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CLAE: A High-Fidelity Nanopore Sequencing Strategy for Read-Level Viral Variant Detection and Environmental RNA Virus
Hannah Yu1,2,3, Sarah Golconda1,2,3, Ga-Eun Lee1,2,3,4
1Center for Retrovirus Research, The Ohio State University, Columbus, OH, 43210, USA.
Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
|September 11, 2025
Summary
Circular- and Linear-Amplicon-Mediated Error Correction (CLAE) enhances Oxford Nanopore Technologies sequencing. This method improves accuracy and yield for long-read sequencing, enabling precise pathogen detection and genome recovery.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- High-fidelity long-read sequencing is crucial for microbial and pathogen profiling.
- Oxford Nanopore Technologies (ONT) offers portable, real-time sequencing but faces challenges in accuracy, read length bias, and throughput.
Purpose of the Study:
- To introduce Circular- and Linear-Amplicon-Mediated Error Correction (CLAE) to overcome limitations of current ONT sequencing.
- To enhance Nanopore sequencing yield and accuracy for long DNA templates.
Main Methods:
- CLAE integrates hairpin ligation, pre-circling, single-stranded DNA linearization, and nickase-based debranching.
- It significantly improves rolling-circle amplification (RCA) efficiency for long DNA templates.
Main Results:
- CLAE achieves Q30-level accuracy in up to 27% of RCA reads.
- It demonstrates throughput exceeding 800 Mb per 100 pores with an N50 of ≈15 Kb.
- CLAE successfully resolved SARS-CoV-2 quasi-species and recovered novel RNA virus genomes.
Conclusions:
- CLAE establishes a versatile, field-compatible platform for high-fidelity viral genome sequencing.
- It broadens ONT's utility in metaviromics, epidemiology, and environmental surveillance.
- CLAE enables precise variant detection and corrects short-read misassemblies.
