Out of five temperatures, only three (59☌, 61☌, and 63☌) yielded the most consistent and greater viral genome coverage with minimal amplicon drops. The sequencing was done in two batches batch one using SQK-LSK109 and batch two using SQK-RBK110.96, each with the sample amplified using ARTIC V3 and Midnight primer, respectively. Gradient PCR tiling was conducted before the sequencing to determine the optimized annealing temperature. Three Delta variant samples with a Ct value of 18, 23, and 25 are used in this study. This study aims to optimize the annealing temperature of the primer set and evaluate the performance of each SQK-LSK109 and SQK-RBK109 library preparation kit, as well as the protocol, respectively. However, a considerable coverage drop in certain genome regions has been observed in experiments using the ARTIC V3 Classic Protocol (ARTIC V3 primer with SQK-LSK109) and Midnight Protocol (Midnight primer and SQK-RBK110.96). Oxford Nanopore Technologies (ONT) has allowed scalable and high-throughput SARS-CoV-2 sequencing. Indonesia International Institute for Life SciencesĪmidst a pandemic caused by the SARS-CoV-2 virus, rapid genomic surveillance of the virus is much needed to support epidemiology monitoring of the pathogen. Optimization of Rapid Turnaround SARS-CoV-2 Sequencing Protocol with Multiplexed PCR Tiling Please use this identifier to cite or link to this item:
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