Cautious Evaluation of Weak SARS-CoV-2 Positive Cases on Xpert Xpress SARS-CoV-2: Formulating a Testing Algorithm in a Hospital Setup
Author(s): Tavisha Dama, Shashikala Shivaprakash, Neetu Biyani and Pratiksha Chheda
Objectives: Due to the sensitivity of the Xpert Xpress SRAS-CoV-2 kit (LOD-0.0200 PFU/ml) and the presence of residual viral RNA from past infections, reporting of higher Ct values is a challenge. Formulating a testing algorithm became important in order to maintain infection control measures in our facility.
Materials and Methods: A retrospective analysis of 747 cases that were tested, between July 2020 to September 2021, by both Xpert Xpress SARS-Cov-2 kit and COVID-19 one-step RT-PCR kit (Meril Diagnostics) (reference method) was carried out. Samples with Ct≥36 on Xpert Xpress SARS-CoV-2 were evaluated further to rule out false positives by correlating with infection history and follow-up data. Data were analysed using Microsoft Excel’s built in Data Analysis Tool Pack capability.
Results: When compared with an ICMR approved kit (COVID-19 onestep RT-PCR kit), gold standard, the Xpert Xpress SARS-COV-2 kit was found to have POA of 70.6% (95% CI: 67.2% to 73.8%), PPA of 100% (95% CI: 97.9% to 100%) and NPA of 61.2% (95% CI: 57% to 65.2%). For cases with Ct ranging from 15-35, results were 100% concordant between Xpert Xpress SARS-CoV-2 and rt-PCR (n=388), however, there was a decrease in concordance as the Ct values increased on Xpert Xpress SARS-CoV-2 (288 cases with Ct≥36). Further evaluation of discordant cases (n=212) revealed 21.2% (45/212) had infection history. Of the remaining 167 cases, follow up swabs were obtained for 42.5% (71/167), out of which 8.4% (6/71) were found to have active infections.
Conclusions: Xpert Xpress SARS-Cov-2 kit can be used as a point of care device in units where urgent results are important. Using an arbitrary cutoff of Ct-36, a testing algorithm was devised where samples with Ct>36 on Xpert Xpress SARS-CoV-2 were repeated by rt-PCR. Repeats positive by rt-PCR were declared as positive, however, the negatives were asked to submit a fresh swab after 48 hours. It was also concluded that higher Ct values need to be cautiously evaluated keeping in mind infection history of the patient and confirmed using an alternate testing method. In case of known positive infection history, Xpert Xpress SARS-CoV-2 should not be used as a preferred method for testing.