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Sanger Sequencing

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...

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Large-Scale SARS-CoV-2 Testing Utilizing Saliva and Transposition Sample Pooling

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Sequencing SARS-CoV-2 from antigen tests.

Ashley Nazario-Toole¹, Holly M Nguyen¹, Hui Xia¹

¹59th Medical Wing, Clinical Investigations and Research Support Laboratory, Joint Base San Antonio-Lackland, San Antonio, TX, United States of America.

|February 8, 2022

Summary

Whole-genome sequencing of SARS-CoV-2 is now feasible using antigen test swabs. This advancement supports continued genomic surveillance despite shifts in diagnostic testing methods.

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Area of Science:

Virology
Genomics
Public Health

Background:

Genomic surveillance is crucial for tracking SARS-CoV-2 variants and informing public health strategies.
Traditional SARS-CoV-2 whole-genome sequencing relies on nasopharyngeal swabs in viral transport media.
A shift towards antigen testing using anterior nasal swabs has occurred, potentially impacting genomic surveillance.

Purpose of the Study:

To develop and validate a workflow for SARS-CoV-2 whole-genome sequencing directly from antigen test swabs.
To assess the feasibility and comparability of genomic data obtained from antigen test swabs versus traditional methods.

Main Methods:

Utilized excess clinical specimens from BinaxNOW™ COVID-19 Ag Card tests.
Adapted existing whole-genome sequencing protocols to accept antigen test-derived swabs as input.
Compared sequencing results with those obtained from RT-PCR assays using nasopharyngeal swabs in viral transport media.

Main Results:

Demonstrated the feasibility of performing SARS-CoV-2 whole-genome sequencing using swabs from antigen tests.
Obtained genomic data from antigen test swabs that is comparable to data from RT-PCR based assays.
Validated a novel input method for genomic surveillance without requiring specialized transport media.

Conclusions:

Whole-genome sequencing from antigen test swabs is a viable alternative for SARS-CoV-2 surveillance.
This method facilitates continued genomic surveillance despite the widespread use of antigen-based diagnostic tests.
The developed workflow supports agile public health responses by maintaining genomic data streams.