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Unveiling Inter- and Intra-Patient Sequence Variability with a Multi-Sample Coronavirus Target Enrichment Approach
Sara Lado1, Jakob Thannesberger1, Kathrin Spettel2,3
1Division of Infectious Diseases and Tropical Medicine, Department of Medicine 1, Medical University of Vienna, 1090 Vienna, Austria.
Viruses
|May 25, 2024
Summary
This study used next-generation sequencing (NGS) to track SARS-CoV-2 evolution, identifying key mutations in viral genes like Spike and Nucleocapsid. The findings highlight the importance of genomic surveillance for understanding emerging variants.
Area of Science:
- Genomics
- Virology
- Molecular Biology
Background:
- The COVID-19 pandemic necessitated rapid understanding of SARS-CoV-2 evolution.
- Genomic surveillance is critical for tracking viral dynamics and host-virus interactions.
Purpose of the Study:
- To explore SARS-CoV-2 evolution using a high-throughput next-generation sequencing (NGS) approach.
- To identify specific viral genes and mutations indicative of viral evolution and selection pressures.
Main Methods:
- Utilized nasal swab and mouthwash samples from COVID-19 patients across diverse geographical regions and infection waves.
- Applied a targeted enrichment protocol and pooling strategy to enhance detection sensitivity in NGS.
- Analyzed mutations across 10 distinct viral gene regions.
Main Results:
- The NGS approach yielded a high number of reads and mutations.
- Envelope, Nucleocapsid, and Open Reading Frame 8 genes exhibited the highest mutation rates.
- Spike and Nucleocapsid genes showed evidence of positive selection, indicating adaptive evolution.
- The pooling strategy successfully detected subtle sequence variability.
Conclusions:
- SARS-CoV-2 evolution is dynamic, influenced by virus-host interplay.
- Continuous genomic surveillance is essential for understanding viral dynamics and emerging variants.
- The described NGS approach is a versatile, fast, and cost-efficient tool for variant screening.
