Research Resources

We are continually aggregating and updating COVID-19 research resources (publications, data tools, and laboratory resources) to support your work. If you have resources that we should add, please send them to us.

Page Content:

General Resources

  • UC Health & CDPH COVID Modeling Consortium  

    The UC Health & CDPH COVID Modeling Consortium unites UC investigators and California public health leaders in a forum to help guide policy decision-making during the COVID-19 pandemic.The consortium aims to facilitate direct, timely engagement and conversation between policymakers and investigators, with bi-weekly discussions focused on high-priority topics such as vaccinations, health equity, economic impact, challenges of new variants, and epidemiological forecasting and nowcasting.

    To learn more or join the conversation, please email us: [email protected].

  • Health and Human Services (HHS) COVID-19 Funding Tracking  
    The information contained on this Tracking Spending-Increasing Accountability (TAGGS) website provides data on the awards made by HHS using emergency supplemental appropriation funding provided in the Coronavirus Preparedness and Response Supplemental Appropriations Act, 2020, the Families First Coronavirus Response Act, the CARES Act (Coronavirus Aid, Relief, and Economic Security Act), the Paycheck Protection Program and Health Care Enhancement Act, and the Coronavirus Response and Relief Supplemental Appropriations Act, 2021.COVID-19 Research Guidelines and Policies
    Refer to the main Office of Research website for all guidelines and policies for safe, effective, and responsible conduct of research during the pandemic.
  • COVID Research Patient and Community Advisory Board (PCAB)  
    The UCSF COVID-19 Research Patient and Community Advisory Board (PCAB) provides review and feedback for UCSF clinical and translational research directly related to COVID-19. Intense public concern about the COVID-19 pandemic and evidence of profound inequities in the pandemic’s toll on communities of color and low-income communities accentuate the importance of community engagement in the conduct of clinical research on COVID-19. The COVID-19 Research PCAB is a group of diverse experts, including patients, leaders of clinical systems, community-based organizations, civic agencies, and other community members who have a stake in the outcomes of COVID-19 research. All investigators conducting COVID-related clinical and community research are strongly encouraged to obtain a consultation from the UCSF COVID-19 PCAB. Request a COVID-19 PCAB review session by requesting a Community-Engaged Research Consultation.
  • UCSF Division of HIV, Infectious Diseases & Global Medicine COVID-19 Website  

    The UCSF Division of HIV, Infectious Diseases & Global Medicine provides a valuable set of informational resources on COVID-19 through its Cross-Campus Infectious Diseases COVID-19 Task Force. This Task Force is made up of infectious disease specialists from ZSFGH, VA, and UCSF hospitals and has been established to provide educational materials, resources, and guidance related to the COVID-19 pandemic.

    Members: Joanne Engel, MD, PhD, Harry Lampiris, MD, Lisa Winston, MD, Annie Luetkemeyer, MD, Chaz Langelier, MD, PhD, Vivek Jain, MD, MAS, Deborah Yokoe, MD, MPH, Sarah Doernberg, MD, MAS, Jennifer Babik, MD, PhD, Monica Gandhi, MD, MPH, Rachel Bystritsky, MD, Ted Ruel, MD, Lynn Ramirez, MD, Charles Chiu, MD, PhD, Bryn Boslett, MD & Chesa Cox, MPH; Co-Chairs & Digest Editors: Brian Schwartz, MD & Diane Havlir, MD; Guest Contributors: Tim Henrich, MD, Rachel Rutishauser, MD, PhD, Emma Bainbridge, MD, MPH, John Szumowski, MD, Akanksha Vaidya, MD, Jennifer Mulliken, MD

    This team provides informative weekly digests with updates on epidemiology, testing, educational resources, ID research and FAQs on these topics. To subscribe to the digest, please fill out our contact form here.

  • Biomedical Advanced Research and Development Authority (BARDA) Coronavirus (COVID-19) Medical Countermeasures 
    The U.S. government is providing a portal for the 2019 novel coronavirus (COVID-19) medical countermeasures task force as a single point of entry for the submission of market research packages and meeting requests from interested stakeholders.  
  • Coronavirus Method Development Community 
    An open-access repository for scientific methods and has a coronavirus method development group. Examples include a protocol for lyophilization of CoronaDetective tests and more generally any QUASR RT-LAMP reaction materials or an automated high-throughput protocol for viral concentration from wastewater using the KingFisher Flex platform.

