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Genomic Epidemiology Data Infrastructure Needs for SARS-CoV-2 Modernizing Pandemic Response Strategies (2020) / Chapter Skim
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3 Current Genomic Epidemiology Efforts Related to SARS-CoV-2
Pages 33-46

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From page 33...
... This chapter provides an overview of select SARS-CoV-2 data sources, identifies limitations of those sources, and highlights breakthrough efforts to combine and analyze genomic sequence data with clinical and epidemiological data for SARS-CoV-2. The proceeding chapter sets out the key considerations for such a framework to bring these data sources together.
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From page 34...
... 2 at NIH serves as a primary repository for all genomic sequencing. In accordance with NIH Data Sharing policies, genomic scientists rapidly deposit and release assembled SARS-CoV-2 genomes and raw metagenomic reads in NCBI's GenBank and SRA databases, linked under BioProjects.
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From page 35...
... . 6  The National COVID Cohort Collaborative is a collaboration among National Center for Advancing Translational Sciences–supported Clinical and Translational Science Awards Program hubs, the National Center for Data to Health, and distributed clinical data networks, with overall stewardship by NIH's National Center for Advancing Translational Sciences.
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From page 36...
... N3C was developed to improve efficiency and accessibility of analyses with COVID-19 clinical data, to expand the ability to analyze coronavirus diseases, and to demonstrate novel approaches for collaborative data sharing. It is governed by a single, central Institutional Review Board (IRB)
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From page 37...
... . By contrast, clusters of SARS CoV-2 genomic sequences seen in Southern and Eastern quadrants in F ­ ebruary/ March, together with epidemiologic data, support multiple local transmissions derived from single sources (super-spreading event)
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From page 38...
... Wadsworth Center The Wadsworth Center,13 the public health laboratory for the New York State Department of Health, was the first laboratory in New York to receive Emergency Use Authorization for SARS-CoV-2 testing. While rapidly expanding its own capacity, Wadsworth supported other commercial and hospital laboratories in the state to develop and ramp up testing capacities for SARS-CoV-2.
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From page 39...
... COG-UK was created to deliver clinically actionable data to local medical centers and the UK government to guide health interventions and policies. Collaborating partners include public health agencies, university laboratories, regional university hubs and health organizations, and sequenc ing centers, including the Wellcome Sanger Insti­ tute.
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From page 40...
... In Washington State, Microsoft's data science team is working with the Washington State Department of Health to build more efficient systems for collecting and managing large volumes of data about disease incidence and hospitalization (Edmond, 2020)
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From page 41...
... Next, they used direct metagenomic sequencing of bronchoalveolar lavage fluid to identify non-human microbial DNA. With some additional targeted sequencing and analysis, they independently identified the complete SARS-CoV-2 genome (Zhou et al., 2020)
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From page 42...
... Its genome scientists ­accessed the reference genome and rapidly acquired full genome sequences of these clinical cases. Phylogenetic analyses were performed using the 2,363 other SARS-CoV-2 genomic sequences deposited in GISAID in March 2020.
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From page 43...
... Public health personnel often have no f­ ormal degree training in public health and thereby lack sufficient training in data science; more trainers in genomic epidemiology are needed to develop ­actionable interventions. Robustly integrating genomic data with clinical and epidemiological data would require a health care and public health system with sufficient infrastructure, coordination, and capacity to integrate and analyze the data.
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From page 44...
... Conclusion: Current sources of SARS-CoV-2 genome sequence data, and current efforts to integrate these data with relevant epide miological and clinical data, are patchy, typically passive, reactive, uncoordinated, and underfunded in the United States. As a result, currently available data are unrepresentative of many important population features, biased, and inadequate to answer many of the pressing questions about the evolution and transmission of the virus, and the relationships of genome sequence variants with viru lence, pathogenesis, clinical outcomes, and the effectiveness of countermeasures.
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From page 45...
... 2020. Amazon, UCSF partner for COVID-19 genome sequencing projects.
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Key Terms

  • genomic epidemiology
  • genomic sequencing
  • data sharing
  • epidemiological data
  • clinical data

  • sequence data
  • sequencing data
  • genomic data
  • genomic sequences
  • genome sequence

  • genome sequences
  • washington state
  • state public
  • health emergency
  • health agencies

  • health laboratories
  • health laboratory
  • national covid
  • global initiative
  • covid cohort

  • advancing translational
  • broad institute
  • cohort collaborative
  • sharing data
  • influenza data

  • genome sequencing
  • current efforts
  • current sources
  • viral genetic
  • emergency response


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