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BioE Coronavirus Response

Several labs in the Bioengineering department are working on COVID-related projects. They are highlighted below so that others can know about these efforts and know who to contact to get involved and help.  By sharing ideas and collaborating, we can make greater progress together. Note: Research on this page is preliminary and not peer reviewed.


Date: March 21, 2020

The Prakash Lab is working on multiple fronts on COVID-19 (protection of health care workers, PPE, opportunities for small business to engage, ventilator shortage and diagnostics).  They will continue to update their progress at:  http://web.stanford.edu/group/prakash-lab/cgi-bin/labsite/publications/

1000x1000: Open distributed manufacturing protocol for high quality (N95 grade) masks for health care worker and citizen protection

Why: It has become clear that the world is under acute shortage of protective gear for health care workers and care givers;  including masks worn to avoid acquiring or passing on an airborne pathogen like SARS-COV2 virus. This is an even more acute challenge with trade restrictions and supply bottlenecks. Since these masks are designed to only be one time use and disposable - with lack of supplies - short cuts are taken which put health care workers at grave risk.
Project plan:  We are envisioning a distributed manufacturing solution for N95 masks - we can 1000x1000 projects. Instead of one plant centrally making 1000N95 masks a day - 1000s of small businesses (2-3 people operation) being able to produce 1000 or more N95 grade masks per day; across the country meeting a million masks a day quota in a distributed fashion. We are developing a nimble, simple, low cost manufacturing setup that allows to make the key ingredients in N95 masks for filtering aerosolized viral particles and integrated quality testing locally. Combined with simple mask design (a simple folding structure); masks can be produced locally (in a back room in a hospital) but still meet high standards if protocols are followed. Our goal is to quickly share exact design, protocol and process for a distributed manufacturing solution for masks to protect health care workers - in a simple instructional format.

“Etch-a-sketch” inspired Ventilator Remote Controller Project
Why: In conversations with physicians and nurses caring for COVID-19 patients globally, it has become evident that they are understaffed and struggling to keep up with such a large population of ARDS patients. Every time a healthcare worker has to go in and out of a COVID-19 patient room, they have to gown up in full PPE beforehand and remove the PPE afterwards. The majority of current mechanical ventilation units available to major hospitals worldwide do not provide a feature to remotely control the settings of a given device. Thus, whenever a ventilator needs to be adjusted, a healthcare worker must put on PPE, enter the room to make adjustments, and remove PPE. This PPE must be either disposed of or processed for reuse so that healthcare workers can work safely in non-patient areas. Furthermore, the process of donning and doffing PPE and entering the room not only takes valuable time for making minor adjustments but also puts the healthcare worker at risk of exposure to SARS-CoV-2. This situation wastes precious time and resources in a situation of shortage of medical supplies.
Project plan: We are building a flexible module that can attach to the outside chasis of a ventilator control touch screen - to enable remote control of ventilator settings using an XY drawing robot and remote knob control. On the other side of the glass door, the health care worker would have an iPAD with the exact same control and could control the adjustment of the setting without coming in and out every time of the room. No ventilator hardware or software is modified in this approach.
The working draft document:  https://docs.google.com/document/d/1Z44YpbulrfZ0txfAJZJqTHFGj67I7Y-cv655t-TL5Mc

Modified "Full-face” snorkeling mask as a reusable PPE for health care worker
Why: PPE is one of the most important protective layers for healthcare workers around the world in a crisis like COVID-19.  Many hospitals have already run out of N95 masks and other PPE, including face masks and face shields. Doctors are trying to reuse and ration masks. The industrial supply chain is unable to scale up to meet current demands. In the US and globally, there is an urgent need for fast stopgap solutions to meet the current demands for PPE.
Project plan: The goal is to modify a “full-face” snorkeling mask and add a 3D-printed part on the ventilation port of the snorkel shield. This 3D-printed part will be a custom attachment which will act as a swap-in replacement for the snorkel tube. As with a snorkel tube, all inhaled air will pass through the attachment; a filter can be added to the attachment for air filtration. Integrating a N95 mask filter for 0.3 um particles into the custom attachment would allow the snorkel mask to function as a simple face shield and provide the same level of protection to a medical health worker as a combination of an N95 mask and a face shield. Moreover we are extensively testing this solution for decontamination and re-use using heat treatment, autoclaving, bleach and other standard decontamination protocols.
The working draft document:  https://docs.google.com/document/d/1J22le3dBZBnNDXGlJLRb38z7v7LaOjKfDeN9f0tFeKY

