Surveillance of the SARS-CoV-2 variants including the quickly spreading mutants by rapid and near real-time sequencing of the viral genome provides an important tool for effective health policy decision making in the ongoing COVID-19 pandemic. Here we evaluated PCR-tiling of short (~400-bp) and long (~2 and ~2.5-kb) amplicons combined with nanopore sequencing on a MinION device for analysis of the SARS-CoV-2 genome sequences. Analysis of several sequencing runs demonstrated that using the long amplicon schemes outperforms the original protocol based on the 400-bp amplicons. It also illustrated common artefacts and problems associated with PCR-tiling approach, such as uneven genome coverage, variable fraction of discarded sequencing reads, including human and bacterial contamination, as well as the presence of reads derived from the viral sub-genomic RNAs.
【초록키워드】 protocol, Decision making, COVID-19 pandemic, Nanopore, Sequencing, variant, Health policy, RNAs, Contamination, Health, Viral, SARS-CoV-2 variants, nanopore sequencing, mutant, Bacterial, Analysis, viral genome, Amplicon, SARS-CoV-2 genome sequences, problems, problem, fraction, genome coverage, reads, sequencing reads, amplicons, approach, effective, evaluated, provide, demonstrated, artefact, outperform, the SARS-CoV-2, the SARS-CoV-2 genome, 【제목키워드】 protocol,