Inconclusive in COVID-19 Reverse TranscriptasePolymerase Chain Reaction Test: A Diagnostic Dilemma

Abstract

Introduction: Cases of COVID 19 pandemic in India has been reported since 30th January 2020. Cases are detected by RTqPCR targeting one or more gene (E/S/N/RdRp/ORF1) based on ICMR guidelines. Results are to be reported as ‘Inconclusive’ if only one target gene is detected in multiplex qPCR. Objective: The present study is aimed to analyze the “Inconclusive” results based on the Ct value of the detected target gene, duration of symptoms of cases and by repeat testing with another fresh sample after 3 days. Methods: This cross-sectional observational study was conducted from June 2020 to December 2020 in a tertiary care hospital in Kolkata. Nasopharyngeal and throat swab from suspected cases were collected and sent to our laboratory for RT-qPCR. Results: A total of 94,443 samples were tested in our laboratory for seven months. 8,455 (8.95%) samples were found to be inconclusive. Out of them, 1287 (15.22%) cases became positive and 3858 (45.63%) became negative after retesting with another fresh sample after 3 days. 1540 (18.21%) cases were lost for follow up. All inconclusive results were correlated with Ct value and duration of the disease symptoms. Maximum cases (64.96%) with Ct value <34, became positive whereas, 72.37% with Ct value >36 became negative on retesting. Most of the cases (28.36%) had symptoms of less than 2 days duration, among positive cases, whereas, 36.86% cases had symptoms of more than 12 days duration among negative cases. 1770 (20.94%) samples were found to be inconclusive again on retesting after 3 days. Most of these cases (46.55%) had a Ct value within 3436 on the first test. Conclusion: All inconclusive samples should always be subjected to further testing after 3 days. There is a chance to get positive results from inconclusive cases whose Ct value is less than 34. Quality control and quality assurance of all processes should be done to check any pre-analytical or analytical fallacies. Clinicians and patients both are to be educated about the probable reasons of inconclusive also.