2020 Project: Scripps Research Institute

Genomic sequencing of SARS-CoV-2 to investigate local and cross-border emergence and spread

What to know

Scripps Research Institute researchers investigated SARS-CoV-2 genomics and molecular epidemiology in Southern California, collaborating with the ÐÇ¿ÕÓéÀÖ¹ÙÍø SPHERES program, California COVIDNet, and county and local public health laboratories. Awarded in 2020, this project expanded collaboration with California laboratories to improve laboratory and bioinformatic methods for cost-effective, high-throughput sequencing.

Decorative image with words "2020" and "SARS-CoV-2"

Findings on SARS-CoV-2 surveillance and investigations

This project:

  • Determined there were several independent introductions of the highly transmissible B.1.1.7 variant in the United States which spread to most states within months.1
  • Described the emergence of SARS-CoV-2 and the role of superspreading during large-scale events during the early outbreak in the United States by using mobility and genomic data.2
  • Developed ViReflow, a user-friendly pipeline enabling rapid analysis of viral sequence dataset. Developed specifically in response to the COVID-19 pandemic, ViReflow is general to any viral pathogen.3
  • Evaluated the amount of SARS-CoV-2 that could be detected from touched versus non-touched indoor surfaces.4
  • Developed improved virus concentration protocols, as well as analysis software for wastewater surveillance. As a result, it was possible to detect emerging variants of concern up to 14 days earlier than through clinical testing.5
  • Developed a rapid and inexpensive pipeline using a molecular test to detect and quantify RNA for SARS-CoV-2. The processing capacity was 6,000 samples per day with next-day result turnaround times.6
  • Developed , an open-source database that tracks more than 40 million combinations of lineages and individual mutations, such as those on the surface of SARS-CoV-2 that helps the virus enter human cells. Then the data are used to provide insights for researchers, public health officials, and the general public. 7
  • Developed , a searchable interface of COVID-19 and SARS-CoV-2 resources including publications, clinical trials, datasets, protocols, and other resources.8

New SARS-CoV-2 dashboards and websites

This project:

  • In partnership with SEARCH alliance, conducted SARS-CoV-2 wastewater monitoring for the San Diego region and provided weekly reporting publicly.
  • Hosted a web portal, , that analyzes and visualizes SARS-CoV-2 genomic data, and Outbreak.info Research Library, and a searchable interface of COVID-19 and SARS-CoV-2 resources including publications, clinical trials, datasets.

New and improved sequencing software tools

This project:

  • Developed ViReflow, a user-friendly viral consensus sequence reconstruction pipeline enabling rapid analysis of viral sequence data set.9
  • Developed —a web portal that analyzes and visualizes SARS-CoV-2 genomic data—and —a searchable interface of COVID-19 and SARS-CoV-2 resources including publications, clinical trials, datasets.78
  • Developed , an analysis framework for SARS-CoV-2 wastewater sequence data.
  • Continues to develop and maintain open-source software for data streaming and analysis, including iVar and INSPECT

Some of this work was supported in part or in full by the BAA award.

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Content Source:
National Center for Emerging and Zoonotic Infectious Diseases (NCEZID)
  1. , medRxiv, 2021.
  2. medRxiv, 2021.
  3. Sci Rep, 2022.
  4. . mSystems, 2022.
  5. Nature, 2022.
  6. , medRxiv, 2021.
  7. , medRxiv. 2021.
  8. bioRxiv, 2022.
  9. Sci Rep, 2022.