Collaboration between clinical and academic laboratories for sequencing SARS-CoV-2 genomes

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  • Wang, Jeremy
    • Affiliation: School of Medicine, Department of Genetics
  • Hawken, Shawn
    • Affiliation: School of Medicine, Department of Pathology and Laboratory Medicine
  • Jones, Corbin D.
    • Affiliation: School of Medicine, Department of Genetics
  • Hagan, Robert S.
    • Affiliation: School of Medicine, Department of Medicine, Division of Pulmonary Diseases and Critical Care Medicine
  • Bushman, Frederic
    • Other Affiliation: University of Pennsylvania
  • Everett, John
    • Other Affiliation: University of Pennsylvania
  • Miller, Melissa B.
    • Affiliation: School of Medicine, Department of Pathology and Laboratory Medicine
  • Rodino, Kyle G.
    • Other Affiliation: University of Pennsylvania
Abstract
  • Genomic sequencing of SARS-CoV-2 continues to provide valuable insight into the ever-changing variant makeup of the COVID-19 pandemic. More than three million SARS-COV-2 genomes have been deposited in GISAID, but contributions from the United States, particularly through 2020, lagged behind the global effort. The primary goal of clinical microbiology laboratories is seldom rooted in epidemiologic or public health testing and many labs do not contain in-house sequencing technology. However, we recognized the need for clinical microbiologists to lend expertise, share specimen resources, and partner with academic laboratories and sequencing cores to assist in SARS-COV-2 epidemiologic sequencing efforts. Here we describe two clinical and academic laboratory collaborations for SARS-COV-2 genomic sequencing. We highlight roles of the clinical microbiologists and the academic labs, outline best practices, describe two divergent strategies in accomplishing a similar goal, and discuss the challenges with implementing and maintaining such programs.
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  • Article
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  • In Copyright
Journal title
  • Journal of Clinical Microbiology
Language
  • English
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  • Postprint

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