Brona Brejova, Kristina Borsova, Viktoria Hodorova, Viktoria Cabanova, Askar Gafurov, Dominika Fricova, Martina Nebohacova, Tomas Vinar, Boris Klempa, Jozef Nosek. Nanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tilingamplicon protocols. PLoS One, 16(10):e0259277. 2021.

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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.