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• SARS-CoV-2 variant surveillance informs vaccine composition and emergency use authorization of monoclonal antibody therapies. • Intermediate methods with the potential to provide more comprehensive mutation coverage than RT-qPCR and more timely results than whole genome sequencing are limited. • The multiplexed SARS-CoV-2 oligonucleotide ligation assay demonstrated 100% overall agreement with whole genome sequencing for Gamma, Delta, and Omicron (BA.1, BA.2, and BA.4/BA.5) variants. 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. [ABSTRACT FROM AUTHOR]