{"doi":"10.1016/j.jviromet.2015.04.022","title":"Performance assessment of the Illumina massively parallel sequencing platform for deep sequencing analysis of viral minority variants","abstract":null,"journal":"Journal of Virological Methods","year":2015,"id":598322,"datarank":0.519860385419959,"base_score":3.4657359027997265,"endowment":3.4657359027997265,"self_citation_contribution":0.519860385419959,"citation_network_contribution":0.0,"self_endowment_contribution":0.519860385419959,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":31,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1533073,"name":"Peter Verhasselt","orcid":null,"position":1,"is_corresponding":false},{"id":1533074,"name":"Joke Reumers","orcid":null,"position":2,"is_corresponding":false},{"id":1533075,"name":"Bie M.P. Verbist","orcid":null,"position":3,"is_corresponding":false},{"id":1016631,"name":"Bart Maes","orcid":"0000-0001-5084-5130","position":4,"is_corresponding":false},{"id":540798,"name":"Jeroen Aerssens","orcid":"0000-0002-9254-4800","position":5,"is_corresponding":false},{"id":1018195,"name":"Kim Thys","orcid":"0000-0002-0400-6915","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Performance assessment of the Illumina massively parallel sequencing platform for deep sequencing analysis of viral minority variants","abstract":"Massively parallel sequencing (MPS) technology has opened new avenues to study viral dynamics and treatment-induced resistance mechanisms of infections such as human immunodeficiency virus (HIV) and hepatitis C virus (HCV). Whereas the Roche/454 platform has been used widely for the detection of low-frequent drug resistant variants, more recently developed short-read MPS technologies have the advantage of delivering a higher sequencing depth at a lower cost per sequenced base. This study assesses the performance characteristics of Illumina MPS technology for the characterization of genetic variability in viral populations by deep sequencing. The reported results from MPS experiments comprising HIV and HCV plasmids demonstrate that a 0.5-1% lower limit of detection can be achieved readily with Illumina MPS while retaining good accuracy also at low frequencies. Deep sequencing of a set of clinical samples (12 HIV and 9 HCV patients), designed at a similar budget for both MPS platforms, reveals a comparable lower limit of detection for Illumina and Roche/454. Finally, this study shows the possibility to apply Illumina's paired-end sequencing as a strategy to assess linkage between different mutations identified in individual viral subspecies. These results support the use of Illumina as another MPS platform of choice for deep sequencing of viral minority species.","is_dataset_classified":null,"base_score":3.4657359027997265,"endowment":3.4657359027997265,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"25917877","pmcid":null,"openalex_id":"https://openalex.org/W1994911328","authors":[],"funders":[],"total_grants":0,"fwci":2.962,"citation_percentile":0.91534203,"influential_citations":0,"citation_trend":[{"year":2015,"count":2},{"year":2016,"count":5},{"year":2017,"count":7},{"year":2018,"count":5},{"year":2019,"count":3},{"year":2020,"count":1},{"year":2021,"count":1},{"year":2022,"count":2},{"year":2023,"count":2},{"year":2024,"count":3}],"oa_status":"closed","license":"https://www.elsevier.com/tdm/userlicense/1.0/","oa_locations":[{"url":"https://api.elsevier.com/content/article/PII:S0166093415001664?httpAccept=text/xml","host_type":"publisher"},{"url":"https://api.elsevier.com/content/article/PII:S0166093415001664?httpAccept=text/plain","host_type":"publisher"},{"url":"https://doi.org/10.1016/j.jviromet.2015.04.022","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/25917877","host_type":"repository"}],"fields_of_study":["Hepatitis C virus research","HIV Research and Treatment","Bacteriophages and microbial interactions","Genetic Variation","HIV","HIV Infections","Hepacivirus","Hepatitis C","High-Throughput Nucleotide Sequencing","Humans","Virology"],"mesh_terms":["Hepatitis C","HIV","Humans","Genetic Variation","Virology","HIV Infections","Hepacivirus","High-Throughput Nucleotide Sequencing"],"keywords":["Illumina dye sequencing","Deep sequencing","Biology","Massive parallel sequencing","DNA sequencing","Sanger sequencing","Virology","Computational biology","Genetics","Genome","Gene","HCV","HIV","Illumina","Massively Parallel Sequencing","Viral Minority"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Good health and well-being"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-28T15:30:21.392792Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}