COVID-19 begins by infection of the respiratory tract epithelium that lines the airways of the nose and lungs. In collaboration with a large number of research laboratories, we have studied the epithelial cells of the airways in diseases including cystic fibrosis, chronic bronchitis, asthma and...

Andrej Sali is applying integrative modeling towards determining the structures of the protein complexes formed by SARS-CoV-2 proteins and human proteins, with the goal of understanding the role of these complexes during viral entry into human cells and viral replication.

Our goal is to generate a single cell resolution spatial atlas of SARS-CoV-2 infection across multiple tissues in patients with severe COVID-19. We aim to determine what specific cell types are targeted by SARS-CoV-2 and characterize the cellular and molecular changes in multiple clinically...

The Kortemme laboratory pursues de novo designed proteins - proteins engineered computationally from scratch - for blocking SARS-CoV-2 entry into human cells by targeting the virus' "spike" protein. De novo designed proteins are a new class of potentially highly stable and potent therapeutic...

We are developing a protein drug as an immediate medical countermeasure against SARS-CoV-2 infection using our unique protein engineering technology. Unfortunately we have no funding for this project and need your support.

Serologic assays are needed to determine SARS-CoV-2 seroprevalence, but poor specificity can overestimate exposures. Here, we built a pan-human coronavirus proteome-wide programmable phage display assay (VirScan) to profile coronavirus antigens specifically enriched by 20 COVID-19 patient serum IgG...

Development of a mouse model that can be used to 1) eliminate a subset of macrophages from the lungs of mice that are permissive for epithelial infection during SARS-CoV-2 infection. These macrophages are heavily recruited during infection, and may play in a role in the detrimental inflammatory...

Drugs that inhibit viral proteins are expected to limit the spread of COVID19. While some of the viral proteins are considered good drug targets, others are more difficult. Our group has specific expertise in technology that allows the identification of drug-like molecules that bind to these...

We have developed a new immunity strategy that leverages a CRISPR epigenetic editing platform with key prophylactic properties. Our approach enables us to robustly and durably silence host proteins required for viral infection or pathogenesis. Our long-term vision is that this strategy can be...

Our lab is working to understand how a range of human-derived antibodies interact with the COVID-19 spike protein. Some of these antibodies are extremely effective at neutralizing the virus, and in fact one is already in clinical trials. Using cryo electron microscopy, we have been able to generate...

We are examining the evolution of several COVID-19/SARS-CoV proteins, including accessory proteins, structural proteins, nucleocapsid, and their interactions with host proteins and genomic RNA. These studies include the assembly of virus like particles and the oligomeric state of nucleocapsid.

Human bronchial epithelial (HBE) cells are infected by SARS-CoV-2. We are studying SARS-CoV-2-related host cell genes in these cells. The work is relevant to understanding why people with various comorbities like asthma and COPD may have different outcomes in COVID-19.

SARS-CoV-2, the novel virus causing the COVID-19 pandemic, uses proteases within our own body to increase its ability to infect our cells. This project aims to see whether genetic variation of certain protease can explain the severity of COVID-19, and also whether developing drugs against our own...

We have generated stable Expi293 cell lines expressing His- or Avi-tagged SARS-CoV2 RBD or spike protein to aid the high demand needed for serological assays.

Characterizing SARS-CoV-2-specific immunity in convalescent individuals

All viruses including coronaviruses hijack specific components of the host cells to facilitate viral entry, viral protein synthesis, genome replication and assembly of new infectious virions. We use CRISPR genetic screens to identify host factors, which are critical for coronavirus infection. This...

Early detection of infection and specific information on tissue damage are the essential steps in assessing novel drug or treatment paradigms for any pathogen. We are leveraging an existing IRB and human blood sample workflow at ZSFG to quickly pivot our project to the discovery of the earliest...

Our laboratory is targeting host factors co-opted by SARS-CoV-2 to support viral replication. We identify the relevant host factors through a close collaboration with Nevan Krogan's lab and the QBI Coronavirus Research Group.

