RT Journal Article
SR Electronic
T1 Validation of Clinical Quality Control Metrics for SARS-CoV-2 Sequencing Using the Ion Torrent Genexus Integrated Sequencer
JF American Society for Clinical Laboratory Science
JO Clin Lab Sci
FD American Society of Chemistry and Laboratory Science
SP 10
OP 18
DO 10.29074/ascls.2025003285
VO 38
IS 1
A1 Leathers, Talbot D.
A1 Zamponi, Martina
A1 Tardif-Kunk, Mackenzie
A1 Garcia, Oyuky
A1 Parker, Kasey N.
A1 Hept, Megan A.
A1 Hines-Battle, Shamir
A1 Harrison, Aaron
A1 Sundin, Tabetha R.
A1 Mollica, Peter A.
YR 2025
UL http://hwmaint.clsjournal.ascls.org/content/38/1/10.abstract
AB 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.