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HiFiViral: A Novel Method for Surveillance of SARS-CoV-2 that is Robust Across Sample Input Quantities and the Evolution of New Variants

The COVID-19 pandemic continues to be a major global epidemiological challenge with the ongoing emergence of new strain lineages that are more contagious, more virulent, drug-resistant, and in some cases evade vaccine-induced immunity. In response, the HiFiViral SARS-CoV-2 kit was developed as a scalable solution for the Sequel II and Sequel IIe Systems. Unlike amplicon sequencing, the HiFiViral SARS-CoV-2 kit uses tiled probes, resulting in robust genome coverage across varying viral input quantities despite the presence of new variants. The use of highly accurate long reads, or HiFi reads, enables comprehensive variant detection, including single nucleotide variants, indels, and structural variants, as well as phasing of variants if multiple strains are present in samples. The fully kitted solution contains all reagents needed for viral enrichment and barcoding up to 384 samples, which can be pooled in a single SMRTbell library and run on a single SMRT Cell 8M. The add-only workflow requires two days in the lab with overnight sequencing and analysis and may be automated to achieve a turnaround time of 24 hours. SMRT Link analysis includes variant calling, HiFi read depth plots, the detection of multiple strains in samples, and consensus sequences ready for submission to public databases. In the talk, Dr. Sarah Kingan, demonstrates performance across a broad range of sample Ct, the accuracy of our variant calling method for viral controls, including variants of concern, and the ability to detect multiple variants down to 20% minor frequency. HiFiViral for SARS-CoV-2 is a cost-effective, convenient, and accurate method for viral sequencing, well-suited for scalable surveillance of a rapidly evolving virus to inform public health decision making.

 

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