ASU scientific team finds new, unique mutation in coronavirus study

SARS-CoV-2 mutation mirrors one found during 2003 SARS outbreak

May 5, 2020

Editor’s note:  This story is being highlighted in ASU Now’s year in review. Read more top stories from 2020.

As the coronavirus pandemic has swept across the U.S., in addition to tracking the number of COVID-19 daily cases, there is a worldwide scientific community engaged in tracking the SARS-CoV-2 virus itself. New coronavirus As the coronavirus pandemic has swept across the U.S., in addition to tracking the number of COVID-19 daily cases, there is a worldwide scientific community engaged in tracking the SARS-CoV-2 virus itself. Efrem Lim leads a team at ASU that looks at how the virus may be spreading, mutating and adapting over time. Download Full Image

Efrem Lim leads a team at Arizona State University that looks at how the virus may be spreading, mutating and adapting over time.

To trace the trail of the virus worldwide, Lim’s team is using a new technology at ASU’s Genomics Facility called next-generation sequencing to rapidly read through all 30,000 chemical letters of the SARS-CoV-2 genetic code, called a genome.

Each sequence is deposited into a worldwide gene bank, run by a nonprofit scientific organization called GISAID. To date, over 16,000 SARS-CoV-2 sequences have been deposited in GISAID’s EpiCoVTM Database. The sequence data shows that SARS-CoV-2 originated from a single source from Wuhan, China, while many of the first Arizona cases analyzed showed travel from Europe as the most likely source.  

Now, using a pool of 382 nasal swab samples obtained from possible COVID-19 cases in Arizona, Lim’s team has identified a SARS-CoV-2 mutation that had never been found before — where 81 of the letters have vanished, permanently deleted from the genome.

The study was published in the online version of the Journal of Virology.  

Lim says as soon as he made the manuscript data available on a preprint server medRxiv, it attracted worldwide interest from the scientific community, including the World Health Organization. 

“One of the reasons why this mutation is of interest is because it mirrors a large deletion that arose in the 2003 SARS outbreak,” said Lim, an assistant professor at ASU’s Biodesign Institute.

During the middle and late phases of the SARS epidemic, SARS-CoV accumulated mutations that attenuated the virus. Scientists believe that a weakened virus that causes less severe disease may have a selective advantage if it is able to spread efficiently through populations by people who are infected unknowingly. 

Teasing apart what exactly this means is of profound interest to Lim and his colleagues. The ASU research team includes LaRinda A. Holland, Emily A. Kaelin, Rabia Maqsood, Bereket Estifanos, Lily I. Wu, Arvind Varsani, Rolf U. Halden, Brenda G. Hogue and Matthew Scotch. 

The ASU virology team had been set up to perform research on seasonal flu viruses, but when the third case of COVID-19 was found in an Arizona individual on Jan. 26, 2020, they knew they had all technical and scientific prowess to rapidly pivot to examining the spread of SARS-CoV-2.

“This was the scientific opportunity of a lifetime for ASU to be able to contribute to understand how this virus is spreading in our community,” Lim said. “As a team, we knew we could make a significant difference.” 

All the positive cases show that the SARS-CoV-2 viral genomes were different from each other, meaning they were independent from each other. This indicates that the new cases were not linked to the first Arizona case in January, but were the result of recent travel from different locations.

In the case of the 81-base pair mutation, because it has never been found before in the GISAID database, it could also provide a clue into how the virus makes people sick. It could also form a new starting point for other scientists to develop antiviral drugs or formulate new vaccines.

SARS-CoV-2 makes accessory proteins that help it infect its human host, replicate and eventually spread from person to person. The genome deletion removes 27 protein building blocks, called amino acids, from the SARS-CoV-2 accessory protein ORF7a.  The protein is very similar to the 2003 SARS-CoV immune antagonist ORF7a/X4.

The ASU team is now hard at work performing further experiments to understand the functional consequences of the viral mutation. The viral protein is thought to help SARS-CoV-2 evade human defenses, eventually killing the cell. This frees up the virus to infect other cells in a cascading chain reaction that can quickly cause the virus to make copies of itself throughout the body, eventually causing serious COVID-19 symptoms eight to 14 days after the initial infection. 

