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Related Experiment Video

Updated: Nov 20, 2025

Quantification and Whole Genome Characterization of SARS-CoV-2 RNA in Wastewater and Air Samples

Quantification and Whole Genome Characterization of SARS-CoV-2 RNA in Wastewater and Air Samples

Published on: June 30, 2023

Partial N Gene Sequencing for SARS-CoV-2 Verification and Pathway Tracing.

Sin Hang Lee¹, Jonathan McGrath², Stephen P Connolly²

¹Milford Molecular Diagnostics Laboratory, Milford, CT, USA.

International Medical Case Reports Journal

|January 20, 2021

Summary

Sequencing SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) nucleocapsid gene amplicons can confirm positive RT-qPCR results and track virus strains. This method helps reduce false positives, preventing unnecessary disruptions from inaccurate COVID-19 diagnoses.

Keywords:

COVID-19 SARS-CoV-2 verification Sanger sequencing false-positive partial N gene sequencing phylogenetically distinct strains single nucleotide mutation virus strain tracing

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Area of Science:

Virology
Genetics
Public Health

Background:

Real-time quantitative polymerase chain reaction (RT-qPCR) tests for SARS-CoV-2 can yield false positives, especially during periods of low virus prevalence.
Accurate confirmation of positive results is crucial for effective disease management and preventing unnecessary public health measures.

Observation:

A case of mild COVID-19 was confirmed using partial sequencing of the SARS-CoV-2 nucleocapsid (N) gene.
The sequencing identified a specific mutation pattern (GGG-to-AAC) linked to strains originating in Continental Europe.
Re-testing reference samples revealed mutations, including one associated with New York state strains and a novel frameshift mutation.

Findings:

Partial N gene sequencing accurately verifies SARS-CoV-2 positive RT-qPCR results.
The method can differentiate between various SARS-CoV-2 strains, aiding in tracking virus transmission.
Identified mutations included known European and New York variants, as well as a novel insertion.

Implications:

Routine sequencing of RT-qPCR positive samples can significantly reduce false-positive diagnoses.
Minimizing false positives can prevent undue public anxiety and avoid unnecessary closures of schools and businesses.
This approach supports more reliable monitoring of SARS-CoV-2 strain movement and evolution.