{"doi":"10.1002/advs.202505978","title":"CLAE: A High‐Fidelity Nanopore Sequencing Strategy for Read‐Level Viral Variant Detection and Environmental RNA Virus Discovery","abstract":"High-fidelity (HF) long-read sequencing enables accurate profiling of microorganisms and pathogens at single-molecule resolution. However, current Oxford Nanopore Technologies (ONT)-a revolutionary platform offering real-time, portable sequencing at relatively low instrumental cost-suffer from severe read-length bias, limited accuracy (often <Q20), and low throughput. Here, Circular- and Linear-Amplicon-Mediated Error Correction (CLAE) is introduced, a biochemical and computational approach that addresses these limitations by integrating hairpin ligation, pre-circling, single-stranded DNA linearization, and targeted nickase-based debranching. CLAE significantly enhances rolling-circle amplification (RCA) efficiency for long DNA templates, markedly improving Nanopore sequencing yield and accuracy. CLAE achieves Q30-level accuracy in up to 27% of RCA reads, throughput exceeding 800 Mb per 100 pores, and an N50 of ≈15 Kb (bacterial genome). Moreover, its bidirectional subreads and high throughput substantially boost accuracy without compromising read length. CLAE is validated by resolving SARS-CoV-2 quasi-species from community wastewater and recovering novel, full-length RNA virus genomes from marine samples. CLAE enables precise variant detection in complex samples and corrects short-read misassemblies, significantly broadening ONT's utility in metaviromics, epidemiology, and environmental surveillance. Thus, CLAE establishes a versatile, field-compatible platform for high-fidelity viral genome sequencing in targeted and agnostic contexts.","journal":"Advanced Science","year":2025,"id":524413,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":4,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9565,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1005567,"name":"Sarah Golconda","orcid":"0000-0001-6398-7285","position":1,"is_corresponding":false},{"id":1397929,"name":"Ga‐Eun Lee","orcid":"0000-0002-5774-5850","position":2,"is_corresponding":false},{"id":1398440,"name":"Dantong Xue","orcid":null,"position":3,"is_corresponding":false},{"id":841587,"name":"Guillermo Domínguez‐Huerta","orcid":"0000-0001-9799-6139","position":4,"is_corresponding":false},{"id":841586,"name":"James M. Wainaina","orcid":"0000-0002-7233-4793","position":5,"is_corresponding":false},{"id":106768,"name":"Benjamin Bolduc","orcid":"0000-0003-2420-0755","position":6,"is_corresponding":false},{"id":1397930,"name":"Shashanka Murthy","orcid":"0000-0001-9690-9320","position":7,"is_corresponding":false},{"id":973927,"name":"Shihyoung Kim","orcid":"0000-0002-8846-2853","position":8,"is_corresponding":false},{"id":616291,"name":"Seth A. Faith","orcid":"0000-0002-0441-9859","position":9,"is_corresponding":false},{"id":591988,"name":"Ji‐Young Lee","orcid":"0000-0002-3301-6434","position":11,"is_corresponding":false},{"id":296503,"name":"Michael Oglesbee","orcid":null,"position":12,"is_corresponding":false},{"id":106774,"name":"Matthew B. Sullivan","orcid":"0000-0001-8398-8234","position":14,"is_corresponding":false},{"id":585611,"name":"Sanggu Kim","orcid":"0000-0003-1228-6168","position":15,"is_corresponding":false},{"id":973928,"name":"Hannah Yu","orcid":"0000-0001-5354-7622","position":0,"is_corresponding":true}],"reference_count":91,"raw_metadata":null,"created_at":"2026-07-19T02:50:12.083054Z","pmid":"40936099","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":[]}