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APR 14, 2021 4:30 PM PDT

How RT-PCR Testing Allows Labcorp to Perform National SARS-CoV-2 Pandemic Surveillance

Sponsored by: PacBio
C.E. Credits: P.A.C.E. CE Florida CE
Speaker
  • Associate Vice President, Research and Development, Laboratory Corporation of America
    Biography

      Brian Krueger, PhD, is an Associate Vice President and Technical Director in R&D at Labcorp. His areas of focus are high throughput exome and genome sequencing, Molecular Microbiology, and high throughput lab automation. He and the Molecular Microbiology R&D group at Labcorp developed and received FDA Emergency Use Authorization for the LabCorp COVID-19 RT-PCR Test.  Recently, Labcorp was awarded a SARS-CoV-2 sequencing surveillance contract with the CDC as a direct result of the R&D team's work in sequencing and characterizing thousands of viral genomes from early on in the pandemic. Dr. Krueger received his PhD in Molecular and Cellular Biology from the University of Iowa in 2009.  He then spent 3 years at the University of Florida employing genetic manipulation and high throughput sequencing techniques to create hundreds of viral mutants of Kaposi Sarcoma Herpesvirus and Murine Herpesvirus 68.  In 2012, Dr. Krueger transitioned from viruses to humans and spent 3 years overseeing Dr. David Goldstein's high throughput human genetics sequencing lab at Duke University and transitioned that lab to Columbia University Medical Center in 2014. He joined Labcorp in 2015 where he has continued to focus on diagnostic assay development in both rare disease genetics and infectious disease.


    Abstract

    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.

    Learning Objectives:

    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.


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