
Clinical and Virologic Outcomes Following Initiation of Antiretroviral Therapy Among Seroconverters in the Microbicide Trials Network-020 Phase III Trial of the Dapivirine Vaginal Ring. PMID:30346511
Analysis of drug resistance in HIV protease. PMID:30343664
Antiretroviral resistance, genotypic characterization and origin of Human Immunodeficiency Virus among the infected wives of Intravenous drug users in Manipur. PMID:30315192
The dawn of precision medicine in HIV: state of the art of pharmacotherapy. PMID:30234392
New antiretroviral agent use affects prevalence of HIV drug resistance in clinical care populations. PMID:30134298
Structural Implications of Genotypic Variations in HIV-1 Integrase From Diverse Subtypes. PMID:30116231
Geographically-stratified HIV-1 group M pol subtype and circulating recombinant form sequences. PMID:30063225
HIV-1 proviral landscapes distinguish posttreatment controllers from noncontrollers. PMID:30024859
Modeling Cumulative Biological Phenomena with Suppes-Bayes Causal Networks. PMID:30013303
A systematic assessment of the availability and clinical drug information coverage of machine-readable clinical drug data sources for building knowledge translation products. PMID:29982512
Within-patient mutation frequencies reveal fitness costs of CpG dinucleotides and drastic amino acid changes in HIV. PMID:29953449
HIV transmission in discordant couples in Africa in the context of antiretroviral therapy availability. PMID:29762171
Field-deployable viral diagnostics using CRISPR-Cas13. PMID:29700266
HIV Resistance Prediction to Reverse Transcriptase Inhibitors: Focus on Open Data. PMID:29671808
Testing for Marginal Linear Effects in Quantile Regression. PMID:29576736
Frequent cross-resistance to rilpivirine among subtype C HIV-1 from first-line antiretroviral therapy failures in South Africa. PMID:29566538
Incomplete inhibition of HIV infection results in more HIV infected lymph node cells by reducing cell death. PMID:29555018
Implication of First-Line Antiretroviral Therapy Choice on Second-Line Options. PMID:29255731
Ex-vivo antiretroviral potency of newer integrase strand transfer inhibitors cabotegravir and bictegravir in HIV type 1 non-B subtypes. PMID:29239896
The L33F darunavir resistance mutation acts as a molecular anchor reducing the flexibility of the HIV-1 protease 30s and 80s loops. PMID:29124158
Analysis of the conformations of the HIV-1 protease from a large crystallographic data set. PMID:29124093
Newly Acquired Infection With Multidrug-Resistant HIV-1 in a Patient Adherent to Preexposure Prophylaxis. PMID:29076941
Prevalence of Pre-antiretroviral-Treatment Drug Resistance by Gender, Age, and Other Factors in HIV-Infected Individuals Initiating Therapy in Kenya, 2013-2014. PMID:29040633
Drug resistance patterns following pharmacy stock shortage in Nigerian Antiretroviral Treatment Program. PMID:29029637
Elucidating the Interdependence of Drug Resistance from Combinations of Mutations. PMID:28915040
Adaptive HIV-1 evolutionary trajectories are constrained by protein stability. PMID:28852572
Stimulus-responsive viral vectors for controlled delivery of therapeutics. PMID:28842318
Improving fold resistance prediction of HIV-1 against protease and reverse transcriptase inhibitors using artificial neural networks. PMID:28810826
High level of HIV-1 drug resistance mutations in patients with unsuppressed viral loads in rural northern South Africa. PMID:28750647
Potential for immune-driven viral polymorphisms to compromise antiretroviral-based preexposure prophylaxis for prevention of HIV-1 infection. PMID:28650381
Decreased emergence of HIV-1 drug resistance mutations in a cohort of Ugandan women initiating option B+ for PMTCT. PMID:28562612
Mutational Correlates of Virological Failure in Individuals Receiving a WHO-Recommended Tenofovir-Containing First-Line Regimen: An International Collaboration. PMID:28365230
Virological Outcomes of Second-line Protease Inhibitor-Based Treatment for Human Immunodeficiency Virus Type 1 in a High-Prevalence Rural South African Setting: A Competing-Risks Prospective Cohort Analysis. PMID:28329393
High Rates of Transmission of Drug-resistant HIV in Aruba Resulting in Reduced Susceptibility to the WHO Recommended First-line Regimen in Nearly Half of Newly Diagnosed HIV-infected Patients. PMID:28329390
GEAR: A database of Genomic Elements Associated with drug Resistance. PMID:28294141
NucAmino: a nucleotide to amino acid alignment optimized for virus gene sequences. PMID:28249562
Prevalence of Transmitted Drug-Resistance Mutations and Polymorphisms in HIV-1 Reverse Transcriptase, Protease, and gp41 Sequences Among Recent Seroconverters in Southern Poland. PMID:28167814
Characterization of the Drug Resistance Profiles of Patients Infected with CRF07_BC Using Phenotypic Assay and Ultra-Deep Pyrosequencing. PMID:28107423
Glycan Alteration Imparts Cellular Resistance to a Membrane-Lytic Anticancer Peptide. PMID:28089756
HIV drug resistance testing among patients failing second line antiretroviral therapy. Comparison of in-house and commercial sequencing. PMID:27894862
Quantitative evaluation of the antiretroviral efficacy of dolutegravir. PMID:27882352
Declining trend in transmitted drug resistance detected in a prospective cohort study of acute HIV infection in Bangkok, Thailand. PMID:27802846
Epistasis and Pleiotropy Affect the Modularity of the Genotype-Phenotype Map of Cross-Resistance in HIV-1. PMID:27678053
Genome-Wide Association Study of HIV Whole Genome Sequences Validated using Drug Resistance. PMID:27677172
A simple and cost-saving phenotypic drug susceptibility testing of HIV-1. PMID:27640883
Automated prediction of HIV drug resistance from genotype data. PMID:27586700
Global Comparison of Drug Resistance Mutations After First-Line Antiretroviral Therapy Across Human Immunodeficiency Virus-1 Subtypes. PMID:27419147
Surveillance of HIV Transmitted Drug Resistance in Latin America and the Caribbean: A Systematic Review and Meta-Analysis. PMID:27355626
Treatment Outcomes and Resistance Patterns of Children and Adolescents on Second-Line Antiretroviral Therapy in Asia. PMID:27355415
The global spread of HIV-1 subtype B epidemic. PMID:27262355
Exploiting Genetic Interference for Antiviral Therapy. PMID:27149616
HIV-1 Protease, Reverse Transcriptase, and Integrase Variation. PMID:27099321
Rapid and Simultaneous Detection of Major Drug Resistance Mutations in Reverse Transcriptase Gene for HIV-1 CRF01_AE, CRF07_BC and Subtype B in China Using Sequenom MassARRAY® System. PMID:27092551
Improving Viral Protease Inhibitors to Counter Drug Resistance. PMID:27090931
An adaptive resampling test for detecting the presence of significant predictors. PMID:27073292
