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.
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
- 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.
- Unlocking capacities of genomics for the COVID-19 response and future pandemics, Nat Methods, 2022.
- Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California. Nature Microbiology 7, 2022.
- Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants. Cell, 2022.
- Limited cross-variant immunity from SARS-CoV-2 Omicron without vaccination. Nature, 2022.
- 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)