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SRX9471388: Nanopore sequencing of SARS-CoV-2 patient isolate
1 OXFORD_NANOPORE (PromethION) run: 95,719 spots, 107M bases, 80.2Mb downloads

Design: PCR amplification of reverse-transcribed SARS-CoV-2 viral RNA with 14 x 2.5kb amplicons, followed by nanopore sequencing
Submitted by: The Garvan Institute
Study: Severe acute respiratory syndrome coronavirus 2 Raw sequence reads
show Abstracthide Abstract
Viral whole-genome sequencing (WGS) provides critical insight into the transmission and evolution of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Long-read sequencing devices from Oxford Nanopore Technologies (ONT) promise significant improvements in turnaround time, portability and cost, compared to established short-read sequencing platforms for viral WGS (e.g., Illumina). However, adoption of ONT sequencing for SARS-CoV-2 surveillance has been limited due to common concerns around sequencing accuracy. To address this, we performed viral WGS with ONT and Illumina platforms on 157 matched SARS-CoV-2-positive patient specimens and synthetic RNA controls, enabling rigorous evaluation of analytical performance. Despite the elevated error rates observed in ONT sequencing reads, highly accurate consensus-level sequence determination was achieved, with single nucleotide variants (SNVs) detected at >99% sensitivity and >99% precision above a minimum ~60-fold coverage depth, thereby ensuring suitability for SARS-CoV-2 genome analysis. ONT sequencing also identified a surprising diversity of structural variation within SARS-CoV-2 specimens that were supported by evidence from short-read sequencing on matched samples. However, ONT sequencing failed to accurately detect short indels and variants at low read-count frequencies. This systematic evaluation of analytical performance for SARS-CoV-2 WGS will facilitate widespread adoption of ONT sequencing within local, national and international COVID-19 public health initiatives.
Sample: nCoV_189
SAMN16729546 • SRS7681738 • All experiments • All runs
Name: nCoV_189
Instrument: PromethION
Strategy: WGS
Selection: PCR
Layout: SINGLE
Runs: 1 run, 95,719 spots, 107M bases, 80.2Mb
Run# of Spots# of BasesSizePublished


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