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As a member of the UCSF QBI Coronavirus research group (QCRG), we study how SARS-CoV2 rewires the behavior of human cells for viral spreading. Our lab uses computational methods to predict virus-human protein interactions and mechanisms that are important for viral infection and could be targeted...

crystallize the two proteases, and develop drugs using three methods based on iterative structure based methods, fragment screening, computer docking followed by crystallography and iterative improvement, and tethering technologies that insert cysteine residues as a 'fishing line' to select...

As part of the QBI Coronavirus Research Group (QCRG), we are studying how SARC-CoV-2 hijacks the ubiquitin proteolysis pathway to evade innate immunity. We leverage comprehensive data sets on virus-host interactions and gene expression profiles during infection to formulate hypotheses that inform...

We are assessing how human lung cells respond to infection by SARS-CoV-2.

For nearly 40 years the UCSF AIDS Specimen Bank (ASB) has collected, processed, stored and distributed biospecimens for UCSF investigators who require secure and safe biospecimen handling for patients with infectious diseases. We have recently expanded our activities to support the collection,...

This study reports clinical and laboratory findings of the first 12 patients diagnosed with COVID19 in the United States, between January 20, 2020 and February 5, 2020.

Emerging reports have associated COVID-19 with a novel coagulopathy which is associated with thromboembolism, organ-failure, and death. In this study, we aim to prospectively characterize coagulation profiles in COVID-19 patients and associated clinical outcomes to support future interventional...

This is a longitudinal study of 896 individuals who complete assessments every 6 six months, starting in August 2020. We collect data on general and COVID-19-specific trauma exposure, PTSD symptoms, depression, anxiety, perceived stress, pandemic threat, protective and risky behaviors for...

Since patients with liver disease are immuno-compromised, it is important to determine their outcomes. The purpose of this study is to analyze the differences in COVID-19 outcomes between patients with and without liver disease. Patients with COVID-19 and/or liver disease will be included.

COVID-19 Screen

Using an anonymous public survey, we collected self-reported information from individuals who had been tested for COVID-19. With the pooled initial responses we have shown predictors for a COVID-19 positive test in a relatively healthy outpatient population include smell or taste change, fever and...

COVID-19 Symptom History

UCSF is participating in the CovidSurg study coordinated by the University of Birmingham through the NIHR Global Surgery Research Unit, a worldwide collaboration of surgeons coming together to understand the implications of COVID-19 on surgical patients. The CovidSurg study aims to determine the 30...

We are developing an imaging technology to visualize the interaction between SARS-CoV-2 virus and the host cells. And using this technology, we are screening and repurposing existing drugs to inhibit the viral interaction with the human cells. By this way, we are hoping to find a quick therapy to...

The aim of this pilot trial is to evaluate the effect of four over the counter antiseptic mouthwash/gargling solutions compared to a control (distilled water) to reduce SARS-CoV-2 load over 4 weeks. In addition, study participants will be assessed for the severity of their clinical symptoms...

We are able to provide collaborative support for studies that will benefit from assays of functional antibodies, including antibody-dependent enhancement and neutralizing activities.

The main purpose of this study was to determine how often patients referred for non-chest imaging studies have findings suggesting the presence of COVID-19. This could potentially be seen, for example, on a CT of the abdomen and pelvis that includes the lung bases or a CT of the neck that includes...

Liver function abnormalities in patients with inflammatory bowel disease

Our lab is working on novel mouse model development to provide tools for study of disease pathogenesis in SARS-CoV-2 infection, including the host immune response.

While the lungs are ground zero, COVID19 tears through organ systems from brain to blood vessels. We see people recover but complain of ongoing problems, including lingering cognitive problems, depression, and anxiety. We have brought together 2 laboratories with complementary techniques ...

We plan to explore children's exposure to opioid and sedatives before, during, and after COVID-19 pandemic in critically ill children.

