ArticleAIDS research and human retroviruses2012
Sequence quality analysis tool for HIV type 1 protease and reverse transcriptase.
Article in AIDS research and human retroviruses, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 36 citations in OpenAlex.
- Integrating Partner Services and Molecular Epidemiology Data to Enhance HIV Transmission Disruption in Rhode Island.Open forum infectious diseases · 2025Article
- HIV drug resistance, early treatment outcomes and impact of guidelines compliance after protease inhibitor-based second-line failure in a dedicated resistance clinic in western Kenya: a retrospective cohort study.Journal of the International AIDS Society · 2025Article
- Dynamics of clustering rates in the Rhode Island HIV-1 epidemic.AIDS (London, England) · 2025Article
- Acquired Human Immunodeficiency Virus Type 1 Drug Resistance in Rhode Island, USA, 2004-2021.The Journal of infectious diseases · 2024Article
- Prospective Evaluation of Routine Statewide Integration of Molecular Epidemiology and Contact Tracing to Disrupt Human Immunodeficiency Virus Transmission.Open forum infectious diseases · 2024Article
- Article
- Added Value of Next Generation over Sanger Sequencing in Kenyan Youth with Extensive HIV-1 Drug Resistance.Microbiology spectrum · 2022Article
- Statewide Longitudinal Trends in Transmitted HIV-1 Drug Resistance in Rhode Island, USA.Open forum infectious diseases · 2022Article
- Longitudinal typing of molecular HIV clusters in a statewide epidemic.AIDS (London, England) · 2021Article
- Next Generation Sequencing for HIV-1 Drug Resistance Testing-A Special Issue Walkthrough.Viruses · 2021Article
- HIV-1 second-line failure and drug resistance at high-level and low-level viremia in Western Kenya.AIDS (London, England) · 2018Article
- Accumulated pre-switch resistance to more recently introduced one-pill-once-a-day antiretroviral regimens impacts HIV-1 virologic outcome.Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2018Article
- High discordance in blood and genital tract HIV-1 drug resistance in Indian women failing first-line therapy.The Journal of antimicrobial chemotherapy · 2018Article
- Etravirine and Rilpivirine Drug Resistance Among HIV-1 Subtype C Infected Children Failing Non-Nucleoside Reverse Transcriptase Inhibitor-Based Regimens in South India.AIDS research and human retroviruses · 2017Article
- Observational
- Global Comparison of Drug Resistance Mutations After First-Line Antiretroviral Therapy Across Human Immunodeficiency Virus-1 Subtypes.Open forum infectious diseases · 2016Article
- Molecular Epidemiology and Transmission Dynamics of Recent and Long-Term HIV-1 Infections in Rural Western Kenya.PloS one · 2016Article
- Treatment failure and drug resistance in HIV-positive patients on tenofovir-based first-line antiretroviral therapy in western Kenya.Journal of the International AIDS Society · 2016Article
- Phylogenetic Investigation of a Statewide HIV-1 Epidemic Reveals Ongoing and Active Transmission Networks Among Men Who Have Sex With Men.Journal of acquired immune deficiency syndromes (1999) · 2015Article
- HIV drug resistance testing by high-multiplex "wide" sequencing on the MiSeq instrument.Antimicrobial agents and chemotherapy · 2015Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
Access to antiretroviral therapy is increasing globally and drug resistance evolution is anticipated. Currently, protease (PR) and reverse transcriptase (RT) sequence generation is increasing, including the use of in-house sequencing assays, and quality assessment prior to sequence analysis is essential. We created a computational HIV PR/RT Sequence Quality Analysis Tool (SQUAT) that runs in the R statistical environment. Sequence quality thresholds are calculated from a large dataset (46,802 PR and 44,432 RT sequences) from the published literature ( http://hivdb.Stanford.edu ). Nucleic acid sequences are read into SQUAT, identified, aligned, and translated. Nucleic acid sequences are flagged if with >five 1-2-base insertions; >one 3-base insertion; >one deletion; >six PR or >18 RT ambiguous bases; >three consecutive PR or >four RT nucleic acid mutations; >zero stop codons; >three PR or >six RT ambiguous amino acids; >three consecutive PR or >four RT amino acid mutations; >zero unique amino acids; or <0.5% or >15% genetic distance from another submitted sequence. Thresholds are user modifiable. SQUAT output includes a summary report with detailed comments for troubleshooting of flagged sequences, histograms of pairwise genetic distances, neighbor joining phylogenetic trees, and aligned nucleic and amino acid sequences. SQUAT is a stand-alone, free, web-independent tool to ensure use of high-quality HIV PR/RT sequences in interpretation and reporting of drug resistance, while increasing awareness and expertise and facilitating troubleshooting of potentially problematic sequences.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.