Sequencing of SARS-CoV-2 genome using different nanopore chemistries

• DOI: 10.1007/s00253-021-11250-w
• Publication Date: 2021-04-01T12:03:06Z
• Authors: Oscar González-Recio; Mónica Gutiérrez-...; Ramón Peiró-Pastor; Pilar Aguilera-Se...; Cristina Cano-Gómez; Miguel Ángel Jimé...; Jovita Fernández-...
• Keywords: Nanopore; 0301 basic medicine; 0303 health sciences; Genome assembly; SARS-CoV-2; Sequence Analysis, RNA; COVID-19; Genome, Viral; 3. Good health; Nanopores; 03 medical and health sciences; Flow cell; Sequencing; Applied Genetics and Molecular Biotechnology

ABSTRACTNanopore sequencing has emerged as a rapid and cost-efficient tool for diagnostic and epidemiological surveillance of SARS-CoV-2 during the COVID-19 pandemic. This study compared results from sequencing the SARS-CoV-2 genome using R9 vs R10 flow cells and Rapid Barcoding Kit (RBK) vs Ligation Sequencing Kit (LSK). The R9 chemistry provided a lower error rate (3.5%) than R10 chemistry (7%). The SARS-CoV-2 genome includes few homopolymeric regions. Longest homopolymers were composed of 7 (TTTTTTT) and 6 (AAAAAA) nucleotides. The R10 chemistry resulted in a lower rate of deletions in timine and adenine homopolymeric regions than R9, at expenses of a larger rate (~10%) of mismatches in these regions.The LSK had a larger yield than RBK, and provided longer reads than RBK. It also resulted in a larger percentage of aligned reads (99% vs 93%) and also in a complete consensus genome.The results from this study suggest that the LSK used on a R9 flow cell could maximize the yield and accuracy of the consensus sequence when used in epidemiological surveillance of SARS-CoV-2.KeypointsSequencing SARS-CoV-2 genome is of great importance for the pandemic surveillanceNanopore offers a low cost and accurate method to sequence SARS-CoV-2 genomeLigation sequencing is preferred rather than the rapid kit using transposases