Q148N, a Novel Integrase Inhibitor Resistance Mutation Associated with Low-Level Reduction in Elvitegravir Susceptibility. PMID:27009474
Exploiting HIV-1 protease and reverse transcriptase cross-resistance information for improved drug resistance prediction by means of multi-label classification. PMID:26933450
More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1. PMID:26882502
Genetic Variability of HIV-1 for Drug Resistance Assay Development. PMID:26875985
Mutations Related to Antiretroviral Resistance Identified by Ultra-Deep Sequencing in HIV-1 Infected Children under Structured Interruptions of HAART. PMID:26807922
Prevalence of K65R in patients treated with tenofovir disoproxil fumarate: recommendations based on the Frankfurt HIV Cohort Study Resistance Database (FHCS-RD). PMID:26746222
Structural studies on molecular mechanisms of Nelfinavir resistance caused by non-active site mutation V77I in HIV-1 protease. PMID:26695135
Identifying representative drug resistant mutants of HIV. PMID:26678327
HIV Drug Resistance Surveillance in Honduras after a Decade of Widespread Antiretroviral Therapy. PMID:26558396
Lessons from Ebola: Improving infectious disease surveillance to inform outbreak management. PMID:26424572
Collaborative Effort for a Centralized Worldwide Tuberculosis Relational Sequencing Data Platform. PMID:26409275
A Population-Structured HIV Epidemic in Israel: Roles of Risk and Ethnicity. PMID:26302493
Global Database-Driven Assessment of HIV-1 Adaptation to the Immune Repertoires of Human Populations. PMID:26246562
Genetic Consequences of Antiviral Therapy on HIV-1. PMID:26170895
Development of Nevirapine Resistance in Children Exposed to the Prevention of Mother-to-Child HIV-1 Transmission Programme in Maputo, Mozambique. PMID:26161559
Trends in Prevalence of HIV-1 Drug Resistance in a Public Clinic in Maputo, Mozambique. PMID:26151752
Comparison of genotypic and virtual phenotypic drug resistance interpretations with laboratory-based phenotypes among CRF01_AE and subtype B HIV-infected individuals. PMID:26147742
Statistical learning and selective inference. PMID:26100887
Transmitted Drug Resistance Mutations in Antiretroviral-Naïve Injection Drug Users with Chronic HIV-1 Infection in Iran. PMID:25962088
Genetic Changes in HIV-1 Gag-Protease Associated with Protease Inhibitor-Based Therapy Failure in Pediatric Patients. PMID:25919760
HIV-1 subtypes and drug resistance profiles in a cohort of heterosexual patients in Istanbul, Turkey. PMID:25916350
A Functional Interplay between Human Immunodeficiency Virus Type 1 Protease Residues 77 and 93 Involved in Differential Regulation of Precursor Autoprocessing and Mature Protease Activity. PMID:25893662
HIV-1 diversity in an antiretroviral treatment naïve cohort from Bushbuckridge, Mpumalanga Province, South Africa. PMID:25889106
Geographic and temporal trends in the molecular epidemiology and genetic mechanisms of transmitted HIV-1 drug resistance: an individual-patient- and sequence-level meta-analysis. PMID:25849352
Lopinavir/Ritonavir Monotherapy as Second-line Antiretroviral Treatment in Resource-Limited Settings: Week 104 Analysis of AIDS Clinical Trials Group (ACTG) A5230. PMID:25694653
Data-intensive analysis of HIV mutations. PMID:25652056
Viral Genetic Diversity and Polymorphisms in a Cohort of HIV-1-Infected Patients Eligible for Initiation of Antiretroviral Therapy in Abuja, Nigeria. PMID:25582324
A SIGNIFICANCE TEST FOR THE LASSO. PMID:25574062
Cross-clade simultaneous HIV drug resistance genotyping for reverse transcriptase, protease, and integrase inhibitor mutations by Illumina MiSeq. PMID:25533166
Defective hydrophobic sliding mechanism and active site expansion in HIV-1 protease drug resistant variant Gly48Thr/Leu89Met: mechanisms for the loss of saquinavir binding potency. PMID:25513833
The HIV mutation browser: a resource for human immunodeficiency virus mutagenesis and polymorphism data. PMID:25474213
Molecular mechanisms and design principles for promiscuous inhibitors to avoid drug resistance: lessons learned from HIV-1 protease inhibition. PMID:25410041
Estimating HIV-1 fitness characteristics from cross-sectional genotype data. PMID:25375675
Structural basis and distal effects of Gag substrate coevolution in drug resistance to HIV-1 protease. PMID:25355911
The lysine 65 residue in HIV-1 reverse transcriptase function and in nucleoside analog drug resistance. PMID:25341667
A "fuzzy"-logic language for encoding multiple physical traits in biomolecules. PMID:25311857
A uniquely prevalent nonnucleoside reverse transcriptase inhibitor resistance mutation in Russian subtype A HIV-1 viruses. PMID:25259833
Low-frequency NNRTI-resistant HIV-1 variants and relationship to mutational load in antiretroviral-naïve subjects. PMID:25256391
Drug susceptibility prediction against a panel of drugs using kernelized Bayesian multitask learning. PMID:25161247
Prediction of HIV drug resistance from genotype with encoded three-dimensional protein structure. PMID:25081370
Identifying selection in the within-host evolution of influenza using viral sequence data. PMID:25080215
Prevalence and virologic consequences of transmitted HIV-1 drug resistance in Uganda. PMID:24960249
Sparse Representation for Prediction of HIV-1 Protease Drug Resistance. PMID:24910813
Prevalence of WHO transmitted drug resistance mutations by deep sequencing in antiretroviral-naïve subjects in Hunan Province, China. PMID:24896087
The HIVToolbox 2 web system integrates sequence, structure, function and mutation analysis. PMID:24886930
The contribution of viral genotype to plasma viral set-point in HIV infection. PMID:24789308
Phylogenetic evidence of HIV-1 sequence evolution in subjects with persistent low-level viraemia. PMID:24699164
Natural polymorphisms and unusual mutations in HIV-1 protease with potential antiretroviral resistance: a bioinformatic analysis. PMID:24629078
Profile of darunavir in the treatment of HIV-infected pediatric and adolescent patients. PMID:24600277
Residual viremia in an RT-SHIV rhesus macaque HAART model marked by the presence of a predominant plasma clone and a lack of viral evolution. PMID:24505452
Southern African Treatment Resistance Network (SATuRN) RegaDB HIV drug resistance and clinical management database: supporting patient management, surveillance and research in southern Africa. PMID:24504151
New insights into the in silico prediction of HIV protease resistance to nelfinavir. PMID:24498124
HIV-1 virologic failure and acquired drug resistance among first-line antiretroviral experienced adults at a rural HIV clinic in coastal Kenya: a cross-sectional study. PMID:24456757
HIV-1 Protease and Substrate Coevolution Validates the Substrate Envelope As the Substrate Recognition Pattern. PMID:24348205