Relatively little is known about COVID-19 infection in children. The ability to test for the virus is limited. However, chest X-ray findings may provide a proxy diagnostic. Specific COVID19 computed tomography findings have been described, but chest x-ray findings have not yet been evaluated....

Relatively little is known about COVID-19 infection in children. The ability to test for the virus is limited. However, chest X-ray findings may provide a proxy diagnostic. Specific COVID19 computed tomography findings have been described, but chest x-ray findings have not yet been evaluated....

Pediatric Otolaryngology practice during COVID pandemic - a survey study

This will be a single site, mechanistic study of asthmatic subjects and healthy, non-asthmatic controls involving a baseline characterization visit and a research bronchoscopy visit. We will identify differences in airway epithelial epigenetic enhancer signatures in asthma, by analyzing freshly...

The goal of this project is to develop engineered variants of the SARS CoV-2 Spike glycoprotein receptor binding domain (RBD) with decreased binding to the human receptor angiotensin converting enzyme 2 (ACE2). Our hypothesis is that decreasing binding of the RBD to ACE2 will increase the titer...

TemPredict is a research study that examines associations between dermal body temperature, heart rate, and other metrics captured by a wearable smartring, and (1) onset of COVID-19 symptoms such as fever, cough, and fatigue, and (2) COVID-19 antibody testing results.

Our lab is interested in dissecting the portal of entry for the novel coronavirus in the human lung. Using sophisticated culturing techniques, cellular phenotyping, and single cell analysis, we hope understand how the virus enters the respiratory track.

Sensing of the virus that causes Covid19 by specific receptors in lung leads to an antiviral response, but it also causes lung inflammation that can be deleterious. Our goal is to study one of the receptors that senses viral RNA, toll-like receptor 7 (TLR7), and we will test it as a potential...

Gastroesophageal reflux disease and the use of proton pump inhibitor medications are both widely prevalent in the population; they have both been mechanistically tied to the development of pneumonia in general but are not well understood as far as COVID-19 is concerned. More importantly, both GERD...

This study is to evaluate the safety and efficacy of different investigational therapeutics in hospitalized adults diagnosed with COVID-19. This study is designed to evaluate multiple interventions compared to placebo. The study subject and study staff will not know whether active drug or placebo...

This is a study to test whether favipiravir, an oral pill that has broad antiviral activity, may be effective at reducing the symptoms of COVID-19 if given early to patients (similar to how Tamiflu is given early for the flu to help shorten the duration of the illness). Participants will receive...

This is a randomized, double-blind, placebo-controlled study to evaluate the efficacy of hydroxychloroquine and azithromycin to prevent hospitalizations and worsening disease in persons with COVID-19. The study is designed to minimize in-person contact between participants and study staff; the...

This clinical trial is testing a promising new therapy for acute respiratory failure in critically ill patients with COVID-19 infections at Zuckerberg San Francisco General Hospital and UCSF Parnassus Medical Center. The therapy is with mesenchymal stromal cells that may decrease lung injury and...

The Azithromycin for COVID-19 Treatment, Investigating Outpatients Nationwide (ACTION) study is a randomized, double-masked, placebo-controlled trial designed to determine whether a single oral dose of azithromycin can prevent hospitalization in patients with COVID-19 who are not currently...

The ColCorona trial is for people newly diagnosed with coronavirus who are not sick enough to need hospitalization. To be eligible, you must be age 40 or older with one additional risk factor such as hypertension, diabetes, asthma, fever of ?38.4∞C (101∞F) within the last 48 hours, or shortness of...

We are a multidisciplinary group of scientists and frontline providers investigating why some people who are infected with COVID-19 have mild symptoms while others develop severe disease. COMET uses multiple cutting edge assays and tests to improve the understanding of how COVID-19 affects the...

The purpose of our study is to rapidly enroll people who are COVID+ (as well as close contacts exposed to COVID+ people but did not get very ill). It is an intensive study with 5 in-person visits, but we do this so that we can understand the early immune response to fight SARS-CoV-2. Your...

