Hunting for COVID-19 variants

The Delta variant of COVID-19 arrived in late July and now accounts for at least 90 percent of the positive cases collected at Clemson University, according to an ongoing study at the university.

“The viral load in the Delta samples we collected is significantly higher than other COVID strains, making it highly transmissible,” said Delphine Dean, director of the university’s Research Education in Disease Diagnosis and Intervention Lab, or REDDI Lab.

So far, no cases of the Lambda or Mu variation have been discovered, said Dean, the Ron and Jane Lindsay family innovation professor of bioengineering.

Dean and a team of Clemson University researchers are analyzing thousands of positive COVID-19 tests in search of emerging variants and other clues of a resurgent health pandemic.

 The work could identify new highly infectious variants resistant to existing vaccines and help map and trace new outbreaks. Information will inform public health officials and scientists working to stifle the COVID-19 pandemic.

“This study gives us real-time feedback to guide decision-making. Surveillance is so critical and Clemson has one of the most robust university-testing programs, so we are in a unique position,” said Hai Yao, the Ernest R. Norville Endowed Chair in Biomedical Engineering.

The interdisciplinary Clemson team is performing genome sequencing on around 2,000 positive samples from COVID-19 tests collected this year, as well as from ongoing tests for the university and surrounding community.  Viral genome sequencing determines the complete genetic code of the virus to help scientists understand its characteristics. This will allow Clemson’s multidisciplinary team to determine how COVID-19 evolves as it is transmitted and determine how different COVID variants will affect public health.

The project is part of a national effort to advance research on the emergence, evolution and pathogenicity of SARS-CoV-2 variants circulating in the United States. The National Institutes of Health invested $15 million in 21 projects around the country. Clemson received $750,000.

Viruses constantly mutate and evolve. While some variants disappear, others persist. The Centers for Disease Control and Prevention is monitoring several variants – Alpha, Beta, Gamma and Delta – that it says appear to spread more quickly and easily than others. Studies suggest current vaccines are effective against these variants, according to the CDC, but more information is needed to understand their emergence and transmission.

The Clemson surveillance project utilizes the REDDI Lab, which was created last year to support the university’s COVID-19 testing strategy. Certified through the Clinical Laboratory Improvement Amendments (CLIA) administered by the Center for Clinical Standards and Quality, REDDI processes around 7,000 COVID-19 tests daily.

The genome sequencing and high-performance computational biology will be conducted at the Clemson University Genomics and Bioinformatics Facility, which is in the College of Science and led by Christopher Parkinson, professor of biological sciences and forestry and environmental conservation.

Lior Rennert and Corey Kalbaugh, assistant professors in the Department of Public Health Sciences, will analyze the data collected to build predictive models that will track the risks of COVID-19 outbreaks and identify segments of the population most at risk. Rennert and Kalbaugh, also an assistant professor of bioengineering, have been central to Clemson’s surveillance-based informative testing program and have helped health officials and others evaluate the effectiveness of COVID-19 mitigation strategies.

In addition to Yao, Dean, Parkinson, Rennert and Kalbaugh, numerous other Clemson experts are working on the project as well:

• Chris Saski, associate professor of plant and environmental sciences;
• Lesslie Pekarek, medical director of Student Health Service;
• Congyue Peng, research assistant professor in the College of Engineering, Computing and Applied Sciences;
• And Stevin Wilson, research associate of biological sciences.

The project is funded through an NIH Center for Biomedical Research Excellence  (COBRE) at Clemson called the S.C. Translational Research Improving Musculoskeletal Health, or SC-TRIMH, led by Yao and Martine LaBerge, chair of the Bioengineering Department. The center was initially funded in 2018 with $11 million from the NIH. Through these COBRE investments, NIH seeks to enhance biomedical research capacity in states of need and build interdisciplinary teams that can tackle medical issues of societal significance.

“This is a great example of how the COBRE program enhances university research that directly benefits society,” said Tanju Karanfil, Clemson vice president for research. “This research will give scientists and policymakers the accurate information they need to protect public health.”

Research reported in this publication is supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number P20GM121342-03S1. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.