Abstract

Introduction: Since its emergence in 2020, the SARS-CoV-2 virus, an RNA virus, has spread globally, causing a pandemic. It mutates frequently, and some mutations may weaken vaccine effectiveness. This research aims to enhance mutation detection using advanced sequencing techniques, crucial for developing strategies to control the spread and impact of COVID-19.

Methods: Here, RNA samples were collected from patients who tested positive for SARS-CoV-2 from April to July 2022, and validated; 613 samples were selected for sequencing.

Results: The results of the study showed that using a new method of next-generation sequencing with 2× tiled primer sets allowed for the accurate identification of new mutations within the SARS-CoV-2 genome. These mutations were analyzed in relation to the characteristics of patients who tested positive for the virus from April to July 2022. This approach improved understanding of how the virus’s genetic variations can influence its behavior and treatment, providing valuable insights for managing the pandemic.

Conclusion: The findings demonstrated the importance of long-read-based NGS analysis and 2× tiled primer sets for determining full SARS-CoV-2 genome sequence with new mutations and understanding the correlation between viral genotypes and patient characteristics for the effective management of SARS-CoV-2.

Keywords: Amplicon; Long-read sequencing; Mutations; Nextgeneration sequencing; SARS-CoV-2