- Deep omics profiling to determine the genomic factors at play in disease severity
Euan Ashley, MB ChB, DPhill; Victoria Parikh, MD; Matthew Wheeler, MD; Carlos Bustamante, PhD; and Manuel Rivas, DPhil
Ashley, Parikh and their team are sequencing genomic information from SARS-CoV-2 and human hosts to better understand the diversity of host responses to the virus. Their work aims to better elucidate genomic details underlying COVID-19 disease severity. To do so, the team will collect de-identified omic and clinical data for 1,000 Stanford patients who tested positive for COVID-19-, including hospitalized patients and patients who were in the intensive care unit.
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Using artificial intelligence to predict drugs that may inhibit COVID-19
Russ Altman, MD, PhD, and other collaborators
Altman and his group have used artificial intelligence to computationally predict six drugs that could inhibit TMPRSS2, a protein that plays a key role in SARS-CoV-2 infections. Altman and his collaborators outside of Stanford Medicine plan to conduct experimental follow-up studies to explore the efficacy of two of the drugs in blocking SARS-CoV-2 from causing infection. While promising, the potential drugs are still part of a preliminary computational analysis and would be dangerous to use clinically at this time.
Investigation of possible oral-fecal transmission of SARS-CoV-2 in the Bay Area
Ami Bhatt, MD, PhD; Angela Rogers, MD, Andrew Rezvani, MD; Niaz Banaei, MD; and Ben Pinsky, MD, PhD
The Bhatt group and collaborators are investigating whether SARS-CoV-2 was circulating through oral-fecal cycles in the Bay Area community. The lab plans to screen stool samples collected through a biobank at Stanford for signs of SARS-CoV-2 from December 2019 through December 2020. Depending on sample availability, the team also plans to research whether a patient’s gut microbiome composition affects gastrointestinal symptoms of COVID-19, as well as other details about how the virus sheds.
Crowdsourcing solutions to better understand molecular structures of COVID-19
Howard Chang, MD, PhD, and Rhiju Das, PhD
The Chang and Das labs are engaging participants of the online-gaming platform Eterna to understand how the RNA genome of SARS-CoV-2 virus might change during the pandemic. Eterna educates and enables its players to “be the virus,” simulating how it shifts its sequence over time to evade diagnostics, therapeutics and vaccines being developed to fight COVID-19. The project seeks to provide RNA-structure-informed predictions and analyses that are not available through other computational efforts, while engaging and educating millions of citizens worldwide through compelling puzzles.
Development of rapid at-home testing for COVID-19
William Greenleaf, PhD
Greenleaf is leading an effort to develop new methods of COVID-19 detection at the point of care to help get around current supply chain problems and allow for rapid screening. The kit in development is meant to function directly in sample swabs and, in principle, could be done at home or in decentralized clinics if users were taught proper swabbing techniques.
Tracking COVID-19 with wearables
Michael Snyder, PhD; Sam Yang, MD, FACEP and Megan Mahoney, MD
Snyder and his team will track biological parameters of individuals who are ill with COVID-19 or at risk for the disease using a smart watch. Their goal is to determine whether they can tell if the smart watch user is becoming ill based on measurements such as heart rate.
Determining pathogenicity of various variants and strains of COVID-19
Michael Snyder, PhD and Ben Pinsky, MD, PhD
Snyder and his group plan to track different variants and strains of COVID-19 and quantitatively determine which ones correlate with different phenotypes, such as levels of pathogenicity. His team also plans to study the false negative rate of COVID-19, seeking to better understand how many people receive a false negative test result during early stages of the disease.
Multi-omics assessment of individuals infected with COVID-19
Michael Snyder, PhD; Sam Yang, MD, FACEP; and Maya Kasowski, PhD
The Snyder group will collect biological samples from individuals ill with COVID-19 and those most at risk for the disease, observing and assessing levels of certain molecules involved in several biological pathways, including metabolism and immune function. The team will use this information to create “omics” profiles to look for potential molecular signatures of COVID-19 infection, as well as signs that an individual might have a strong adverse reaction to the virus.