TAS iGEM Team Creates COVID-19 Test for International Competition

The Taipei American School Director of Scientific Research, Mr. Jude Clapper, is an animated speaker, even on the worst of days. As he sits in front of me along with his colleagues, Dr. Jonathan Hsu and Dr. Nicholas Ward, his excitement is palpable.

"The kids are unbelievably motivated this year because they're genuinely interested in the science," he says. "We don't have to push them at all."

The "kids" in question? Taipei American School's 2020 International Genetically Engineered Machines team.

Each year's iGEM team is composed of students in Grades 11 and 12 who enroll in the course Honors Research in synthetic Biology, which is co-taught by Clapper, Hsu and Ward across two different class periods. This year's iGEM team hopes to continue its record of success at the annual iGEM Giant Jamboree, which is usually hosted in Boston each fall but which will be hosted virtually this year due to the world health crisis brought on by the novel coronavirus COVID-19.

This year's team is led by Wilson H. ('21), a quiet and quick-witted young man, whose independent research was recently published in the 2020 American Society of Clinical Oncology Meeting Library, the world's largest oncology conference. Wilson was voted as the project head "unanimously" by his peers, who hold great respect for his skills in graduate-level research and in leading the team's multi-step research process. 

Both Clapper and Hsu agree: "Wilson? He's on another level. He thinks on a different level, almost like a graduate student. He wanted a very serious project for this year's team, something that could cure cancer or the like. He is very application based."

Originally, Wilson and the 2020 iGEM team discussed a few alternative research ideas, but many of the first ideas had to be discarded because they were more appropriate for multi-year research projects that were "not particularly feasible for the time frame of an iGEM project," according to Clapper. Other discarded ideas included "how to heal a broken heart," how to get more out of your sleep cycle, reducing plastic waste, a solution for coral bleaching, and researching the enzyme in pineapples that produces a "tingling feeling" for some in order to use it to help with menstrual cramps.

Eventually, the team narrowed down their project to two potential topics: one group was interested in attempting to create a form of internal "body armor" made from the materials within lobster shells. According to Wilson, the material - chiten - could, theoretically be used to grow an additional endoskeleton within humans that would provide additional strength and support for the body. The second faction within the team was interested in what would eventually become this year's project: a home test for influenza A, influenza B, and COVID-19.

However, including a test for COVID-19 was not originally part of the scope of this year's project.

In February, right after Chinese New Year, the novel coronavirus influenza began to become more prevalent in Asia, the team realized that there was another research opportunity to be had. "As soon as China realized it was becoming an outbreak, they released the sequence of the virus genome, which made it publicly accessible for us during our first distance learning session," said Clapper. "Wilson, without any sort of teacher assisting him literally went out on his own, found the sequence of the two strains of influenza and COVID-19 and did several forms of bioinformatic analysis of the genomes."

In March, when the United States began to feel the strain of the virus and the lack of test kits became a concern globally, the TAS iGEM team quickly realized that this project's potential impact was greater than they had anticipated. "This is a real problem right now and we are designing a kit that will be very useful, not just for the United States but for the entire world," said Hsu.

The idea of "impact" is a large component of the iGEM competition philosophy. Every team needs to show that their research project has a component that they call "human practice." The idea behind this concept is that each project needs to be relevant and helpful to humanity.

The students have been working in earnest on this project since January, despite a total of four weeks spent away from campus as the school enacted two sessions of distance learning.

Both the teachers and students agree that they are actually ahead of schedule for their project this year, even with those weeks spent apart from one another.

The iGEM Giant Jamboree will be hosted virtually in the fall of 2020, and so the TAS team will work throughout the spring, summer, and early fall to complete their project, which is, essentially, an at-home test kit for influenza A, B, and COVID-19. 

"Currently this type of test is a gold standard for most virus or coronavirus tests. Basically, it identifies a piece of the DNA where the genetic sequence of the virus is. If you're infected, you carry that virus in your own body. The test uses a sample out of that person, like saliva or another viral particle carrier. The test can detect if there is DNA in your sample and the color changes based on the presence of that DNA."

Hsu and Clapper describe it as essentially a "ph" test for those who are less familiar with this type of test, known as a PCR-based test. "When you measure the pH of your pool or your water, you put in a stick of paper and it changes color based on the equipment. That's the whole principle behind our work. If it's a little bit more acidic, then it changes color. This is what is happening in our test because if you have the DNA of one of these viruses, the test makes a lot more copies of it every time, which then changes the color of the liquid," explained Clapper and Hsu.

Their current results show a minimum detection time of around 30 minutes for each of the 3 viruses. Additionally, their test can detect extremely small amounts of virus targets. Other existing detection methods (lateral flow rapid tests, real-time Polymerase Chain Reaction (PCR) tests, blood serology, and viral cell cultures) each have their own shortcomings: common false negatives, expensive instruments, and time-consuming processes. In short, their test works by a simple color change over time—the reaction starts out pink but gradually becomes yellow in the presence of a virus.

The team's second part of their research is trying to make sure that these tests could be used by people in their own homes, without much margin of error for people to self-identify color changes. The team is collecting results with time-lapse videos and writing an analysis software program that can automatically analyze the color changes in the videos using a cell phone. This allows the user to measure the color change with a simple phone camera and will eventually be easily adaptable to personal home-use. 

Project head, Wilson H., knows that it's possible that many other schools are also trying to produce similar tests to this project. He thinks that ultimately the TAS project has two advantages: it's fast and it's accurate. "It's sensitive and specific," he said, "which are the two parts of accuracy. It also operates at room temperature, which means that you don't have to work in a special lab in order to process the results."

Wilson and his other team members feel grateful for the synthetic biology program at TAS. "It has really opened up a lot of opportunities," he said. "When I started upper school, I was actually focusing more on the engineering side of learning, like in robotics competitions. But I eventually realized that my true passion is biology and chemistry. It's something where I can truly expand my knowledge and what I want to do in the future."

The TAS iGEM team worked throughout the spring and summer to finish up their project in order to present their work at the iGEM 2020 Virtual Giant Jamboree held on November 14-22.

According to Clapper, the summer was a critical time for the project's success. "We have validated the sensitivity of our initial test results," said Clapper. "Additionally we are developing a prototype in order to show a proof of concept of how a saliva-based virus detection kit would work."

The TAS iGEM students did not stop there, however. The team reached out to other local schools to provide education about synthetic biology and general information about COVID - 19.

After a busy summer of research and teaching, the iGEM team was happy to get back to school in August. One reason was that the campus had been renovated while they were gone. The scientific research classes moved into a renovated, state-of-the-art Sandy R Puckett Memorial Research Laboratory, which is on the first floor of the Dr. Sharon D. Hennessy Building affectionately known as H-Block. 

"They have set up shop quickly and are working constantly to give the final results that will be presented in poster, oral and webpage format during the virtual iGEM jamboree in Nov 2020," Clapper said.