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Is SNP Genotyping a Better Approach for Monitoring for Known Variants of Concern

C.E. Credits: P.A.C.E. CE Florida CE
Speaker
  • Distinguished Professor and Director, The Genome Center, Genome and Biomedical Sciences Facility, University of California, Davis
    Biography

      After studying Natural Sciences at Cambridge University, Richard Michelmore joined the faculty of University of California at Davis in 1982. Richard was the founding Director of the Genome Center at UC Davis in 2003. He is currently a Distinguished Professor in the Departments of Plant Sciences, Molecular & Cellular Biology, and Medical Microbiology & Immunology. His multidisciplinary research utilizes molecular, genetic, and evolutionary approaches to plant genomics and he has published over 200 scientific papers. In particular, he aims to exploit such approaches for information-driven deployment of resistance genes in crop plants to provide more durable disease resistance. In addition, he is interested in fostering research to enhance global food security. His interests also include applications of DNA sequencing to all areas of biology and its increasing impact on society. In response to the current pandemic, he has been a major contributor to the team providing rapid, high throughput testing for SARS-CoV-2 to the UC Davis campus and the City of Davis and is now deploying rapid genotyping to monitor for variants of concern.


    Abstract

    At UC Davis we have implemented rapid, inexpensive, high throughput testing for SARS-Cov-2 using technology repurposed from the agricultural biotechnology sector.  As part of Healthy Davis Together, this is providing at least weekly testing for the campus and the City of Davis.   The workflow involves testing saliva samples from asymptomatic individuals without RNA extraction.  To date, we have processed over 400,000 tests and identified more than 1,700 positive individuals.  The IntelliQube qPCR machine is not the rate limiting step, which provides the opportunity for high throughput genotyping of all positive samples for variants of SARS-CoV-2.  Evolution of the virus is inevitable and it is critical to monitor for variants of concern that have higher transmissibility and/or reduce the effectiveness of vaccines.  Genotyping using SNPs that discriminate between known variants of concern is more efficient, less expensive, technically less demanding, and importantly much more rapid than sequencing.  It will not, however, discover new variants and is therefore complementary to sequencing.  In collaboration with LGC, we have developed and deployed 14 SNP assays that can distinguish all the current variants of concern and interest in a redundant fashion.  All positive samples are assayed and genotypes assigned within a few days of sample collection.  Non-wildtype genotypes are validated by sequencing.  This provides rapid resulting to the county health authorities.  In summary, robust genotyping technology is available for monitoring large numbers of positive samples on a global scale; this will be particularly important in geographical areas where sequencing is not feasible.  The regulatory framework for this is more challenging than the technical aspects.

    Learning Objectives:

    1. Why is it important to monitor for variants of SARS-CoV-2?

    2. What are the relative advantages of SNP genotyping and sequencing for surveillance?


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