The Translational Genomics Research Institute, an affiliate of City of Hope, has joined with The Pathogen and Microbiome Institute at Northern Arizona University and the Department of Ecology and Evolutionary Biology at the University of Arizona to form a union dedicated to tracking the spread and evolution of coronavirus in Arizona.
Harnessing the power of state-of-the-art technology and big data analysis, researchers at the newly formed Arizona COVID-19 Genomics Union, or ACGU, want to better understand how the virus may be evolving, how it is transmitted and how it is moving through the general population. This molecular epidemiological approach combines traditional epidemiology methods with evolutionary modeling based on high-resolution analysis of the virus' genome.
ACGU will sequence samples from COVID-19 patients to analyze the virus' genetic codes, track its different strains, show where each sample originates from and where it may have been transmitted, and — possibly — reveal details that could provide critical information for diagnostics, antiviral drug targets and vaccine development. TGen already is receiving samples from across Arizona as part of its testing efforts.
"Only by using genomic sequencing and advanced analyses can we begin to fully understand this disease at the molecular level, looking for keys to unlock its mysteries," said David Engelthaler, co-director and associate professor of the Translational Genomics Research Institute's Pathogen and Microbiome Division, the infectious disease branch in Flagstaff known as TGen North. "We have the ability to sequence the genome of every strain from every patient — that's what we are working toward."
Engelthaler is Arizona's former state epidemiologist and state biodefense coordinator. He was previously with the Centers for Disease Control and Prevention and has led investigations of local, national and international disease outbreaks for over 25 years, starting with Arizona's hantavirus outbreak in 1993 to 1994. He will coordinate the new ACGU's genomic sequencing of the SARS-CoV-2 virus, which causes COVID-19.
The union's other co-founders are two of Arizona's leading infectious-disease scientists: Paul Keim of Northern Arizona University and Michael Worobey of the University of Arizona.
Worobey is head of the UArizona Department of Ecology and Evolutionary Biology and a member of university's BIO5 Institute. He is known around the world for his work on viral pandemics. Using genomic epidemiology, he has definitively tracked the origins and worldwide spread of HIV and also determined why the 1918 Spanish influenza pandemic killed millions of young adults.
"Molecular analysis of viruses provides crucial clues about how pandemics begin and how to fight them," Worobey said. "We will be capitalizing upon Arizona's wealth of talent and infrastructure in this endeavor."
Keim is a world expert in pathogens such as plague and anthrax. He worked with the FBI to crack the anthrax letters case in the wake of 9/11. At NAU, he is a Regents Professor of Biology, holds an endowed chair in microbiology and is executive director of the Pathogen and Microbiome Institute. He is a Distinguished Professor at TGen, co-director of TGen North and will serve as director the ACGU.
"Genome sequences are ideal for distributed scientific research efforts and the Arizona union will rely heavily on national and global studies to track the disease. Nevertheless, it is critical that regional experts engage in this process to maximize the benefits for Arizona citizens," Keim said.
The Arizona COVID-19 Genomics Union is similar to other groups across the globe working to gain a foothold on the new coronavirus. Rapid sharing of data and analysis has been, and continues to be, critical to scientific, medical and public health understanding of the virus. The first U.S. epicenter of COVID-19 — Seattle — is also home to NextStrain, the internet home for genome tracking of this and other pathogens. The Arizona COVID-19 Genomics Union will make its findings public and work with NextStrain and other coalitions worldwide.
The consortium of Arizona scientists hope that their regional sequencing will give Arizona health care providers and public policymakers an edge in responding to the pandemic.