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

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.