Superinfection with drug-resistant HIV is rare and does not contribute substantially to therapy failure in a large European cohort. PMID:24219163
Selection of RNAi-based inhibitors for anti-HIV gene therapy. PMID:24175213
Potential elucidation of a novel CTL epitope in HIV-1 protease by the protease inhibitor resistance mutation L90M. PMID:24015196
The individualized genetic barrier predicts treatment response in a large cohort of HIV-1 infected patients. PMID:24009493
The prevalence of transmitted resistance to first-generation non-nucleoside reverse transcriptase inhibitors and its potential economic impact in HIV-infected patients. PMID:23991151
Non-nucleoside reverse transcriptase inhibitor (NNRTI) cross-resistance: implications for preclinical evaluation of novel NNRTIs and clinical genotypic resistance testing. PMID:23934770
Prototypical Recombinant Multi-Protease-Inhibitor-Resistant Infectious Molecular Clones of Human Immunodeficiency Virus Type 1. PMID:23796938
Elevated hypermutation levels in HIV-1 natural viral suppressors. PMID:23791226
SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments. PMID:23761454
Selection of drug-resistant feline immunodeficiency virus (FIV) encoding FIV/HIV chimeric protease in the presence of HIV-specific protease inhibitors. PMID:23720716
Nucleoside reverse transcriptase inhibitor resistance mutations associated with first-line stavudine-containing antiretroviral therapy: programmatic implications for countries phasing out stavudine. PMID:23687292
In vitro HIV-1 evolution in response to triple reverse transcriptase inhibitors & in silico phenotypic analysis. PMID:23613794
L74V increases the reverse transcriptase content of HIV-1 virions with non-nucleoside reverse transcriptase drug-resistant mutations L100I+K103N and K101E+G190S, which results in increased fitness. PMID:23535575
CancerDR: cancer drug resistance database. PMID:23486013
Transmission patterns of HIV-subtypes A/AE versus B: inferring risk-behavior trends and treatment-efficacy limitations from viral genotypic data obtained prior to and during antiretroviral therapy. PMID:23469241
Comprehensive in vitro analysis of simian retrovirus type 4 susceptibility to antiretroviral agents. PMID:23365453
Structural and thermodynamic basis of amprenavir/darunavir and atazanavir resistance in HIV-1 protease with mutations at residue 50. PMID:23365446
Prevalent polymorphisms in wild-type HIV-1 integrase are unlikely to engender drug resistance to dolutegravir (S/GSK1349572). PMID:23295935
QColors: an algorithm for conservative viral quasispecies reconstruction from short and non-contiguous next generation sequencing reads. PMID:23202421
Collinearity of protease mutations in HIV-1 samples with high-level protease inhibitor class resistance. PMID:23085775
What do molecules do when we are not looking? State sequence analysis for stochastic chemical systems. PMID:22977098
Correlated electrostatic mutations provide a reservoir of stability in HIV protease. PMID:22969420
Prediction of mutational tolerance in HIV-1 protease and reverse transcriptase using flexible backbone protein design. PMID:22927804
Lys66 residue as a determinant of high mismatch extension and misinsertion rates of HIV-1 reverse transcriptase. PMID:22925131
Cost-effectiveness of tenofovir instead of zidovudine for use in first-line antiretroviral therapy in settings without virological monitoring. PMID:22905175
Maraviroc observational study: the impact of expanded resistance testing and clinical considerations for antiretroviral regimen selection in treatment-experienced patients. PMID:22881368
A Perturbation Method for Inference on Regularized Regression Estimates. PMID:22844171
Global analysis of sequence diversity within HIV-1 subtypes across geographic regions. PMID:22822410
Minor protease inhibitor mutations at baseline do not increase the risk for a virological failure in HIV-1 subtype B infected patients. PMID:22719859
Panel of prototypical recombinant infectious molecular clones resistant to nevirapine, efavirenz, etravirine, and rilpivirine. PMID:22664973
Modeling HIV-1 drug resistance as episodic directional selection. PMID:22589711
Surveillance of HIV drug resistance in children receiving antiretroviral therapy: a pilot study of the World Health Organization's generic protocol in Maputo, Mozambique. PMID:22544205
Prevalence of HIV drug resistance before and 1 year after treatment initiation in 4 sites in the Malawi antiretroviral treatment program. PMID:22544204
HIV-1 phenotypic reverse transcriptase inhibitor drug resistance test interpretation is not dependent on the subtype of the virus backbone. PMID:22496845
Lopinavir/ritonavir monotherapy after virologic failure of first-line antiretroviral therapy in resource-limited settings. PMID:22441252
Factors limiting the transmission of HIV mutations conferring drug resistance: fitness costs and genetic bottlenecks. PMID:22432052
Virologic failures on initial boosted-PI regimen infrequently possess low-level variants with major PI resistance mutations by ultra-deep sequencing. PMID:22355307
Standardized comparison of the relative impacts of HIV-1 reverse transcriptase (RT) mutations on nucleoside RT inhibitor susceptibility. PMID:22330916
Genetic diversity of recently acquired and prevalent HIV, hepatitis B virus, and hepatitis C virus infections in US blood donors. PMID:22293432
The HIVdb system for HIV-1 genotypic resistance interpretation. PMID:22286876
Endogenous or exogenous spreading of HIV-1 in Nordrhein-Westfalen, Germany, investigated by phylodynamic analysis of the RESINA Study cohort. PMID:22262052
A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes. PMID:22172090
Emerging trends of drug-resistant HIV-1 among drug-treated patients in former blood donors in Hubei, China: a three-year surveillance from 2004 to 2006. PMID:22160938
The impact of molecular manipulation in residue 114 of human immunodeficiency virus type-1 reverse transcriptase on dNTP substrate binding and viral replication. PMID:22153297
The evolution of HIV: inferences using phylogenetics. PMID:22138161
Directed HIV-1 evolution of protease inhibitor resistance by second-generation short hairpin RNAs. PMID:22064528
Reverse transcriptase drug resistance mutations in HIV-1 subtype C infected patients on ART in Karonga District, Malawi. PMID:21995490
Drug resistance mutations in HIV pol sequences from Argentinean patients under antiretroviral treatment: subtype, gender, and age issues. PMID:21936717
Sequence quality analysis tool for HIV type 1 protease and reverse transcriptase. PMID:21916749
Biochemical, inhibition and inhibitor resistance studies of xenotropic murine leukemia virus-related virus reverse transcriptase. PMID:21908397
STRUCTURED, SPARSE REGRESSION WITH APPLICATION TO HIV DRUG RESISTANCE. PMID:21892380
