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

Alexander T Matelski; Nikhut I Siddique; Philip Mead; Tommaso Raimondi; Laura C Jorgenson; Omar Calderon; Kory Harman; John J Farrell

The Bland-Altman plot for inter-rater reliability determined that 96.5% of inter-rater difference 109 was within two standard deviations (average difference = 2.0 CCEs; SD = 6.1). The majority of both 110 positive and negative samples had at least one CCE/hpf, with an average of 3.7 CCEs/hpf in positive 111 samples and 3.2 CCEs/hpf in negative samples (p=0.18). However, 19% of negative samples had no CCEs 112 visible on microscopy, while just 6% of positive samples exhibited the same ( This study demonstrated a meaningful difference in identifiable CCEs on microscopic review 118 between NPS that were negative or positive by RT-PCR for respiratory pathogens. There was greater 119 association between lack of identifiable CCEs and RT-PCR negative NPS, which we posit is partially 120 attributable to inadequately collected swabs. This feature also demonstrated a useful discriminatory 121 NPV. Given this finding, microscopic review of CCEs using simple, inexpensive reagents and equipment 122 could be a helpful step in the diagnostic algorithm for upper respiratory viral infection. Situations in 123 which there is high clinical suspicion but a negative RT-PCR may benefit from rapid microscopic review 124 using a streamlined, benchside version of this protocol, which could save limited resources like NPS, viral 125 transport media, and RT-PCR kits. 126