As SARS-CoV-2 continues to circulate and evolve, so too does our ability to study it. It’s now clear that multiple strains of SARS-CoV-2 can co-exist in different tissues and that the virus can evolve resistance to monoclonal antibodies during an infection. New recombinants like “deltacron” have also been discovered that mix-and-match genomic segments from circulating variants. With this many complexities to navigate and world case counts still in the millions, it’s more important than ever to deploy robust tools like full-genome sequencing for variant surveillance.
Microbiology labs can now submit SARS-CoV-2-positive samples for full-genome sequencing instead of using PCR assays for variant detection. Full-genome sequencing can detect novel mutations—eliminating the need for revalidation when a new variant emerges.
In a recent report1, Dr. Jennifer Dien Bard describes how her microbiology lab at Children’s Hospital Los Angeles (CHLA) implemented variant surveillance during the emergence of the Omicron variant. All SARS-CoV-2-positive qPCR samples with a viral titer of Ct < 30 were genotyped with NGS. These samples were run in batches of 14 performed twice weekly. With this method, CHLA reported variants within 30 hours of initial qPCR detection, all with a workflow that required only 10 minutes of wet-lab hands-on time. This workflow also required minimal training thanks to on-board library preparation and sequencing with a complete SARS-CoV-2 NGS assay and integrated data analysis with built-in software that automatically listed mutations and calls SARS-CoV-2 variants. With minimal hands-on time, flexible throughput, and rapid sequencing, an integrated sequencer was a great fit for routine SARS-CoV-2 genomic sequencing at CHLA, delivering actionable results in a single day.
All-in-one NGS systems make it easy to implement full-genome sequencing for microbial and infectious disease research applications, including pathogen identification, epidemiological investigations, antimicrobial resistance profiling, and variant surveillance – all within as little as one-day turnaround time.
For Research Use Only. Not for use in diagnostic procedures.
1. Fissel, J. A., Mestas, J., Chen, P. Y., Flores-Vazquez, J., Truong, T. T., Bootwalla, M., Maglinte, D. T., Gai, X., & Dien Bard, J. (2022). Implementation of a Streamlined SARS-CoV-2 Whole-Genome Sequencing Assay for Expeditious Surveillance during the Emergence of the Omicron Variant. Journal of clinical microbiology, 60(4), e0256921. https://doi.org/10.1128/jcm.02569-21