Efficient identification of human immunodeficiency virus type 1 mutants resistant to a protease inhibitor by using a random mutant library. PMID:21876045
The higher barrier of darunavir and tipranavir resistance for HIV-1 protease. PMID:21871444
Cell-to-cell spread of HIV permits ongoing replication despite antiretroviral therapy. PMID:21849975
Nonnucleoside reverse transcriptase inhibitor-resistant HIV is stimulated by efavirenz during early stages of infection. PMID:21835788
Missing data on the estimation of the prevalence of accumulated human immunodeficiency virus drug resistance in patients treated with antiretroviral drugs in north america. PMID:21813792
Accessory mutations maintain stability in drug-resistant HIV-1 protease. PMID:21762813
Dynamics of preferential substrate recognition in HIV-1 protease: redefining the substrate envelope. PMID:21762811
Randomized trial of time-limited interruptions of protease inhibitor-based antiretroviral therapy (ART) vs. continuous therapy for HIV-1 infection. PMID:21738668
HIVToolbox, an integrated web application for investigating HIV. PMID:21647445
Genetic draft and quasi-neutrality in large facultatively sexual populations. PMID:21625002
Role of induced fit in limiting discrimination against AZT by HIV reverse transcriptase. PMID:21548586
Identification of new, emerging HIV-1 unique recombinant forms and drug resistant viruses circulating in Cameroon. PMID:21513545
Dose-response curve slope is a missing dimension in the analysis of HIV-1 drug resistance. PMID:21502494
HIV-1 integrase inhibitor resistance and its clinical implications. PMID:21459813
Intensity of deoxycytidine deamination of HIV-1 proviral DNA by the retroviral restriction factor APOBEC3G is mediated by the noncatalytic domain. PMID:21300806
Performance of the Abbott RealTime HIV-1 viral load assay is not impacted by integrase inhibitor resistance-associated mutations. PMID:21289145
Human immunodeficiency virus type 1 resistance or cross-resistance to nonnucleoside reverse transcriptase inhibitors currently under development as microbicides. PMID:21282453
Proteochemometric modeling of the susceptibility of mutated variants of the HIV-1 virus to reverse transcriptase inhibitors. PMID:21179544
Early virologic failure and the development of antiretroviral drug resistance mutations in HIV-infected Ugandan children. PMID:21099693
Cohort profile: The PharmAccess African (PASER-M) and the TREAT Asia (TASER-M) monitoring studies to evaluate resistance--HIV drug resistance in sub-Saharan Africa and the Asia-Pacific. PMID:21071386
Call for a quality standard for sequence-based assays in clinical microbiology: necessity for quality assessment of sequences used in microbial identification and typing. PMID:21068275
Drug resistance mutations in drug-naive HIV type 1 subtype C-infected individuals from rural Malawi. PMID:20950147
Constraints on HIV-1 diversity from protein structure. PMID:20881050
Higher levels of Zidovudine resistant HIV in the colon compared to blood and other gastrointestinal compartments in HIV infection. PMID:20836880
HIV-1 protease mutations and protease inhibitor cross-resistance. PMID:20660676
Cellular HIV-1 DNA levels in drug sensitive strains are equivalent to those in drug resistant strains in newly-diagnosed patients in Europe. PMID:20544014
Nucleic acid template and the risk of a PCR-Induced HIV-1 drug resistance mutation. PMID:20539818
Prevalence and clinical significance of HIV drug resistance mutations by ultra-deep sequencing in antiretroviral-naïve subjects in the CASTLE study. PMID:20532178
Constrained patterns of covariation and clustering of HIV-1 non-nucleoside reverse transcriptase inhibitor resistance mutations. PMID:20462946
Predicting tipranavir and darunavir resistance using genotypic, phenotypic, and virtual phenotypic resistance patterns: an independent cohort analysis of clinical isolates highly resistant to all other protease inhibitors. PMID:20368406
Combinations of mutations in the connection domain of human immunodeficiency virus type 1 reverse transcriptase: assessing the impact on nucleoside and nonnucleoside reverse transcriptase inhibitor resistance. PMID:20194692
Only slight impact of predicted replicative capacity for therapy response prediction. PMID:20140263
The mutation T477A in HIV-1 reverse transcriptase (RT) restores normal proteolytic processing of RT in virus with Gag-Pol mutated in the p51-RNH cleavage site. PMID:20122159
Detecting and understanding combinatorial mutation patterns responsible for HIV drug resistance. PMID:20080674
HIV-1 reverse transcriptase drug-resistance mutations in chronically infected individuals receiving or naïve to HAART in Cameroon. PMID:20029816
Non-nucleoside reverse transcriptase inhibitor outcomes among combination antiretroviral therapy-treated adults in Botswana. PMID:20023437
Identification of structural mechanisms of HIV-1 protease specificity using computational peptide docking: implications for drug resistance. PMID:20004167
Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease. PMID:19758465
Nonpolymorphic human immunodeficiency virus type 1 protease and reverse transcriptase treatment-selected mutations. PMID:19721070
Human immunodeficiency virus type 1 protease-correlated cleavage site mutations enhance inhibitor resistance. PMID:19706699
Transmitted antiretroviral drug resistance among acute and recent HIV infections in North Carolina from 1998 to 2007. PMID:19704170
Host sequence motifs shared by HIV predict response to antiretroviral therapy. PMID:19627600
Are all subtypes created equal? The effectiveness of antiretroviral therapy against non-subtype B HIV-1. PMID:19331584
The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance. PMID:19304876
Prevalence of drug-resistant HIV-1 in rural areas of Hubei province in the People's Republic of China. PMID:19295329
The folding free-energy surface of HIV-1 protease: insights into the thermodynamic basis for resistance to inhibitors. PMID:19150359
Distinct resistance mutation and polymorphism acquisition in HIV-1 protease of subtypes B and F1 from children and adult patients under virological failure. PMID:18992847
Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores. PMID:18718947
Minority human immunodeficiency virus type 1 variants in antiretroviral-naive persons with reverse transcriptase codon 215 revertant mutations. PMID:18715933
Predicting drug resistance of the HIV-1 protease using molecular interaction energy components. PMID:18704937
An ontology-driven method for hierarchical mining of temporal patterns: application to HIV drug resistance research. PMID:18693909
HIV-1 drug resistance mutations: an updated framework for the second decade of HAART. PMID:18615118
Selecting anti-HIV therapies based on a variety of genomic and clinical factors. PMID:18586740
