This article was originally published here
J Clin Microbiol. September 22, 2021: JCM0064921. doi: 10.1128 / JCM.00649-21. Online before printing.
ABSTRACT
Background: Rapid and effective methods are needed to sequence the SARS-CoV-2 genome to track genetic mutations and identify new and emerging variants during the ongoing pandemic. Objective: to evaluate the performance of the SARS-CoV-2 AmpliSeq research panel and the S5 complement analysis tools for the analysis of the whole SARS-CoV-2 genome sequence and to compare the results with those obtained with the analysis process ARTIC based on MiSeq, using metrics such as depth, coverage, and single nucleotide variant (SNV) call match. Methods: A total of 191 clinical samples and a single isolated culture were extracted and sequenced with AmpliSeq technology and analysis tools. Of the 191 clinical samples, 83 (Ct 15.58 - 32.54) were also sequenced using an Illumina MiSeq based method with the ARTIC analysis process for direct comparison. Results: 176 of the 191 clinical samples sequenced in the S5XL and prepared using the SARS-CoV-2 research panel, had almost complete coverage (> 98%) of the viral genome, with an average depth of 5031x. Similar coverage levels (> 98%) were observed for 81/83 primary samples sequenced with both methods tested. The sample with the lowest viral load (Ct of 32.54) achieved 89% coverage with the MiSeq method and did not achieve sequencing with the AmpliSeq method. The consensus sequences produced by each method were identical in 81/82 samples, in areas of equal coverage, with only one difference present in one sample. Conclusions: The AmpliSeq approach is as effective as the Illumina-based method that uses ARTIC V3 amplification to sequence SARS-CoV-2 directly from patient samples in a range of viral loads (Ct 15.56-32.54 , median = 22.18). The AmpliSeq workflow is very easily automated with the Ion Chef and S5 instruments and requires less training and experience with NGS preparation than the Illumina workflow.
PMID:34550806 | DOI:10.1128 / JCM.00649-21
