Finding the Middle Ground with the Clinical Laboratory's Role in SARS-CoV-2 Genomic Surveillance

Continued replacement of the dominant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages, and associated surges, highlights the importance of genomic surveillance to identify the next possible threats. Despite concerted efforts between clinical laboratories and public health to generate sequence data, the United States has lagged in percentage of SARS-CoV-2 cases sequenced. A more simple and cost-effective option is needed to allow front-line clinical laboratories to perform high-throughput surveillance and refer important samples for slow and expensive next-generation sequencing (NGS). In this issue of the Journal of Clinical Microbiology, A. Babiker, K. Immergluck, S. D. Stampfer, A. Rao, et al. (J Clin Microbiol 59:e01446-21, 2021, https://doi.org/10.1128/JCM.01446-21) describe a rapid and flexible multiplex single-nucleotide polymorphism (SNP) assay targeting mutations associated with Alpha, Beta/Gamma, and, added later, Delta variants. They show 100% accuracy in characterized variant pools and clinical samples confirmed by NGS. Such an approach could be a happy medium in the role of front-line laboratories to assist with critically needed high-throughput genomic surveillance.