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SARS-CoV-2 Sequencing for Variant Surveillance.

Julie Woolworth Hirschhorn¹, Jaclyn Dunne²

¹Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA. woolworj@musc.edu.

Methods in Molecular Biology (Clifton, N.J.)

|April 11, 2023

Summary

This summary is machine-generated.

Next-generation sequencing enables comprehensive analysis of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome. This method offers scalability and cost-effectiveness for viral surveillance, despite some bioinformatics challenges.

Keywords:

COVID-19 Next-generation sequencing SARS-CoV-2 Variants

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Area of Science:

Virology
Genomics
Molecular Biology

Background:

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic surveillance is crucial for understanding viral evolution and transmission.
Next-generation sequencing (NGS) technologies offer powerful tools for comprehensive viral genome analysis.

Purpose of the Study:

To describe a modified FDA Emergency Use Authorization (EUA) procedure for the genomic sequencing of SARS-CoV-2.
To outline the advantages and disadvantages of using NGS for SARS-CoV-2 surveillance.

Main Methods:

Detailed description of a modified EUA procedure for SARS-CoV-2 whole-genome sequencing.
Emphasis on specimen quality, genome coverage, and annotation for successful sequencing.

Main Results:

NGS provides scalable, high-throughput, and cost-effective full genome analysis of SARS-CoV-2.
Challenges include expensive instrumentation, reagent costs, longer time-to-result, and complex bioinformatics.

Conclusions:

The described NGS procedure, a research use only (RUO) version, facilitates robust SARS-CoV-2 genomic surveillance.
Understanding the technical considerations is key to optimizing SARS-CoV-2 genomic sequencing.