Consensus drug resistance mutations for epidemiological surveillance: basic principles and potential controversies. PMID:18575192
Genotypic susceptibility scores and HIV type 1 RNA responses in treatment-experienced subjects with HIV type 1 infection. PMID:18462083
Viral population estimation using pyrosequencing. PMID:18437230
Comparison of algorithms that interpret genotypic HIV-1 drug resistance to determine the prevalence of transmitted drug resistance. PMID:18427201
Proteochemometric modeling of HIV protease susceptibility. PMID:18402661
Analysis of correlated mutations in HIV-1 protease using spectral clustering. PMID:18375964
Stability analysis of mixtures of mutagenetic trees. PMID:18366778
Sequence editing by Apolipoprotein B RNA-editing catalytic component [corrected] and epidemiological surveillance of transmitted HIV-1 drug resistance. PMID:18356601
Conservation patterns of HIV-1 RT connection and RNase H domains: identification of new mutations in NRTI-treated patients. PMID:18335052
Molecular mechanisms of FIV infection. PMID:18289701
An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope. PMID:18039027
Prevalence of darunavir resistance-associated mutations: patterns of occurrence and association with past treatment. PMID:17955436
Mapping protease inhibitor resistance to human immunodeficiency virus type 1 sequence polymorphisms within patients. PMID:17913806
Distinguishing functional amino acid covariation from background linkage disequilibrium in HIV protease and reverse transcriptase. PMID:17726544
Differential drug resistance acquisition in HIV-1 of subtypes B and C. PMID:17710130
DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations. PMID:17576693
X-ray crystal structures of human immunodeficiency virus type 1 protease mutants complexed with atazanavir. PMID:17537865
Selection of mutations in the connection and RNase H domains of human immunodeficiency virus type 1 reverse transcriptase that increase resistance to 3'-azido-3'-dideoxythymidine. PMID:17507476
HIV-1 subtype B protease and reverse transcriptase amino acid covariation. PMID:17500586
Both human immunodeficiency virus cellular DNA sequencing and plasma RNA sequencing are useful for detection of drug resistance mutations in blood samples from antiretroviral-drug-naive patients. PMID:17442799
Adaptation to human populations is revealed by within-host polymorphisms in HIV-1 and hepatitis C virus. PMID:17397261
Ontology-driven mapping of temporal data in biomedical databases. PMID:17238664
Prediction of HIV mutation changes based on treatment history. PMID:17238630
N88D facilitates the co-occurrence of D30N and L90M and the development of multidrug resistance in HIV type 1 protease following nelfinavir treatment failure. PMID:17209774
HIV-1 protease and reverse transcriptase mutations for drug resistance surveillance. PMID:17197813
The HIV positive selection mutation database. PMID:17108357
Genotypic predictors of human immunodeficiency virus type 1 drug resistance. PMID:17065321
In vitro human immunodeficiency virus type 1 resistance selections with combinations of tenofovir and emtricitabine or abacavir and lamivudine. PMID:16982781
Rationale and uses of a public HIV drug-resistance database. PMID:16921473
Use of the l1 norm for selection of sparse parameter sets that accurately predict drug response phenotype from viral genetic sequences. PMID:16779091
Web resources for HIV type 1 genotypic-resistance test interpretation. PMID:16652319
DR_SEQAN: a PC/Windows-based software to evaluate drug resistance using human immunodeficiency virus type 1 genotypes. PMID:16524459
Inhibitory effects of archetypical nucleic acid ligands on the interactions of HIV-1 nucleocapsid protein with elements of Psi-RNA. PMID:16522643
SVARAP and aSVARAP: simple tools for quantitative analysis of nucleotide and amino acid variability and primer selection for clinical microbiology. PMID:16515699
HIV-1 pol mutation frequency by subtype and treatment experience: extension of the HIVseq program to seven non-B subtypes. PMID:16514293
Effectiveness of nonpeptide clinical inhibitor TMC-114 on HIV-1 protease with highly drug resistant mutations D30N, I50V, and L90M. PMID:16480273
HIV-1 Protease and reverse-transcriptase mutations: correlations with antiretroviral therapy in subtype B isolates and implications for drug-resistance surveillance. PMID:15995959
Insertions in the human immunodeficiency virus type 1 protease and reverse transcriptase genes: clinical impact and molecular mechanisms. PMID:15980322
Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity. PMID:15965030
Drug resistance and antiretroviral drug development. PMID:15845781
Impact of HIV-1 subtype and antiretroviral therapy on protease and reverse transcriptase genotype: results of a global collaboration. PMID:15839752
Comparison of the precision and sensitivity of the Antivirogram and PhenoSense HIV drug susceptibility assays. PMID:15764961
Immunologic pressure within class I-restricted cognate human immunodeficiency virus epitopes during highly active antiretroviral therapy. PMID:15731259
Molecular dynamics simulations of 14 HIV protease mutants in complexes with indinavir. PMID:15597206
Association of a novel human immunodeficiency virus type 1 protease substrate cleft mutation, L23I, with protease inhibitor therapy and in vitro drug resistance. PMID:15561868
Nucleotide specificity of HIV-1 reverse transcriptases with amino acid substitutions affecting Ala-114. PMID:15548134
Distribution of human immunodeficiency virus type 1 protease and reverse transcriptase mutation patterns in 4,183 persons undergoing genotypic resistance testing. PMID:15273130
Evolution of resistance to drugs in HIV-1-infected patients failing antiretroviral therapy. PMID:15238768
Mutation D30N is not preferentially selected by human immunodeficiency virus type 1 subtype C in the development of resistance to nelfinavir. PMID:15155216
Characterization of a subtype D human immunodeficiency virus type 1 isolate that was obtained from an untreated individual and that is highly resistant to nonnucleoside reverse transcriptase inhibitors. PMID:15113918
HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs. PMID:15044738
Positive selection detection in 40,000 human immunodeficiency virus (HIV) type 1 sequences automatically identifies drug resistance and positive fitness mutations in HIV protease and reverse transcriptase. PMID:15016892
Increased G-->A transition frequencies displayed by primer grip mutants of human immunodeficiency virus type 1 reverse transcriptase. PMID:14694133
Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes. PMID:12824435
Rationale and uses of a public HIV drug-resistance database PubMed citations: 171.