The goal of this study was to collect clinical information and collect biomarkers on hospitalized subjects with COVID-19. This study was subsumed into the COMET study, a larger cross-site research project at UCSF.

LIINC is a study of volunteers who were previously infected with SARS-CoV-2 (also known as novel coronavirus or COVID-19) who have recovered from acute infection. The study is designed to provide a specimen bank of samples with carefully characterized clinical data. LIINC specimens will be used to...

PRIORITY (Pregnancy CoRonavIrus Outcomes RegIsTrY) is a nationwide study of pregnant or recently pregnant people who are either under investigation for Coronavirus infection (COVID-19) or have been confirmed to have COVID-19. This study is being done to help patients and healthcare providers better...

As a sub-study of PRIORITY, a national registry of COVID-19 in pregnancy and postpartum, we are building a perinatal biorepository of biospecimens from the pregnant and postpartum mother and her infant, including blood, placenta, cord blood, infant heelstick, and breastmilk. These samples will be...

Information about patient risk factors for COVID-19 infection and disease severity are primarily captured by electronic health records systems in the form of clinical notes. To answer important questions about the epidemiology of COVID-19, we need computational tools to 'mine' this data out of...

Our group, Amend at UCSF, is conducting quantitative and qualitative research with correctional officers and policy leaders to understand the organizational responses to COVID-19 in prisons and jails throughout the US and to investigate the impacts of COVID-19 on the health and well-being of...

To help fight the novel coronavirus now plaguing humanity, the COVID-19 Citizen Science (CCS) project will allow anyone in the world age 18 or over to become a citizen scientist advancing understanding of the disease. Based around a smartphone app, participants will be asked to complete an initial...

UCSF investigators worked with colleagues around the world to establish the COVID-19 Global Rheumatology Alliance registry (rheum-covid.org) to create an open platform for rapid data collection and dissemination during the pandemic. COVID-19 has potential to severely affect those with rheumatologic...

Developing models and algorithms based on principles in statistics and machine learning to understand COVID-19.

Developmental Epidemiological Study of Children born through Reproductive Technology (DESCRT)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread internationally and in the US. As of the beginning of April, more than 1 million cases of coronavirus disease 2019 (COVID-19, the disease caused by SARS-CoV-2) and more than 56,000 deaths have been reported worldwide....

The Global Hidradenitis Suppurativa and COVID-19 Registry is an international pediatric and adult database to monitor and report outcomes of COVID-19 occurring in hidradenitis suppurativa (HS) patients. We will use these data to better understand risk of infection and clinical course, track...

The aim of this study is to examine health care providers' perceptions of how they and their facilities are prepared to identify and manage COVID-19 cases. In addition, we will examine how perceived preparedness to respond to COVID-19 is associated with provider stress and burnout. The study is...

Immune basis of racial disparities in COVID-19 patients

We aim to use mathematical modeling and machine learning approaches to build decision-making technologies to improve the risk assessment, prevention, and control of healthcare-associated infections (HAI) and antimicrobial resistant infections (ARI).

Our proposed technologies will account...

This study uses electronic health record data from the Department of Veteran Affairs to examine COVID-19 outcomes in people with psychiatric disorders compared to people with no psychiatric disorders. Outcomes include risk for breakthrough infections following COVID-19, and hospitalization and...

The University of California Health System, with 19 health professional schools, 5 academic medical centers, and 12 hospitals, has built a research data set with all SARS-CoV-2 tested patient care data, to enable safe, secure, respectful, and regulated deidentified clinical research.

UC San Francisco epidemiologists and infectious disease specialists are partnering with several community organizations and the San Francisco Department of Public Health (SFDPH) to offer comprehensive, voluntary SARS-CoV-2 (the virus that causes COVID-19) testing to residents of the Bayview,...

