Table 4.

Potential reasons for COVID RT-PCR test discrepancy.

1. Differences in pre-analytical variables: a. Sample collection kit i. Viral transport media ii. Swab type b. How diligently the sample is collected i. Sometimes the collector is afraid to collect sample properly; sometime the patient gags or does not cooperate; sometimes the tonsil and posterior pharyngeal wall or mid inferior portion of inferior turbinate cannot be easily reached) c. Sample transport conditions d. Sample storage conditions e. Timing of the test (samples taken in relation to symptom; sample taken in relation to sub-clinical infection duration) 2. Differences in analytical variables: a. RNA extraction method i. Spin column extraction ii. Magnetic bead extraction iii. Automated RNA extraction instrument and kit type b. PCR kit used: we use three different kits: Seegene, Altona, True PCR; Every kit may have differences in i. Genes detected ii. Analytical sensitivity (Limit of detection) iii. Clinical sensitivity and specificity 3. Differences in Post analytical variables: a. CT cut-off used to call positive (True PCR: 35; Seegene 40; Altona 45) b. Number of genes and type of genes for calling a sample positive c. Sometimes the borderline cases just over the cut-off may be called positive or vice versa The discrepancy is likely to be less with low CT values (CT < 35); and significantly more after that (CT > 35 or low viral load situation) Also note CT values may be affected by all the factors mentioned as above. Some experts are of the view that as COVID is a new disease with no proven anti-viral treatment or vaccine, reporting borderline situation as positive is perhaps safer than doing it otherwise