ArticleNucleic acids research2009
A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 94 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
94 citing papers in PubMed.
- Prevalence and Phylogenetic Characterization of Hepatitis C Virus Among Indian Men Who Have Sex With Men: Limited Evidence for Sexual Transmission.The Journal of infectious diseases · 2020Trial
- Baseline Polymorphisms and Emergence of Drug Resistance in the NS3/4A Protease of Hepatitis C Virus Genotype 1 following Treatment with Faldaprevir and Pegylated Interferon Alpha 2a/Ribavirin in Phase 2 and Phase 3 Studies.Antimicrobial agents and chemotherapy · 2015Trial
- Trial
- Detection of transmission clusters of HIV-1 subtype C over a 21-year period in Cape Town, South Africa.PloS one · 2014Trial
- CAMELLIA: an alignment-free pipeline integratingNAR genomics and bioinformatics · 2026Article
- HIV-1 prevalence, drug resistance, and associated factors in the urban Ethiopian population.Scientific reports · 2025Article
- VITALdb: to select the best viroinformatics tools for a desired virus or application.Briefings in bioinformatics · 2025Article
- Sexual Networks and Behavioral Characteristics of HIV-Positive Male Military Members, Female Sex Workers, and Male Civilians.AIDS and behavior · 2025Article
- A new lineage nomenclature to aid genomic surveillance of dengue virus.PLoS biology · 2024Article
- A new lineage nomenclature to aid genomic surveillance of dengue virus.medRxiv : the preprint server for health sciences · 2024Article
- Genome-wide diversity of Zika virus: Exploring spatio-temporal dynamics to guide a new nomenclature proposal.Virus evolution · 2022Article
- Explainable deep neural networks for novel viral genome prediction.Applied intelligence (Dordrecht, Netherlands) · 2022Article
- WalkIm: Compact image-based encoding for high-performance classification of biological sequences using simple tuning-free CNNs.PloS one · 2022Article
- A Tale of Three Recent Pandemics: Influenza, HIV and SARS-CoV-2.Frontiers in microbiology · 2022Review
- Molecular Epidemiology of HIV-1 Infected Migrants Followed up in Portugal: Trends between 2001-2017.Viruses · 2020Article
- Computational MHC-I epitope predictor identifies 95% of experimentally mapped HIV-1 clade A and D epitopes in a Ugandan cohort.BMC infectious diseases · 2020Article
- A cross-sectional study to characterize local HIV-1 dynamics in Washington, DC using next-generation sequencing.Scientific reports · 2020Article
- Global and regional dispersal patterns of hepatitis B virus genotype E from and in Africa: A full-genome molecular analysis.PloS one · 2020Article
- 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.Antimicrobial agents and chemotherapy · 2019Article
- A MiSeq-HyDRA platform for enhanced HIV drug resistance genotyping and surveillance.Scientific reports · 2019Article
34 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
Human immunodeficiency virus type-1 (HIV-1), hepatitis B and C and other rapidly evolving viruses are characterized by extremely high levels of genetic diversity. To facilitate diagnosis and the development of prevention and treatment strategies that efficiently target the diversity of these viruses, and other pathogens such as human T-lymphotropic virus type-1 (HTLV-1), human herpes virus type-8 (HHV8) and human papillomavirus (HPV), we developed a rapid high-throughput-genotyping system. The method involves the alignment of a query sequence with a carefully selected set of pre-defined reference strains, followed by phylogenetic analysis of multiple overlapping segments of the alignment using a sliding window. Each segment of the query sequence is assigned the genotype and sub-genotype of the reference strain with the highest bootstrap (>70%) and bootscanning (>90%) scores. Results from all windows are combined and displayed graphically using color-coded genotypes. The new Virus-Genotyping Tools provide accurate classification of recombinant and non-recombinant viruses and are currently being assessed for their diagnostic utility. They have incorporated into several HIV drug resistance algorithms including the Stanford (http://hivdb.stanford.edu) and two European databases (http://www.umcutrecht.nl/subsite/spread-programme/ and http://www.hivrdb.org.uk/) and have been successfully used to genotype a large number of sequences in these and other databases. The tools are a PHP/JAVA web application and are freely accessible on a number of servers including: http://bioafrica.mrc.ac.za/rega-genotype/html/, http://lasp.cpqgm.fiocruz.br/virus-genotype/html/, http://jose.med.kuleuven.be/genotypetool/html/.
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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.