The COVID-19 pandemic threatens to overwhelm the U.S. healthcare system. There is no proven therapeutic or vaccine for the novel coronavirus causing this pandemic. We have created a UC COVID19 Genomics Consortium (UCGC) to collectively share and enroll patients in a joint effort to better...

University of California Health COVID Research Data Sets (CORDS)

We have conducted six focus groups across all levels of residents in surgery. We are analyzing the qualitative data. In general we have three major findings. The pandemic has shed light on the role of competency based education as opposed to establishing standards by numbers of cases and...

Using a national survey of OHNS residency programs, we queried resident concerns and roles during the initial stages and peak of the COVID-19 pandemic. The survey results showed OHNS residency programs responded quickly with policy changes to minimize risks of viral transmission and exposure. In...

This project is a collection of resources from faculty affiliated with Healthforce Center at UCSF primarily focused on workforce surge planning, including research on workforce and staffing and alternative care sites for practitioners to implement in the field. Website link: https://healthforce....

In the wake of the COVID-19 pandemic, administrative and clinical leaders are having to make difficult decisions and policy changes about family presence and involvement in order to prevent the virus' transmission without a clear understanding of how these changes will impact patient care. The...

Impact of COVID-19 on distribution of imaging resources

Impact of COVID-19 on Patients Awaiting Total Hip and Knee Arthroplasty: A multi-institutional Survey

COVERED is a 20 site Centers for Disease Control sponsored public surveillance study, in which we are trying to assess the attributable risk of providing emergency care to patients with COVID, and to identify ways to reduce that risk. To answer these questions, we are enrolling emergency...

During the COVID-19 pandemic, telemedicine use is increasing without practice guidelines specific adolescent health. This study summarizes obstacles to the implementation of telemedicine for adolescents, and proposed solutions. Observations made during this process have implications for the...

Telemedicine has the potential to improve access to HIV care both during and after the COVID-19 pandemic. However, implementation of telemedicine also has the potential to widen health disparities if measures are not taken to address access barriers faced by vulnerable popualtions. This study is...

The SARS-Cov-2 (COVID19) pandemic has led to striking care and disease disparities. A confluence of factors places vulnerable communities at risk for COVID19 and for poor outcomes. In particular, low-income communities, non-US born communities, and communities of color may face unique challenges,...

Vitamin D has a number of beneficial actions on the immune system. Vitamin D deficient individuals are predisposed to a number of viral infections and respiratory illnesses. We would like to determine if vitamin D deficiency is a determinant of who progresses in their illness following COVID-19...

The COVID-19 pandemic and associated large-scale social distancing efforts to reduce viral transmission have led to dramatic changes in human behaviors associated with traumatic injury. While overall injury rates have decreased, there are apparent changes in injury patterns, mechanisms, and...

Although the effects of the COVID-19 pandemic on the public's anxiety levels have been well documented by traditional media, little is known about the impact on frontline medical providers. In mid-March 2020, we initiated a longitudinal study to assess multiple factors affecting emergency medicine...

The purpose of this project is to understand the impact of the ongoing COVID-19 pandemic on the social well-being, psychological health, and health care use of older adults in San Francisco.

Covid-19 and the associated lockdowns may impact access and use of reproductive health care globally, including in India. Using facebook surveys, we are in the process of collecting both panel and cross sectional data from women and men across India about the impact of the COVID-19 pandemic on...

Mental health needs and service status in young adults with autism spectrum disorders

Preventing Inter-Generational Transmission of Stress Vulnerability and Obesity in at-risk Populations

Since COVID-19, many anecdotal reports of stigma and discrimination have been made by healthcare providers, especially those who are Asian American/Native Hawaiian/Pacific Islander (AANHPI), due to harmful racist stereotypes (e.g., Chinese virus, Kung Flu). This is a non-random online survey of ...

Due to the COVID-19 pandemic this has limited in-person clinical experiences for trainees. Our team has developed brief, virtual standardized patient encounters to allow medical students to build skills in obtaining an adolescent social history from standardized patients with the opportunity for...