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A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance.

Lori Bourassa1, Garrett A Perchetti1, Quynh Phung1

  • 1Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA.

Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology
|June 25, 2021
PubMed
Summary

A SARS-CoV-2 nucleocapsid mutation (D399N) significantly reduced the sensitivity of the Quidel Sofia antigen test. This highlights the need to monitor viral variants impacting diagnostic accuracy.

Keywords:
AntigenFalse negativeNucleocapsidQuidelSars-cov-2Sofia 2Variant

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Area of Science:

  • Clinical Microbiology
  • Virology
  • Molecular Diagnostics

Background:

  • SARS-CoV-2 variants pose challenges to diagnostic test performance.
  • Antigen tests have generally been unaffected by viral variation to date.
  • The Quidel Sofia SARS Antigen FIA test's sensitivity was investigated.

Purpose of the Study:

  • To investigate a case of a high viral load specimen testing negative on the Quidel Sofia SARS Antigen FIA test.
  • To identify mutations in SARS-CoV-2 variants affecting antigen test performance.
  • To assess the impact of specific nucleocapsid mutations on antigen test sensitivity.

Main Methods:

  • Whole genome sequencing to identify viral mutations.
  • Testing of clinical specimens with identified mutations on different antigen assays.
  • Testing of recombinant nucleocapsid proteins with specific mutations.

Main Results:

  • A SARS-CoV-2 isolate with D399N and T205I nucleocapsid mutations was identified.
  • The D399N mutation caused an approximate 1000-fold loss in sensitivity for the Quidel Sofia test.
  • The D399N mutation did not affect the Abbott BinaxNOW or Quidel Quickvue tests.
  • The T205I mutation did not impact the performance of either Sofia or BinaxNOW tests.

Conclusions:

  • Routine pathogen genomics can identify diagnostic challenges posed by viral variants.
  • Antigenic diversity outside the spike protein is critical for SARS-CoV-2 diagnostic development.
  • The D399N mutation necessitates careful monitoring for its potential impact on diagnostic sensitivity.