Lim points out that only 16,000 SARS-CoV-2 genomes have been sequenced to date, which is less than 0.5% of the strains circulating. There are currently more than 3.5 million confirmed COVID-19 cases worldwide. 

Lim’s group has teamed up with TGen, UArizona and Northern Arizona University to continue tracking different genetic strains of the new coronavirus. Together, the newly formed Arizona COVID-19 Genomics Union (ACGU) hopes to use big data analysis and genetic mapping to give Arizona health care providers and public policy makers an edge in fighting the growing pandemic. 

The work was supported by NSF STC Award 1231306, NIH grants R01 LM013129, R00 DK107923, the J.M. Kaplan Foundation’s One Water One Health, Arizona State University Foundation project 30009070), and ASU Core Facilities Seed Funding. 

Joe Caspermeyer

Manager (natural sciences), Media Relations & Strategic Communications


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ASU entrepreneurs pitch via video for online Demo Day competition

ASU startups pitch their ventures online for more than $312,000 in funding.
May 5, 2020

More than $312,000 awarded to startups

Sometimes even a small amount of money makes a huge difference. An Arizona State University student took the $4,000 that she won in a Demo Day competition a year ago and created a company in her native Ghana to help feed children.

Already successful, Freda Sarfo, a master’s degree student in global logistics, won another $5,000 at last week’s Demo Day entrepreneurship competition, which she’ll use to expand her social enterprise, called Tropical Almond.

Like most everything else this semester, Demo Day was held online. At a typical Demo Day event, the founders pitch to a panel of judges at SkySong in Scottsdale throughout the day, and an awards ceremony is held in the evening. This semester, 85 ventures put together five-minute video pitches, which the judges reviewed last week. The awards were announced during an online presentation on May 1.

In her pitch video, Sarfo described growing up with a single mother in Ghana, where 1 out of 7 children dies of malnutrition. Women have few job opportunities to support their families.

The area is lush with tropical almond trees (different from the sweet almonds found in the United States), which produce hard-shelled nuts. Because the trees are planted for shade, the nuts often go to waste. Children become adept at shaking the trees to get at the nuts.

“Tropical almonds were our favorite and we were never hungry,” she said in her video.

In 2017, Sarfo came to ASU as a Mastercard Foundation Scholar, where she launched her business, Tropical Almond. With the $4,000 she won last year, she built a small processing facility in Ghana. She pays women to collect and crack the fallen nuts, which are then cold pressed. The oil is packaged and sold as a hair product for black women. The nut byproduct is processed into nutritious snacks. For every bottle of almond oil sold, one bag of high-protein snacks is donated. In the first three months, she sold 350 bottles through her online store.

Sarfo hopes to eventually start a tropical almond orchard in Ghana to produce a reliable source for the oil and more jobs.

“We’ve been able to feed over 100 kids with our protein-dense snack,” she said. “Through our outreach program, where we educate people on the benefits of the trees, we have been able to prevent more than 1,000 trees from being cut down and provide revenue for over 100 single mothers.”

Sarfo’s prize was among the more than $312,000 that was distributed during the Spring 2020 Demo Day online awards ceremony.

Unique circumstances like the pandemic fuel innovation, and that’s when ASU entrepreneurs step up, said Ji Mi Choi, associate vice president of entrepreneurship and innovation at ASU.

“No one is saying, ‘We’ll hunker down and see you on the other side when this is over,” she said during the awards event.

She described one major effort: Teams at ASU, led by the interdisciplinary Luminosity Lab, have stepped up to address the crisis by creating an online platform, called the PPE Response Network, to match hospitals that need safety gear to people, organizations and businesses that can make the items with 3D printers, she said.

In addition, the Devils Invent hackathon pivoted to help during the pandemic. Normally, it’s a 48-hour event in which teams work on several problems. But this semester, it was converted to an online format in which everyone worked on one problem for Banner Hospital — how to control visitors and still provide information to patients’ families. The hospital is now working with two student teams on refining their ideas.

“We’ve been tested in real time and we can say, ‘Yes, we’ve been having a positive impact,’” Choi said.

All of the startups who pitched at Demo Day are part of Venture Devils, the umbrella for funding, space and mentorship in the office of Entrepreneurship and Innovation at ASU.

