Diagnostic evaluation of nCoV-QS, nCoV-QM-N, and nCoV-OM detection kits based on rRT-PCR for detection of SARS-CoV-2 in Ecuador.

Background: Ecuador was harshly impacted by COVID-19, in the region was the epicenter of the pandemic with the highest mortality rates and with the lowest rates of processed samples. Real-time reverse transcription PCR assays are essential to identify and manage the SARS-CoV-2 outbreak. Because of the global emergency, in Ecuador several commercial kits were introduced for use without clinical validation. In this manner, having the need to perform an evaluation with clinical samples before use for population screening.

Objective: This study aimed to evaluate the diagnostic performance of the nCoV-QS, nCoV-QM-N, nCoV-OM detection kits lately available in Ecuador, against the LightMix kit using nasopharyngeal swab (NPS) samples.

Materials And Methods: 198 nasopharyngeal samples were used (66 fresh NPS and 132 RNA stored samples). All samples were analyzed for SARS-CoV-2 with nCoV-QS, nCoV-QM-N, nCoV-OM detection kits and compared the concordance (Cohen's Kappa index, positive percentage agreement and negative percentage agreement) to LightMix as reference detection kit.

Results: The 198 samples presented strong concordance (96% nCoV-QM-N, 100% nCoV-OM and 100% nCoV-QS). The individual performance of each gene showed that the nCoV-OM kit had a higher number of samples detected with the (52.5%) and (53.5%) genes. The combined genes demonstrated that of nCoV-OM and nCoV-QS kits presented a higher percentage of detection with 52.5% and 48.5%, respectively. Finally, the detection rate and cycle threshold were not different between , , and target genes.

Conclusion: The nCoV-QS, nCoV-QM-N, and nCoV-OM Detection kits have comparable diagnostic performance to the emergency approved LightMix kit for SARS-CoV-2 detection in suspected COVID-19 patients.