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Performance of COVIDSeq and Swift Normalase Amplicon SARS-CoV-2 Panels for SARS-CoV-2 Genome Sequencing: Practical Guide and Combining FASTQ Strategy

Authors :
Hosoon Choi
Munok Hwang
Dhammika H. Navarathna
Jing Xu
Janell Lukey
Chetan Jinadatha
Source :
Journal of Clinical Microbiology. 60
Publication Year :
2022
Publisher :
American Society for Microbiology, 2022.

Abstract

The whole genomic sequencing (WGS) of SARS-CoV-2 has been performed extensively and is playing a crucial role in fighting against COVID-19 pandemic. Obtaining sufficient WGS data from clinical samples is often challenging especially from the samples with low viral load. We evaluated two SARS-CoV-2 sequencing protocols for their efficiency/accuracy and limitations. Sequence coverage of >95% was obtained by Swift normalase amplicon SARS-CoV-2 panels (SNAP) protocol for all the samples with Ct ≤ 35 and by COVIDSeq protocol for 97% of samples with Ct ≤ 30. Sample RNA quantitation obtained using digital PCR provided more precise cutoff values. The quantitative digital PCR cutoff values for obtaining 95% coverage are 10.5 copies/μL for SNAP protocol and 147 copies/μL for COVIDSeq protocol. Combining FASTQ files obtained from 2 protocols improved the outcome of sequence analysis by compensating for missing amplicon regions. This process resulted in an increase of sequencing coverage and lineage call precision.

Details

ISSN :
1098660X and 00951137
Volume :
60
Database :
OpenAIRE
Journal :
Journal of Clinical Microbiology
Accession number :
edsair.doi.dedup.....d568846eaa1e2eb466a933945fc9d40d