171 articles citing: Rationale and uses of a public HIV drug-resistance database

Viruses Previously Identified in Brazil as Belonging to HIV-1 CRF72_BF1 Represent Two Closely Related Circulating Recombinant Forms, One of Which, Designated CRF122_BF1, Is Also Circulating in Spain. PMID:35694315
HIV-1 Evolutionary Dynamics under Nonsuppressive Antiretroviral Therapy. PMID:35446121
Guide RNAs containing universal bases enable Cas9/Cas12a recognition of polymorphic sequences. PMID:35338140
Mortality from drug-resistant tuberculosis in high-burden countries comparing routine drug susceptibility testing with whole-genome sequencing: a multicentre cohort study. PMID:35252901
Limits to detecting epistasis in the fitness landscape of HIV. PMID:35041711
Prevalent subtypes and one-year outcomes of an HIV-cohort from an urban Philippine center. PMID:34941127
Rising rates of recent preexposure prophylaxis exposure among men having sex with men newly diagnosed with HIV: antiviral resistance patterns and treatment outcomes. PMID:34873084
Adherence, resistance, and viral suppression on dolutegravir in sub-Saharan Africa: implications for the TLD era. PMID:34848579
Participants Switching to Second-Line Antiretroviral Therapy with Susceptible Virus Display Inferior Adherence and Worse Outcomes: An Observational Analysis. PMID:34788110
Characterization of HIV-1 Epidemic in Kyrgyzstan. PMID:34721358
CODEHOP-Mediated PCR Improves HIV-1 Genotyping and Detection of Variants by MinION Sequencing. PMID:34668751
Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C. PMID:34491984
Intrapatient Development of Multi-Class Drug Resistance in an Individual Infected with HIV-1 CRF01_AE. PMID:34471364
SHARED: An International Collaboration to Unravel Hepatitis C Resistance. PMID:34452444
Revertant mutation V48G alters conformational dynamics of highly drug resistant HIV protease PRS17. PMID:34419931
Second-generation mother-to-child HIV transmission in South Africa is characterized by poor outcomes. PMID:34270488
RHIVDB: A Freely Accessible Database of HIV Amino Acid Sequences and Clinical Data of Infected Patients. PMID:34178036
HIV-1 viral blips are associated with repeated and increasingly high levels of cell-associated HIV-1 RNA transcriptional activity. PMID:34148986
HIV Protease: Historical Perspective and Current Research. PMID:34066370
Emergence of Human Immunodeficiency Virus-1 Drug Resistance During the 3-Month World Health Organization-Recommended Enhanced Adherence Counseling Period in the CART-1 Cohort Study. PMID:34046513
Longitudinal typing of molecular HIV clusters in a statewide epidemic. PMID:34033589
Fundamental Identifiability Limits in Molecular Epidemiology. PMID:34009339
Drug Design Strategies to Avoid Resistance in Direct-Acting Antivirals and Beyond. PMID:33410674
Prevalence of pretreatment HIV drug resistance in key populations: a systematic review and meta-analysis. PMID:33369131
Predominance of positive epistasis among drug resistance-associated mutations in HIV-1 protease. PMID:33085662
Virological failure, HIV-1 drug resistance, and early mortality in adults admitted to hospital in Malawi: an observational cohort study. PMID:32890497
Occurrence of the S230R integrase strand inhibitor mutation in a treatment-naïve individual case report. PMID:32629687
Epidemiological data analysis of viral quasispecies in the next-generation sequencing era. PMID:32568371
The HIV care continuum and HIV-1 drug resistance among female sex workers: a key population in Guinea-Bissau. PMID:32532294
Close-up: HIV/SIV intasome structures shed new light on integrase inhibitor binding and viral escape mechanisms. PMID:32506843
A near full-length HIV-1 genome from 1966 recovered from formalin-fixed paraffin-embedded tissue. PMID:32430331
Near point-of-care, point-mutation test to detect drug resistance in HIV-1: a validation study in a Mexican cohort. PMID:32205723
Current Trends in Diagnostics of Viral Infections of Unknown Etiology. PMID:32074965
Phylodynamic Analysis Complements Partner Services by Identifying Acute and Unreported HIV Transmission. PMID:32012700
Structural basis of second-generation HIV integrase inhibitor action and viral resistance. PMID:32001525
Highly drug-resistant HIV-1 protease reveals decreased intra-subunit interactions due to clusters of mutations. PMID:31920003
Characterizing Protein-Ligand Binding Using Atomistic Simulation and Machine Learning: Application to Drug Resistance in HIV-1 Protease. PMID:31877249
SNAPPy: A snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing. PMID:31768265
Moderately High Tenofovir Diphosphate in Dried Blood Spots Indicates Drug Resistance in Viremic Persons Living with HIV. PMID:31750768
Epistasis and entrenchment of drug resistance in HIV-1 subtype B. PMID:31591964
Raltegravir-Induced Adaptations of the HIV-1 Integrase: Analysis of Structure, Variability, and Mutation Co-occurrence. PMID:31551948
Prevalence and Correlates of Pre-Treatment HIV Drug Resistance among HIV-Infected Children in Ethiopia. PMID:31546824
Picomolar to Micromolar: Elucidating the Role of Distal Mutations in HIV-1 Protease in Conferring Drug Resistance. PMID:31361460
Mapping the drivers of within-host pathogen evolution using massive data sets. PMID:31289267
NNRTI-induced HIV-1 protease-mediated cytotoxicity induces rapid death of CD4 T cells during productive infection and latency reversal. PMID:31242909
A MiSeq-HyDRA platform for enhanced HIV drug resistance genotyping and surveillance. PMID:31222149
Highly Drug-Resistant HIV-1 Protease Mutant PRS17 Shows Enhanced Binding to Substrate Analogues. PMID:31172041
Role of co-expressed APOBEC3F and APOBEC3G in inducing HIV-1 drug resistance. PMID:31025011
Low rates of nucleoside reverse transcriptase inhibitor and nonnucleoside reverse transcriptase inhibitor drug resistance in Botswana. PMID:30946161
PERSIA for Direct Fluorescence Measurements of Transcription, Translation, and Enzyme Activity in Cell-Free Systems. PMID:30920800
Seroprevalence of HCV, HBV and HIV in two inner-city London emergency departments. PMID:30869036
Patterns of hepatitis B virus S gene escape mutants and reverse transcriptase mutations among genotype D isolates in Jordan. PMID:30867996
Constrained Mutational Sampling of Amino Acids in HIV-1 Protease Evolution. PMID:30721995
Prevalence and persistence of transmitted drug resistance mutations in the German HIV-1 Seroconverter Study Cohort. PMID:30650082
GLUE: a flexible software system for virus sequence data. PMID:30563445
Structural Adaptation of Darunavir Analogues against Primary Mutations in HIV-1 Protease. PMID:30543749
Antiretroviral resistance, genotypic characterization and origin of Human Immunodeficiency Virus among the infected wives of Intravenous drug users in Manipur. PMID:30315192
Towards Personalized Medicine: An Improved De Novo Assembly Procedure for Early Detection of Drug Resistant HIV Minor Quasispecies in Patient Samples. PMID:30310253
Insight into treatment of HIV infection from viral dynamics models. PMID:30129208
Sanger and Next Generation Sequencing Approaches to Evaluate HIV-1 Virus in Blood Compartments. PMID:30096879
HIV-1 proviral landscapes distinguish posttreatment controllers from noncontrollers. PMID:30024859
PharmGKB summary: atazanavir pathway, pharmacokinetics/pharmacodynamics. PMID:29517518
