Finding the middle ground with the clinical laboratory's role in SARS-CoV-2 genomic surveillance.

Graf, Erin H

Continued replacement of the dominant 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 U.S. has lagged behind in percent 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. In this issue of the Journal of Clinical Microbiology, Babiker et al (J Clin Microbiol 59:e01446-21, 2021, https://doi.org/10.1128/JCM.01446-21) describe a rapid and flexible multiplex SNP assay targeting mutations associated with Alpha, Beta/Gamma and, later added, 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.