Sequencing of Sars-CoV-2 genome using different Nanopore chemistries

González-Recio, Oscar; Gutiérrez-Rivas, Mónica; Peiró-Pastor, Ramón; Aguilera-Sepúlveda, Pilar; Cano-Gómez, Cristina; Jiménez-Clavero, Miguel Ángel; Fernández-Pinero, Jovita

Nanopore 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. Keypoints Sequencing SARS-CoV-2 genome is of great importance for the pandemic surveillance Nanopore offers a low cost and accurate method to sequence SARS-CoV-2 genome Ligation sequencing is preferred rather than the rapid kit using transposases