Effect of not vortexing nasopharyngeal and throat swabs on SARS-CoV-2 nucleic acid detection: A pilot study

Jamil N Kanji; Kanti Pabbaraju; Anita Wong; Candace Beitku; Ashwin Deo; Seema Kailey; Raymond Ma; Graham Tipples; Nathan Zelyas

doi:10.1016/j.jviromet.2022.114468

Effect of not vortexing nasopharyngeal and throat swabs on SARS-CoV-2 nucleic acid detection: A pilot study

J Virol Methods. 2022 Mar:301:114468. doi: 10.1016/j.jviromet.2022.114468. Epub 2022 Jan 17.

Authors

Jamil N Kanji¹, Kanti Pabbaraju², Anita Wong², Candace Beitku³, Ashwin Deo³, Seema Kailey³, Raymond Ma³, Graham Tipples⁴, Nathan Zelyas⁵

Affiliations

¹ Public Health Laboratory, Alberta Precision Laboratories, Calgary, AB, Canada; Division of Infectious Diseases, Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Pathology & Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Laboratory Medicine & Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada. Electronic address: jamil.kanji@ahs.ca.
² Public Health Laboratory, Alberta Precision Laboratories, Calgary, AB, Canada.
³ Public Health Laboratory, Alberta Precision Laboratories, Edmonton, AB, Canada.
⁴ Public Health Laboratory, Alberta Precision Laboratories, Edmonton, AB, Canada; Department of Medical Microbiology & Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada; Li Ka Shing Institute for Virology, University of Alberta, Edmonton, AB, Canada.
⁵ Department of Laboratory Medicine & Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada; Public Health Laboratory, Alberta Precision Laboratories, Edmonton, AB, Canada.

Abstract

The processing of swabs for respiratory virus detection involves vortexing while still in the viral transport medium (VTM). The effect of not vortexing swabs prior to analysis has not been studied extensively for SARS-CoV-2 detection, and presents an opportunity to improve pre-analytic laboratory workflow. We aimed to assess the impact of not vortexing nasopharyngeal/throat swabs submitted in VTM for SARS-CoV-2 testing. To assess the impact of not vortexing swabs, 277 swab samples were tested for SARS-CoV-2 RNA in paired vortexed and non-vortexed aliquots using eight routine nucleic acid amplification assays. We compared the qualitative (positive/negative) and semi-quantitative (cycle threshold, Ct) results. Following discordant analysis, all but one non-vortexed sample had the same qualitative result as the vortexed sample. 27.4 % of samples were SARS-CoV-2 positive. Comparison of Ct values revealed an apparent reduction in human cellular nucleic acid in the non-vortexed samples (mean Ct values of 24.0 and 26.5 for vortexed and non-vortexed samples, respectively, p < 0.0001) and increased Ct values for non-vortexed samples using a laboratory-developed SARS-CoV-2 assay (mean Ct values of 4.1 and 4.2 for vortexed and non-vortexed samples, respectively; p < 0.0001), but this was not observed for a more automated commercial SARS-CoV-2 assay (mean Ct values of 15.2 for both vortexed and non-vortexed samples, respectively; p = 0.68). While vortexing swabs appears to improve the recovery of cellular material, it does not have an appreciable impact on the qualitative sensitivity of SARS-CoV-2 nucleic acid tests, which may support omission of this step and simplification of front-end sample processing.

Keywords: PCR; Qualitative; SARS-CoV-2; Sample processing; Vortex.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19 Testing
COVID-19*
Humans
Nasopharynx
Pharynx
Pilot Projects
RNA, Viral / genetics
SARS-CoV-2*
Specimen Handling / methods

Substances

RNA, Viral