Whole genome sequencing (WGS) of SARS-CoV-2 is performed for surveillance of variants of concern (VOCs). Oxford Nanopore Technology (ONT) is preferred for field deployment compared to Illumina. The key advantage of ONT for outbreak genomic surveillance is:
- A Higher base-calling accuracy (>99.9% per base) compared to all short-read platforms
- B Lower cost per base making it the most economical platform for high-throughput surveillance
- C Real-time long-read sequencing with faster time-to-result (4–6 hours from library prep) and portable MinION device deployable in field laboratories ✓
- D Ability to sequence RNA directly without reverse transcription, eliminating cDNA synthesis errors
Explanation
Oxford Nanopore Technology (ONT) MinION sequencer uses nanopore-based direct sequencing of long DNA/cDNA reads. Its key advantages for outbreak surveillance are: (1) portability — the MinION device is USB-powered, weighs <100g, enabling field deployment; (2) speed — sequencing begins in real-time, with first results in 4–6 hours; (3) long reads (>10 kb) enabling full-genome assembly with fewer amplicons. Limitations include lower per-base accuracy (~97–98%) compared to Illumina (~99.9%). Illumina (short-read, ~150 bp) has higher accuracy and throughput but requires >24 hours and fixed infrastructure. For SARS-CoV-2 VOC detection (spike gene mutations), ONT ARTIC protocol using multiplexed tiling PCR amplicons followed by nanopore sequencing was extensively used in COVID-19 genomic surveillance.
Reference: Ananthanarayan & Paniker's Textbook of Microbiology, 11th ed.
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Written and medically reviewed by the StethoPrep medical team.