The winning ventures from this semester’s Demo Day:

Amazon Alexa Venture Challenge: There were two $10,000 winners: BisbeeBaby, a platform that collects data from baby products, and EqualComm, a technology that provides real-time American Sign Language interpretation or text captioning for audio events. EqualComm was launched by Dylan Lang, a computer science and business entrepreneurship major who is president of the “deaf Devils at ASU” student organization. Other winners were Parts Detect, $5,000, and Easy Voice and Morality, $2,500 each.

Ashton Family Venture Challenge: Dima Building Innovators, created by Andres Sandoval, a graduate student in systems engineering, won $10,000. He invented a device to make construction safer during plumbing installation.

Edson Student Entrepreneur Initiative: Three student-led ventures won $20,000 each: GreyDyne, a software platform to detect seizures from EEG data that was co-founded by accounting major Nathan Gottlieb; IMD Solutions, a health care technology created by a team of five ASU undergraduates majoring in biomedical engineering; and Storm Stick, a device invented by Jason Miller to decontaminate fire scenes. Other ventures that were awarded funding were NeXST Rehab, $15,000; Dext Technologies, VBeck and Navi Concierge Nurses, $10,000 each; and Stonne Products, Selleh Lake Restoration, PeerSquared, BigUp and Accelerated Cycles, $5,000 each.

eSeed Social Impact Challenge: The Pauline Foundation, started by Pauline Nalumansi, a graduate student in the Thunderbird School of Global Management, won $6,000. Nalumansi won $5,000 at the Demo Day last fall for the nonprofit she created to help empower at-risk youth in Uganda, her home country. Other winners in this category were Ahwatukee Christmas, a Christmas tree removal and donation business started by finance major Connor Hogan and engineering management major Dillon Newgaard, and Memory Glass, a facial-recognition device for people with impaired memories invented by mechanical engineering major Andrew Deros, $2,500 each.

eSeed Challenge Accelerator: The five $5,000 winners were Introhm, Blastr Wrapz, StreamWork, Prescient Technologies and Crystal Sonic. Other winners were Selleh Lake Restoration and Opti-Rims, $2,500 each, and Altion Security, $1,000.

Mastercard Foundation Scholars Program: Besides Sarfo, the other winners were Comprehensive Rehabilitation Services and Shine Gardens, $4,000 each; VBeck and Resin, $3,000 each; Mtendere Library, $1,500, and Suntaa Shea and FJ Breeds, $1,000 each.

Phoenix Rising Venture Challenge: This was a new competition funded by ASU’s Global Sport Institute in collaboration with Phoenix Rising, which was seeking ideas that would promote the soccer team. Hat-Tec, a customizable hat storage and display hanger, won $15,000 and a beta test with the team. The founder, Domenic Fotino, earned a degree in technological entrepreneurship and management from ASU. Rachel Masterson, a student in the Thunderbird School of Global Management who created a venture called Futbar, won an offer to create a collaborative event with the team.

Retail Devils: This challenge is funded by Follett and was started as a pathway for student entrepreneurs to get their creations into the Sun Devil Bookstores. Winners were Better Family Products, $5,000; Strax Gear, $3,000, and Bare Sprouts, $2,000.

Sarsam Family Venture Challenge: Padma Agrobotics won $15,000 for its invention of weed-killing robots. Compass for Courage won $10,000. Ryan Stoll, a postdoctoral scholar in the psychology department and co-founder of Compass for Courage, has won thousands of dollars in previous venture competitions. Compass for Courage makes an interactive curriculum for children that uses board games to help them learn skills to overcome anxiety.

C.J. Allen, who earned an MBA at ASU in 2009 and is senior manager for the Alexa Smart Home program at Amazon, was one of the Demo Day judges.

“The virtual format changed the experience as a judge and changed the way we were able to connect with teams,” he said. “But what didn’t change was the quality of the ideas and pitches. I leave truly inspired by everyone.”

Top image: Freda Sarfo, a master’s degree student in global logistics, won $5,000 at last week’s Demo Day for her venture, Tropical Almond, a social enterprise based in Ghana. She's shown here pitching at the 2019 Demo Day. Photo by Charlie Leight/ASU Now

Mary Beth Faller

Reporter , ASU News