Coronavirus target enrichment approach reveals intra-patient sequence variability

Amid the global challenges posed by the COVID-19 pandemic, unraveling the genomic intricacies of the SARS-CoV-2 virus becomes increasingly pivotal. This study delves into the broader landscape of viral evolution and the host-pathogen interplay, adding depth to our comprehension of the dynamic forces driving the past pandemic. This research introduces an innovative high-throughput next-generation sequencing (NGS) approach for a thorough exploration of SARS-CoV-2 genomic diversity. Leveraging nasal swab and mouthwash specimens from COVID-19 patients across diverse geographical regions during sequential infection waves (May 2020 to March 2021), the study incorporated a targeted enrichment protocol and pooling strategy to heighten detection sensitivity. The approach exhibited remarkable efficiency, generating high number of reads, and mutations distributed across 10 distinct viral gene regions. Sequencing was performed at the Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna under the project ID JMF-2105-04.