2021 Project: University of California, San Francisco (UCSF)

Actionable, Real-Time Genomic Surveillance of SARS-CoV-2 in California.

What to know

UCSF created an integrated network to combine rapid viral sequencing with epidemiologic and clinical data. Awarded in 2021, this project established a real-time network with local, state, and federal public health agencies to track and monitor the evolution and spread of COVID-19. By using techniques to sequence SARS-CoV-2 genomes from infected patients and then sharing data with public health agencies through the network, researchers sought to improve contract tracing and public health responses.

Decorative image with words "2021" and "SARS-CoV-2"

Findings on SARS-CoV-2 surveillance and investigations

This project:

  • Determined SARS-CoV-2 transmission could occur from fully vaccinated symptomatic index patients to vaccinated and unvaccinated household contacts. 1
  • Explored the application of genomic and computational methods for efficient data-driven response to the COVID-19 pandemic. 2
  • Explored the associations between vaccine breakthrough infections in the San Francisco Bay Area and SARS-CoV-2 variants in early 2021. 3

Findings on SARS-CoV-2 variant characteristics

This project:

  • Determined differences in antibody titers in Delta versus Omicron vaccine breakthrough infections.4
  • Showed that without vaccination, Omicron infection induced a weak and limited humoral response that might not confer broad protection against non-Omicron variants. 5
  • Determined differences in antibody titer for Delta and in Omicron BA.1 and BA.2 variants in unvaccinated individuals and in breakthrough infections. 6

New SARS-CoV-2 dashboards and websites

Data from this contract contributes directly to several dashboards published as Campus Health Updates for UCSF: https://www.ucsf.edu/campus-health-updates

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Content Source:
National Center for Emerging and Zoonotic Infectious Diseases (NCEZID)
  1. Contact-Tracing Outcomes Among Household Contacts of Fully Vaccinated Coronavirus Disease 2019 (COVID-19) Patients: San Francisco, California, 29 January-2 July 2021, Clinical Infectious Diseases, 2021.
  2. Unlocking capacities of genomics for the COVID-19 response and future pandemics, Nat Methods, 2022.
  3. Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California. Nature Microbiology 7, 2022.
  4. Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants. Cell, 2022.
  5. Limited cross-variant immunity from SARS-CoV-2 Omicron without vaccination. Nature, 2022.
  6. Neutralizing Immunity Induced Against the Omicron BA.1 and BA.2 Variants in Vaccine Breakthrough Infections | The Journal of Infectious Diseases | Oxford Academic (oup.com)