Microscopic Review of Nasopharyngeal Swabs as a Means of Benchside Quality Assurance

Nasopharygneal swabs (NPS) are the collection modality recommended by the Centers for Disease Control and Prevention (CDC) for reverse-transcription polymerase chain reaction (RT-PCR) testing for SARS-CoV2. NPS gather both extracellular material and human respiratory epithelial cells and, when used with RT-PCR, have reliable sensitivity for detection of viral infection. However, at our institution, we identified a 1.7% re-order rate within 7-days for NPS for respiratory pathogen RT-PCR, which we hypothesize may be due to low confidence in adequate sample collection. We sought to identify an inexpensive and accessible strategy for benchside quality assurance of NPS adequacy by observing microscopic content of viral transport media. For 801 NPS samples collected in November 2019, we air-dried and safranin-stained aliquots of viral transport media on glass slides. We then counted morphologically distinct ciliated columnar epithelial cells (CCEs). 19% of samples negative by RT-PCR for respiratory pathogens had no CCEs, while just 6% of positive samples exhibited the same. Pearsons Chi-squared test was used to compare presence of CCEs between samples that were positive and negative for respiratory pathogens by RT-PCR (p=3.3x10-38). The negative predictive value (NPV) of finding no identifiable CCEs on microscopy was 85%. We posit that samples without identifiable CCEs may have been inadequately collected. The basic, benchside protocol using inexpensive laboratory reagents that we describe here could help improve accuracy and accessibility of NPS and RT-PCR testing for SARS-CoV2 and other respiratory pathogens while conserving limited resources in the face of a pandemic.