Validation of Clinical Quality Control Metrics for SARS-CoV-2 Sequencing Using the Ion Torrent Genexus Integrated Sequencer

ABSTRACT Since its emergence in 2019, SARS-CoV-2 has infected millions globally, with novel variants arising through mutations that enhance virulence or immune evasion. Given the shortage of qualified laboratory professionals during this time, clinical platforms exhibiting minimal hands-on time gained popularity. One such platform, Thermo Fisher Scientific’s Ion Torrent Genexus, provided sequencing capabilities to short-staffed laboratories, yet standard quality control metrics for this platform remain limited. In this study, we established quality metrics for accurate variant calling on the Genexus Integrated Sequencer. Upper respiratory specimens positive for SARS-CoV-2 were sequenced and rigorously assessed using the proposed metrics. We sequenced 339 patient specimens and 89 controls across varying viral loads. Among positive controls that met the metrics, 100% were assigned correct lineages, while 86% of negative controls appropriately failed quality thresholds. The proposed metrics provide a framework for accurate SARS-CoV-2 variant identification on the Genexus platform, offering a model for clinical laboratories adopting this technology for reliable sequencing and variant tracking.