Mechanism of Darunavir (DRV)'s High Genetic Barrier to HIV-1 Resistance: A Key V32I Substitution in Protease Rarely Occurs, but Once It Occurs, It Predisposes HIV-1 To Develop DRV Resistance. PMID:29511083
Combination Therapy with Tenofovir Disoproxil Fumarate/Emtricitabine/Elvitegravir/Cobicistat Plus Darunavir Once Daily in Antiretroviral-Naive and Treatment-Experienced Patients: A Retrospective Review. PMID:29385867
Implication of First-Line Antiretroviral Therapy Choice on Second-Line Options. PMID:29255731
Analysis of the conformations of the HIV-1 protease from a large crystallographic data set. PMID:29124093
Prevalence of Pre-antiretroviral-Treatment Drug Resistance by Gender, Age, and Other Factors in HIV-Infected Individuals Initiating Therapy in Kenya, 2013-2014. PMID:29040633
Drug resistance patterns following pharmacy stock shortage in Nigerian Antiretroviral Treatment Program. PMID:29029637
Elucidating the Interdependence of Drug Resistance from Combinations of Mutations. PMID:28915040
Adaptive HIV-1 evolutionary trajectories are constrained by protein stability. PMID:28852572
HIV drug resistance against strand transfer integrase inhibitors. PMID:28583191
Using drug exposure for predicting drug resistance - A data-driven genotypic interpretation tool. PMID:28394945
Analysis of HIV Integrase Resistance in Black Men Who Have Sex with Men in the United States. PMID:28384058
Inference of Epistatic Effects Leading to Entrenchment and Drug Resistance in HIV-1 Protease. PMID:28369521
FunResDB-A web resource for genotypic susceptibility testing of Aspergillus fumigatus. PMID:28340175
Clinical and biological insights from viral genome sequencing. PMID:28090077
Quantitative evaluation of the antiretroviral efficacy of dolutegravir. PMID:27882352
Declining trend in transmitted drug resistance detected in a prospective cohort study of acute HIV infection in Bangkok, Thailand. PMID:27802846
The feasibility of incorporating Vpx into lentiviral gene therapy vectors. PMID:27790625
Genome-Wide Association Study of HIV Whole Genome Sequences Validated using Drug Resistance. PMID:27677172
A Triazinone Derivative Inhibits HIV-1 Replication by Interfering with Reverse Transcriptase Activity. PMID:27634404
Surveillance of HIV Transmitted Drug Resistance in Latin America and the Caribbean: A Systematic Review and Meta-Analysis. PMID:27355626
Treatment Outcomes and Resistance Patterns of Children and Adolescents on Second-Line Antiretroviral Therapy in Asia. PMID:27355415
3-Hydroxypyrimidine-2,4-dione-5-N-benzylcarboxamides Potently Inhibit HIV-1 Integrase and RNase H. PMID:27283261
Exploiting Genetic Interference for Antiviral Therapy. PMID:27149616
Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource. PMID:27087306
Polymorphic substitution E157Q in HIV-1 integrase increases R263K-mediated dolutegravir resistance and decreases DNA binding activity. PMID:27084918
Phenotypic Coreceptor Tropism in Perinatally HIV-infected Youth Failing Antiretroviral Therapy. PMID:27078121
Drug-Drug Interactions Based on Pharmacogenetic Profile between Highly Active Antiretroviral Therapy and Antiblastic Chemotherapy in Cancer Patients with HIV Infection. PMID:27065862
Clinical use of whole genome sequencing for Mycobacterium tuberculosis. PMID:27004841
Towards Better Precision Medicine: PacBio Single-Molecule Long Reads Resolve the Interpretation of HIV Drug Resistant Mutation Profiles at Explicit Quasispecies (Haplotype) Level. PMID:26949565
Genetic Determinants of Drug Resistance in Mycobacterium tuberculosis and Their Diagnostic Value. PMID:26910495
A Follow-Up of the Multicenter Collaborative Study on HIV-1 Drug Resistance and Tropism Testing Using 454 Ultra Deep Pyrosequencing. PMID:26756901
Quantifying Next Generation Sequencing Sample Pre-Processing Bias in HIV-1 Complete Genome Sequencing. PMID:26751471
Prevalence of K65R in patients treated with tenofovir disoproxil fumarate: recommendations based on the Frankfurt HIV Cohort Study Resistance Database (FHCS-RD). PMID:26746222
The HIV Treatment Gap: Estimates of the Financial Resources Needed versus Available for Scale-Up of Antiretroviral Therapy in 97 Countries from 2015 to 2020. PMID:26599990
HIV Drug Resistance Surveillance in Honduras after a Decade of Widespread Antiretroviral Therapy. PMID:26558396
Collaborative Effort for a Centralized Worldwide Tuberculosis Relational Sequencing Data Platform. PMID:26409275
Dolutegravir-Selected HIV-1 Containing the N155H and R263K Resistance Substitutions Does Not Acquire Additional Compensatory Mutations under Drug Pressure That Lead to Higher-Level Resistance and Increased Replicative Capacity. PMID:26246578
The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies. PMID:26228431
Genetic Consequences of Antiviral Therapy on HIV-1. PMID:26170895
Comparison of genotypic and virtual phenotypic drug resistance interpretations with laboratory-based phenotypes among CRF01_AE and subtype B HIV-infected individuals. PMID:26147742
Deep sequencing of protease inhibitor resistant HIV patient isolates reveals patterns of correlated mutations in Gag and protease. PMID:25894830
A Functional Interplay between Human Immunodeficiency Virus Type 1 Protease Residues 77 and 93 Involved in Differential Regulation of Precursor Autoprocessing and Mature Protease Activity. PMID:25893662
A microbiological revolution meets an ancient disease: improving the management of tuberculosis with genomics. PMID:25810419
Drug-resistance mechanisms and tuberculosis drugs. PMID:25706840
Lopinavir/Ritonavir Monotherapy as Second-line Antiretroviral Treatment in Resource-Limited Settings: Week 104 Analysis of AIDS Clinical Trials Group (ACTG) A5230. PMID:25694653
Clinical application of whole-genome sequencing to inform treatment for multidrug-resistant tuberculosis cases. PMID:25673793
Integrated analysis of residue coevolution and protein structures capture key protein sectors in HIV-1 proteins. PMID:25671429
Dolutegravir resistance mutation R263K cannot coexist in combination with many classical integrase inhibitor resistance substitutions. PMID:25653436
Cross-clade simultaneous HIV drug resistance genotyping for reverse transcriptase, protease, and integrase inhibitor mutations by Illumina MiSeq. PMID:25533166
Unraveling the web of viroinformatics: computational tools and databases in virus research. PMID:25428870
The lysine 65 residue in HIV-1 reverse transcriptase function and in nucleoside analog drug resistance. PMID:25341667
Drug resistance in non-B subtype HIV-1: impact of HIV-1 reverse transcriptase inhibitors. PMID:25254383
Predicting virus mutations through statistical relational learning. PMID:25238967
Deep sequencing: becoming a critical tool in clinical virology. PMID:24998424
Prevalence and virologic consequences of transmitted HIV-1 drug resistance in Uganda. PMID:24960249
The Cluster Elastic Net for High-Dimensional Regression With Unknown Variable Grouping. PMID:24817772
The contribution of viral genotype to plasma viral set-point in HIV infection. PMID:24789308
Exposure to MIV-150 from a high-dose intravaginal ring results in limited emergence of drug resistance mutations in SHIV-RT infected rhesus macaques. PMID:24586674