A multiplex ELISA based diagnostics for COVID19
Collaborators: Peter Kim (Stanford), CZ BioHub, Shalin Mehta Lab (BioHub)
Why: Ramp up on PCR based COVID-19 tests has allowed for limited testing availability; but serological based new tests are needed rapidly at scale. This is also true considering conditions in LMIC countries.
Project plan: With progress on recombinant expression of viral proteins and ongoing work in Peter Kim Lab and BioHub on developing ELISA reagents - we are rapidly putting together an automated modular diagnostics platform to conduct a multi-plex low-cost micro-spotting based ELISA test compatible with Octopi based scanning/imaging platform. This complimentary approach will be useful for surveillance as well as diagnostics.


Date: March 18, 2020

Computational screens identify possible drug candidates to treat Covid-19

Using computational screens against the human protein TMPRSS2 that is necessary for attachment and infection of human cells by Coronaviruses, the Altman lab identified several drugs, including two that are on the market today, that should be further evaluated for their potential therapeutic benefits.

Specifically, they discovered that there is one anticoagulant — nafomastat -- that was a high hit. Nafomastat is noteworthy since it came up positive in a screen for MERS in 2016. Nafomastat is being clinically tested in Japan. This is a validation of their approach, which identified at least 2 other high-scoring candidates. Two experimental groups are already doing assays on these drugs.  If you can provide these drugs to researchers for their assays, that could be useful. If you are a drug company with internal assays for checking these drugs, please go for it and let the Altman lab know if you need help!

Their preprint can be found here: https://chemrxiv.org/articles/Homology_Modeling_of_TMPRSS2_Yields_Candidate_Drugs_That_May_Inhibit_Entry_of_SARS-CoV-2_into_Human_Cells/12009582/1

The report of the Japanese nafomastat trial:  https://www.bloomberg.com/news/articles/2020-03-18/japanese-researchers-to-test-blood-thinner-for-virus-treatment

The 2016 paper upon which it is based:  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5075056/


Date: March 14, 2020

New genetic method of using CRISPR to eliminate COVID-19 virus genomes in cells 

The Stanley Qi Lab has developed a CRISPR-based countermeasure against COVID.  The paper is available on bioRxiv (in preprint form and not yet peer reviewed), and it describes a new genetic method of using CRISPR to eliminate COVID-19 virus genomes in cells. This provides an alternative approach to traditional vaccines which may take another 12-18 months to develop. The work is a collaboration with David Lewis and Drew Endy, led by Marie La Russa in Stanley's lab, and supported by DARPA.

The preprint can be found here: www.biorxiv.org/content/10.1101/2020.03.13.991307v1

Read about "Could Crispr Be Humanity's Next Virus Killer?" in WIRED (March 18, 2020)

Industry and other labs can connect with the Stanley Qi Lab at:  stanley.qi@stanford.edu


Date:  March 14, 2020

Scientific meeting on AI & COVID-19

Russ Altman is  leading the organization of a scientific virtual meeting on AI & COVID-19, to be held April 1, 2020.  The event will convene experts from Stanford and beyond to advance the understanding of the virus and its impact on society.  Please RSVP on the website and save the date; details and agenda will be communicated soon.


Date: February 21, 2020

AI algorithms identify potential T-cell and B-cell epitopes

The Altman Lab has run AI algorithms on the virus to look for virus coat protein targets and also peptides that are likely to be presented by MHC cells.  

They used computational tools from structural biology and machine learning to identify 2019-nCoV T-cell and B-cell epitopes based on viral protein antigen presentation and antibody binding properties. These epitopes can be used to develop more effective vaccines and identify neutralizing antibodies.

The preprint can be found here:  https://www.biorxiv.org/content/10.1101/2020.02.19.955484v1