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Related Experiment Video

Updated: Oct 16, 2025

Author Spotlight: Advancing Pathogen Diagnostics with Standardized LAMP

Author Spotlight: Advancing Pathogen Diagnostics with Standardized LAMP

Published on: September 8, 2023

Fast SARS-CoV-2 Variant Detection Using Snapback Primer High-Resolution Melting.

Joseph C Lownik^1,2, Jared S Farrar², Grayson W Way²

¹Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.

Diagnostics (Basel, Switzerland)

|October 23, 2021

Summary

A new, rapid, and inexpensive method using snapback primer-based high-resolution melting can detect over 20 high-consequence SARS-CoV-2 spike mutations. This test distinguishes between viral variants in under 2 hours for less than $10 per sample.

Keywords:

COVID testing COVID-19 PCR SARS-CoV-2 high-resolution melting snapback primer

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Last Updated: Oct 16, 2025

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Area of Science:

Virology
Molecular Biology
Genetics

Background:

The COVID-19 pandemic, caused by SARS-CoV-2, has infected over 200 million people globally.
The emergence of numerous SARS-CoV-2 variants necessitates rapid and sensitive detection methods.
Current whole-genome sequencing for variant tracking is costly and requires specialized infrastructure.

Purpose of the Study:

To present a fast, inexpensive, and accessible assay for detecting SARS-CoV-2 variants.
To identify over 20 high-consequence mutations in the SARS-CoV-2 spike protein.
To offer a viable alternative to whole-genome sequencing for variant surveillance.

Main Methods:

Development of a snapback primer-based high-resolution melting (HRM) assay.
Utilizing HRM to detect specific mutations in the SARS-CoV-2 spike gene.
Assay validation for speed, cost-effectiveness, and accuracy in variant lineage identification.

Main Results:

The developed assay successfully detects over 20 high-consequence SARS-CoV-2 spike mutations.
The methodology can distinguish between multiple SARS-CoV-2 variant lineages.
The entire testing process is completed in approximately 2 hours.
The cost per sample is less than $10.

Conclusions:

Snapback primer-based HRM is a feasible, rapid, and inexpensive method for SARS-CoV-2 variant detection.
This assay provides a valuable tool for tracking viral evolution and informing public health responses.
The accessibility of this method can broaden the scope of variant surveillance beyond specialized laboratories.