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Performance of COVIDSeq and Swift normalase amplicon SARS-CoV-2 panels for SARS-CoV-2 Genomes Sequencing: Practical Guide and Combining FASTQ Strategy (preprint)
medrxiv; 2022.
Preprint
in English
| medRxiv | ID: ppzbmed-10.1101.2021.12.30.21268553
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/L for SNAP protocol and 147 copies/L 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.
Full text:
Available
Collection:
Preprints
Database:
medRxiv
Main subject:
COVID-19
Language:
English
Year:
2022
Document Type:
Preprint
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