Literature Resources

Datasets & Visualization Tools

Clinical 

Communication

Epidemiology and Population Health 

  • covidcounties.org: open-source platform tracking the current trends of the COVID-19 pandemic at the county level (December 2020 release)
    Management of the COVID-19 pandemic has proven to be a significant challenge to policy makers. This is in large part due to uneven reporting and the absence of open-access visualization tools to present local trends and infer healthcare needs. covidcounties.org represents a powerful open-source platform to empower non-data scientists to track the current trends of the COVID-19 pandemic at the US county level, using time series plots and maps, to help facilitate policy and healthcare decisions which can help improve outcomes. This application is accompanied by a manually curated dataset that catalogs all major public policy actions made at the state-level, as well as technical validation of the primary data. Finally, the underlying code for the site is also provided as open source, enabling others to validate and learn from this work. We welcome volunteers (both technical and non-technical) to help us to further develop CovidCounties (https://covidcounties.org/buttelabcovid/www/volunteers.html).
  • Collection of Live Information Regarding National Epidemic Prevention
    Collects and gathers information of hospitals, hotels, factories, logistics, donations, contributions, prevention, and treatment to help organizations and people collaborate.
  • Impact of Health Disparities on COVID-19 Outcomes 
    The National Academies of Sciences, Engineering, and Medicine have a long history of gathering leading experts to share the latest research and information on health equity. A new National Academies resource, Conversations on COVID-19: Impacts on Communities of Color, includes conversations with experts on a variety of topics related to minority health and COVID-19, as well as information and resources from the National Academies on issues related to health equity.
    Learn more about the impact of health disparities on COVID-19 outcomes by visiting nationalacademies.org/covid-19-minority-impacts. 
  • Novel Corona Virus 2019 Dataset 
    Daily updated information on the number of affected cases, deaths, and recovery from 2019 Novel Coronavirus. 
  • UCSF Health Atlas
    Interactive population health mapping website that curates publicly available data and visualizes it at the census tract level.

Omic

  • Repository of Coronavirus Genomes
    Sequences of genomes that are similar to 2019-nCoV / SARS-CoV-2.
  • SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology and Surveillance (SPHERES)
    CDC is leading the SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology and Surveillance (SPHERES), a new national genomics consortium to coordinate SARS-CoV-2 sequencing across the United States. The SPHERES consortium includes 37 state and local public health laboratories, several large regional and national clinical diagnostic corporations, and academic and non-profit leaders in pathogen genomics, bioinformatics, and public health from across the country. Moreover, the consortium aligns federal laboratories and public health agencies with international genomics efforts and engages the private sector in efforts to better understand the genomics and patterns of SARS-CoV-2 transmission across the United States.
  • SARS-CoV-2 Sequencing Resources
    A crowd-sourced collection of information, documentation, protocols, and other resources for public health laboratories sequencing SARS-CoV-2 coronavirus samples.

Other Research 

  • Promiscuous 2.0: a resource for drug repositioning
    The development of new drugs for diseases is a time-consuming, costly and risky process. In recent years, many drugs could be approved for other indications. This repurposing process allows to effectively reduce development costs, time and, ultimately, save patients’ lives. During the ongoing COVID-19 pandemic, drug repositioning has gained widespread attention as a fast opportunity to find potential treatments against the newly emerging disease. In order to expand this field to researchers with varying levels of experience, we made an effort to open it to all users (meaning novices as well as experts in cheminformatics) by significantly improving the entry-level user experience. The browsing functionality can be used as a global entry point to collect further information with regards to small molecules (∼1 million), side-effects (∼110 000) or drug-target interactions (∼3 million). The drug-repositioning tab for small molecules will also suggest possible drug-repositioning opportunities to the user by using structural similarity measurements for small molecules using two different approaches. Additionally, using information from the Promiscuous 2.0 Database, lists of candidate drugs for given indications were precomputed, including a section dedicated to potential treatments for COVID-19. All the information is interconnected by a dynamic network-based visualization to identify new indications for available compounds. Promiscuous 2.0 is unique in its functionality and is available at http://bioinformatics.charite.de/promiscuous2.

Data Computing Resources

  • US Census TOPx COVID-19 Solutions

    TOPx, modeled on The Opportunity Project (TOP), is an innovation program led by Census Open Innovation Labs at the U.S. Census Bureau. Through technology development sprints, TOPx, engages government, technologists and communities to co-create digital products that serve the public using federal open data. To date, more than 1,500 people, 30 federal agencies, and hundreds of organizations have participated in TOP sprints - resulting in over 135 new open data tools including apps, websites, mapping tools, data visualizations, games and more.

    The Department of Health and Human Services, in partnership with the U.S. Census Bureau, facilitated a TOPx technology development sprint focused on a pressing national challenge. In the midst of the COVID-19 pandemic, ensuring that diagnostic data from testing devices is harmonized, automated, and shared with public health authorities and other key stakeholders is essential. Unfortunately, this process is not currently occurring because diagnostic devices and tests have not previously been coupled with applications or digital software tools. Through this sprint, 12 technology teams, which were selected from the HHS COVID-19 At-Anywhere Diagnostics Design-a-thon, developed digital products to ensure this information is transmitted efficiently, securely and accurately to key stakeholders, including federal, state, local and tribal governments, patients, providers, employers, schools, consumers and others.

  • UCSF AWS COVID19
    Researchers at UCSF that wish to conduct COVID-19 related research and obtain Amazon Web Services (AWS) credits to cover the cost of the computing resources for that research can contact IT for help in planning and submitting the ask for credits. Please contact Ryan Hunt and/or reply to the survey.

Laboratory Materials

  • SARS-CoV-2 Replicon (cDNA) for Various Gene Cloning Purposes
    Contact Nevan Krogan for more information
  • Lung Organoid Model: A collection of labs are assembling a rapid-translation pathway based on organoids and lung culture systems. For information about plugging into the program/platform, please contact ImmunoX.
  • SARS-CoV-2 virus: All work with SARS-CoV-2 must be performed under Biosafety Level 3 (BSL3) containment. To work with the virus at UCSF you must have access to a BSL3 facility, and you must have an approved Biological User Authorization that describes all experimental procedures and biohazard mitigation. For more information, contact Anita Sil.