ArticleNucleic acids research2014
COMET: adaptive context-based modeling for ultrafast HIV-1 subtype identification.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 264 papers, 1 of them a synthesis that pooled it.
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Who cites it
264 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Expanded Spectrum of Antiretroviral-Selected Mutations in Human Immunodeficiency Virus Type 2.The Journal of infectious diseases · 2020Pooled it
- Detection of HIV-1 Transmission Clusters from Dried Blood Spots within a Universal Test-and-Treat Trial in East Africa.Viruses · 2022Trial
- Patterns of pretreatment drug resistance mutations of very early diagnosed and treated infants in Botswana.AIDS (London, England) · 2021Trial
- Molecular footprints of a traveling epidemic: CRF01_AE-cluster 5 (01_C5) might spread across Northeast and South China via middle-aged MSM.Emerging microbes & infections · 2026Article
- Genetic Subtypes, Pretreatment Drug Resistance, and Associated Factors Among Individuals Newly Diagnosed With HIV-1 in Zhejiang Province From 2022 to 2024: Cross-Sectional Study.JMIR public health and surveillance · 2026Article
- Untangling the effects of within-host and between-host natural selection in viruses with applications to evolution of HIV-1 co-receptor usage.Journal of the Royal Society, Interface · 2026Article
- HIV drug resistance and treatment success in the Republic of Congo: Implications for optimized treatment.HIV medicine · 2026Article
- HIV-1 integrase inhibitor resistance in viraemic-treated individuals and baseline capsid diversity relevant to future lenacapavir therapy.The Journal of antimicrobial chemotherapy · 2026Article
- Article
- Nationwide Molecular Epidemiology of HIV-1 in Uruguay (2007-2021): Lineage Diversity, BF1 Recombinant Complexity and Epidemiological Patterns.Journal of the International AIDS Society · 2026Article
- HIV-1 virome profiling using HIV-PULSE to guide therapeutic and curative interventions.EBioMedicine · 2026Article
- Emerging Trends in HIV-1 Sub-Subtype A6 in Belgium: Transmission Dynamics, Drug Resistance, and Subtyping Tool Evaluation.Viruses · 2026Article
- Development of a Subsequence Correlation Coefficient Feature Vector Method for High-Resolution HIV-1 Subtype Classification - China, 2004-2022.China CDC weekly · 2026Article
- HIV-1 subtype diversity trends in a Northern California cohort.AIDS (London, England) · 2026Article
- Article
- Novel integrase mutations linked to genotypic DTG resistance in African non-B HIV-1 strains: the DTG RESIST study.The Journal of antimicrobial chemotherapy · 2026Article
- Geographical and temporal trends of HIV-1 subtypes and drug resistance in China: a nationwide study over two decades (2003-2024).The Journal of general virology · 2026Article
- Detection of HIV-1 Resistance Mutations to Antiretroviral Therapy and Cell Tropism in Russian Patients Using Next-Generation Sequencing.Pathogens (Basel, Switzerland) · 2026Article
- Real-world Prevalence of Nonintegrase INSTI Resistance-Associated Mutations and Virological Outcomes in People Who Have Recently Acquired HIV-1 in the United Kingdom.The Journal of infectious diseases · 2026Article
- Evaluating HIV-1 Transmitted Drug Resistance and Clustering in Newly Diagnosed Patients in Romania (2019-2022).Viruses · 2026Article
204 more citing papers are in PubMed but not listed here.
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5 authors.
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Abstract
Viral sequence classification has wide applications in clinical, epidemiological, structural and functional categorization studies. Most existing approaches rely on an initial alignment step followed by classification based on phylogenetic or statistical algorithms. Here we present an ultrafast alignment-free subtyping tool for human immunodeficiency virus type one (HIV-1) adapted from Prediction by Partial Matching compression. This tool, named COMET, was compared to the widely used phylogeny-based REGA and SCUEAL tools using synthetic and clinical HIV data sets (1,090,698 and 10,625 sequences, respectively). COMET's sensitivity and specificity were comparable to or higher than the two other subtyping tools on both data sets for known subtypes. COMET also excelled in detecting and identifying new recombinant forms, a frequent feature of the HIV epidemic. Runtime comparisons showed that COMET was almost as fast as USEARCH. This study demonstrates the advantages of alignment-free classification of viral sequences, which feature high rates of variation, recombination and insertions/deletions. COMET is free to use via an online interface.
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