Dealing with inconclusive SARS-CoV-2 PCR samples-Our experience.

Area of Science:

• Virology
• Infectious Diseases
• Molecular Diagnostics

Background:

• Early confirmation of SARS-CoV-2 is vital for managing COVID-19 patients and contacts.
• Standard RT-PCR diagnostics detect two or three unique viral sequences.
• Interpreting inconclusive samples positive for only one SARS-CoV-2 gene presents a challenge.

Purpose of the Study:

• To analyze the frequency and characteristics of inconclusive SARS-CoV-2 RT-PCR results.
• To determine the proportion of inconclusive samples representing true infections versus false positives.

Main Methods:

• Retrospective analysis of 16,364 naso-oropharyngeal swabs tested for SARS-CoV-2.
• Evaluation of amplification plots for inconclusive samples (positive for N-gene only).
• Review of patient medical records for COVID-19 testing history and demographics.

Main Results:

• 136 (0.8%) inconclusive samples were identified, positive only for the N-gene.
• Of analyzed inconclusive samples, 48% had prior SARS-CoV-2 positivity, 14% had subsequent positivity.
• 37% of inconclusive samples were classified as false positives.

Conclusions:

• A significant portion of inconclusive SARS-CoV-2 RT-PCR results indicate early or late-stage infection.
• The presence of false positives necessitates individual patient assessment based on clinical and epidemiological data.
• Separate analysis of each inconclusive result is recommended for accurate COVID-19 diagnosis.