Oropharyngeal Secretion as Alternative for SARS-CoV-2 Detection

Area of Science:

• Virology
• Infectious Diseases
• Diagnostic Testing

Background:

• Accurate detection of SARS-CoV-2 RNA is crucial for managing COVID-19 patients.
• Nasopharyngeal swabs (NPSs) are commonly used but may yield false negatives.
• Oropharyngeal secretions (OSs) present an alternative sampling method.

Purpose of the Study:

• To evaluate if OS sampling enhances SARS-CoV-2 RNA detection via nucleic acid amplification testing (NAAT).
• To compare the diagnostic accuracy of OS versus NPS sampling methods.
• To assess the consistency and differences between OS and NPS sampling.

Main Methods:

• Two prospective studies were conducted.
• Study 1: 75 COVID-19 patients with negative NPS NAAT results were re-tested using OS.
• Study 2: Paired OS and NPS samples from 50 COVID-19 patients were analyzed using NAAT, with McNemar's test and kappa statistic applied.

Main Results:

• Two patients in Study 1 showed positive SARS-CoV-2 RNA in OS samples.
• McNemar's test revealed a statistically significant difference (P=0.021) in NAAT results between OS and NPS in Study 2.
• Cohen's kappa coefficient indicated fair consistency (0.244) between OS and NPS.
• NPS testing risked discharging 59% of infectious patients, versus 14% with OS testing.

Conclusions:

• OS sampling appears to improve the accuracy of SARS-CoV-2 RNA detection by NAAT.
• The NPS method carries a higher risk of false negatives, potentially leading to premature discharge of infectious patients.
• Further research with larger sample sizes is recommended to confirm these findings, noting viral RNA detection does not confirm infectivity.