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Evaluation of a multiplexed oligonucleotide ligation assay for SARS-CoV-2 variant identification. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology Solis, D., Sibai, M., Kung, F., Break, T. J., Harkins, S. B., Huang, C., Yamamoto, F., Sahoo, M. K., Wohlstadter, J. N., Sigal, G. B., Pinsky, B. A. 2023; 162: 105444

Abstract

SARS-CoV-2 variant surveillance informs vaccine composition and decisions to de-authorize antibody therapies. Though detailed genetic characterization requires whole-genome sequencing, targeted mutation analysis may complement pandemic surveillance efforts.This study investigated the qualitative performance of a multiplex oligonucleotide ligation assay targeting 19 spike mutations using 192 whole genome sequenced upper respiratory samples representing SARS-CoV-2 variants of concern.Initial valid results were obtained from 95.8% [95% confidence interval (CI): 92.0 - 98.2; 184/192] of samples. All eight invalid samples were valid on repeat testing. When comparing SARS-CoV-2 oligonucleotide ligase assay SARS-CoV-2 variant calls with whole genome sequencing, overall positive percent agreement was 100% (95% CI: 98.1 - 100.0; 192/192), as was the positive and negative percent agreement for each of the tested variants; Gamma, Delta, Omicron BA.1, BA.2, and BA.4/BA.5.This multiplexed oligonucleotide ligation assays demonstrated accurate SARS-CoV-2 variant typing compared to whole genome sequencing. Such an approach has the potential to provide improved turnaround compared to sequencing and more detailed mutation coverage than RT-qPCR.

View details for DOI 10.1016/j.jcv.2023.105444

View details for PubMedID 37043903