Next-Generation Sequencing to Help Monitor Patients Infected with HIV: Ready for Clinical Use? PMID:24585216
Residual viremia in an RT-SHIV rhesus macaque HAART model marked by the presence of a predominant plasma clone and a lack of viral evolution. PMID:24505452
HIV-1 Protease and Substrate Coevolution Validates the Substrate Envelope As the Substrate Recognition Pattern. PMID:24348205
The Need for Development of New HIV-1 Reverse Transcriptase and Integrase Inhibitors in the Aftermath of Antiviral Drug Resistance. PMID:24278679
Selection of RNAi-based inhibitors for anti-HIV gene therapy. PMID:24175213
Potential elucidation of a novel CTL epitope in HIV-1 protease by the protease inhibitor resistance mutation L90M. PMID:24015196
Use of nucleoside reverse transcriptase inhibitor-only regimens in HIV-infected children and adolescents. PMID:24008749
The prevalence of transmitted resistance to first-generation non-nucleoside reverse transcriptase inhibitors and its potential economic impact in HIV-infected patients. PMID:23991151
HIV-1 Genetic Variability and Clinical Implications. PMID:23844315
Elevated hypermutation levels in HIV-1 natural viral suppressors. PMID:23791226
SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments. PMID:23761454
Selection of drug-resistant feline immunodeficiency virus (FIV) encoding FIV/HIV chimeric protease in the presence of HIV-specific protease inhibitors. PMID:23720716
Genomics and outbreak investigation: from sequence to consequence. PMID:23673226
L74V increases the reverse transcriptase content of HIV-1 virions with non-nucleoside reverse transcriptase drug-resistant mutations L100I+K103N and K101E+G190S, which results in increased fitness. PMID:23535575
Significantly improved HIV inhibitor efficacy prediction employing proteochemometric models generated from antivirogram data. PMID:23436985
Comprehensive in vitro analysis of simian retrovirus type 4 susceptibility to antiretroviral agents. PMID:23365453
Prevalent polymorphisms in wild-type HIV-1 integrase are unlikely to engender drug resistance to dolutegravir (S/GSK1349572). PMID:23295935
HIV Drug Resistance and the Advent of Integrase Inhibitors. PMID:23180144
Rapid whole-genome sequencing for investigation of a suspected tuberculosis outbreak. PMID:23175259
Timeliness of clinic attendance is a good predictor of virological response and resistance to antiretroviral drugs in HIV-infected patients. PMID:23145079
In vivo anti-HIV activity of the heparin-activated serine protease inhibitor antithrombin III encapsulated in lymph-targeting immunoliposomes. PMID:23133620
Comparison of predicted susceptibility between genotype and virtual phenotype HIV drug resistance interpretation systems among treatment-naive HIV-infected patients in Asia: TASER-M cohort analysis. PMID:23095645
Prolonged and substantial discordance in prevalence of raltegravir-resistant HIV-1 in plasma versus PBMC samples revealed by 454 "deep" sequencing. PMID:23049972
Prevalence of and viral outcomes associated with primary HIV-1 drug resistance. PMID:23049668
What do molecules do when we are not looking? State sequence analysis for stochastic chemical systems. PMID:22977098
Maraviroc observational study: the impact of expanded resistance testing and clinical considerations for antiretroviral regimen selection in treatment-experienced patients. PMID:22881368
Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PMID:22876174
Development of elvitegravir resistance and linkage of integrase inhibitor mutations with protease and reverse transcriptase resistance mutations. PMID:22815755
A combined screening platform for HIV treatment failure and resistance. PMID:22563383
BF integrase genes of HIV-1 circulating in São Paulo, Brazil, with a recurrent recombination region. PMID:22485165
Lopinavir/ritonavir monotherapy after virologic failure of first-line antiretroviral therapy in resource-limited settings. PMID:22441252
Factors limiting the transmission of HIV mutations conferring drug resistance: fitness costs and genetic bottlenecks. PMID:22432052
Study of genotypic and phenotypic HIV-1 dynamics of integrase mutations during raltegravir treatment: a refined analysis by ultra-deep 454 pyrosequencing. PMID:22238474
Optimal antiviral switching to minimize resistance risk in HIV therapy. PMID:22073250
Directed HIV-1 evolution of protease inhibitor resistance by second-generation short hairpin RNAs. PMID:22064528
Role of HIV Subtype Diversity in the Development of Resistance to Antiviral Drugs. PMID:21994627
The higher barrier of darunavir and tipranavir resistance for HIV-1 protease. PMID:21871444
Nonnucleoside reverse transcriptase inhibitor-resistant HIV is stimulated by efavirenz during early stages of infection. PMID:21835788
High-throughput identification of genetic interactions in HIV-1. PMID:21522176
Dose-response curve slope is a missing dimension in the analysis of HIV-1 drug resistance. PMID:21502494
A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase. PMID:21441930
Human immunodeficiency virus type 1 resistance or cross-resistance to nonnucleoside reverse transcriptase inhibitors currently under development as microbicides. PMID:21282453
Development of a low bias method for characterizing viral populations using next generation sequencing technology. PMID:21042592
Computational analysis of HIV-1 protease protein binding pockets. PMID:20925403
Co-lethality studied as an asset against viral drug escape: the HIV protease case. PMID:20565756
Effects of the V82A and I54V mutations on the dynamics and ligand binding properties of HIV-1 protease. PMID:20195662
Non-nucleoside reverse transcriptase inhibitor outcomes among combination antiretroviral therapy-treated adults in Botswana. PMID:20023437
Prevalence of drug-resistant HIV-1 in rural areas of Hubei province in the People's Republic of China. PMID:19295329
Identification and recovery of minor HIV-1 variants using the heteroduplex tracking assay and biotinylated probes. PMID:18948297
Directly administered antiretroviral therapy for HIV-infected drug users does not have an impact on antiretroviral resistance: results from a randomized controlled trial. PMID:18193497
Comprehensive viral oligonucleotide probe design using conserved protein regions. PMID:18079152
http://dx.doi.org/10.1101/866715

Tags:

Tags
More detailed information about this field from each metasource.

phenotype
metasource: Fairsharing.org
version: None

treatment
metasource: Fairsharing.org
version: None

protein sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

databases of individual protein families
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

viral genome databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

genetic variation
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:43.648520

immunology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:43.648520

preclinical and clinical studies
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:43.648520

mapping
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:43.648520

sequencing
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:43.648520

phenotype treatment protein sequence protein family genomics viral genome genetic variation immunology preclinical and clinical studies mapping sequencing

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