When SARS-CoV-2 reached the United States in late January 2020, Labcorp immediately began development of an RT-PCR test to aid in detection and diagnosis of COVID-19 in infected patients. As a result of developing this assay, Labcorp has unprecedented access to positive SARS-CoV-2 samples nationwide and has leveraged that access to implement a comprehensive SARS-CoV-2 Sequencing Surveillance program. This pipeline uses residual extraction material from positive samples and converts those samples into high throughput sequencing libraries using 1,200bp overlapping amplicons. Sequencing proceeds on the Pacific Biosciences Sequel II using HiFi CCS reads. Sequencing reads are used to generate a consensus sequence that is used to identify the lineage and clade of each sample that meets the minimum coverage criteria. To date, Labcorp has sequenced over 15,000 samples in real time and has submitted those sequences to public repositories in collaboration with the US Centers for Disease control. Labcorp’s surveillance program has been able to track the spread of SARS-CoV-2 variants across the US, including the observation of the increased prevalence of B.1.1.7 and detection of the first case of B.1.351. This work could serve as a model for future public and private collaborations with respect to national infectious disease surveillance.
1. Understand the difference between RT-PCR testing and whole genome sequencing
2. Explain why sequencing based pandemic surveillance is so important to the national response to virus spread.