A collaborative of researchers from UC Berkeley, the University of California, San Francisco (UCSF), Stanford University, and Gladstone Institutes, a biomedical research nonprofit, as well as 50 scientific volunteers, have created a pop-up lab that utilizes robotics to test more people for COVID-19. Two senior investigators from Gladstone Institutes and a UC Berkeley professor are also developing a fast, inexpensive field test that utilizes mobile phone technology. This test will diagnose the next two strains of the virus that are expected to develop, COVID-20 and COVID-21.
The robotics equipment in the pop-up lab at UC Berkeley engages in automated, safe sample handling and sample plate preparation for patient swabs inputted into polymerase chain reaction (PCR) machines. After the samples are prepped, the PCR machines can test over 700 samples in 90 minutes. The equipment will allow hundreds of tests to be analyzed relatively quickly.
The mobile phone technology is helping the researchers create a different type of test that does not utilize a lab or advanced machinery. The new test could be administered in a home, workplace, or airport, far from a hospital.
Both the current and upcoming tests involve the extraction of ribonucleic acid (RNA) from human cells. It is important to gather RNA because the coronavirus carries its genetic material in RNA. Viewing the RNA allows for a determination as to whether a patient has contracted a coronavirus.
Learning from the lab
The first instrument that utilizes robotics is the Hamilton STARlet, which takes samples from cotton nose and throat swabs in beakers. The machine inserts the samples into wells in rows of gridded polycarbonate plates. This machine also records who provided each sample. Each plate has 96 wells, in contrast to machines that process one sample at a time. The second machine, the Hamilton Vantage, pipettes TRIzol, a chemical solution that separates RNA from DNA and protein, into the wells.
The Hamilton Vantage then seals the plates, preparing them for insertion into the PCR machine. The PCR machine then engages in a process of heating and cooling the samples while producing many copies of the sequences of RNA present in nose and throat cells, which is called thermal cycling.
Scientists can then use a technique called gel electrophoresis to separate the RNA fragments by size and charge. The bands of the RNA generated through the process have a pattern specific to COVID-19. The lab is expected to be able to initially process over 1,000 samples in 24 hours. Later, it will ramp up testing to 3,000 samples a day if needed.
The machines will first be used to process test kits from UC Berkeley students, faculty, and staff. They will then be used to diagnose patients at clinics and medical centers in the East Bay. If needed, the lab will begin testing for patients around the Bay Area and throughout California.
Using mobile phone tech for testing
The mobile phone technology involves the use of a mobile phone camera. This technology is being incorporated into a test that can be easily adapted for future viral epidemics. This test also requires access to the Internet for data.
Dr. Melanie Ott, senior investigator of the Gladstone Institute of Virology and Immunology and a professor of medicine at the University of California, San Francisco, and Dr. Jennifer Doudna, senior investigator of the Gladstone Institute of Data Science and Biotechnology and executive director of the Innovative Genomics Institute at UC Berkeley, are partnering with Dr. Dan Fletcher, bioengineering faculty scientist at Lawrence Berkeley National Laboratory, on this project.
Ott said the team has requested and received assistance from mobile phone manufacturers to understand the limitations and utility of the mobile phone technology incorporated into the test. The test will compare RNA from a patient’s sample to the RNA sequences of the current and potentially other strains of the novel coronavirus.
The new test will utilize a CRISPR-based method to find a specific bit of RNA inside a human cell. CRISPR is an acronym for “clustered regularly interspaced short palindromic repeats.” The method works by inserting a specific protein, called Cas13, along with a piece of guide RNA into a sample. If the guide RNA finds viral RNA that matches its sequence, Cas13 becomes activated. Cas13 cleaves, or cuts, the viral RNA.
The researchers add a probe RNA that is also cleaved by the activated Cas13. When that probe is cleaved, it releases fluorescent light. The light can be detected by a mobile phone camera.