Arizona COVID-19 Genomics Union Tracks Virus Strains in State

Sep 16, 2020

Initial findings reported by the Arizona COVID-19 Genomics Union suggest that following Arizona’s first reported case of COVID-19 in late January, the state experienced no cases that went undetected and was COVID-free until at least 11 distinct incursions occurred between mid-February and early April.

The results were published in mBio, an open access journal published by the American Society for Microbiology, earlier this month.

Researchers at UArizona are among founders of the Arizona COVID-19 Genomics Union, whose mission is to crack the genetic code of SARS-CoV-2 – the virus that causes COVID-19. (Image: Pixabay)Faculty at the Translational Genomics Research Institute (TGen) – an affiliate of City of Hope – along with faculty at Northern Arizona University, the University of Arizona and Arizona State University launched the ACGU in early April with the express purpose of tracking the causative agent of COVID-19: how it evolves and how it spreads into, within and out of Arizona.

The ACGU sequenced the SARS-CoV-2 genomes in as many virus-positive patient samples in Arizona as possible, and working with Arizona’s public health officials, applied the results toward statewide efforts to test and track patients, as well as provide guidance for Arizona public policy makers.

Quick action by ASU and Maricopa County public health officials, ACGU scientists agree, likely kept the first identified COVID-19 patient in Arizona — a student who had just returned from Hubei, the Chinese province where the disease originated — from igniting an outbreak, and prevented Arizona from becoming an early epicenter.

“This is a great example of how a rapid and thorough public health response can be successful in preventing the spread of this disease,” said ACGU Director Paul Keim, Regents’ Professor of Biological Sciences and Cowden Endowed Chair in Microbiology at NAU and executive director of the NAU Pathogen and Microbiome Institute.

“Similar steps could be taken when shaping future efforts to reopen businesses and schools, even though the virus continues to circulate and people remain susceptible,” added Dr. Keim, who is also a Distinguished Professor and co-director of TGen’s Pathogen and Microbiome Division.

Michael Worobey, PhDMichael Worobey, PhD, an ACGU co-founder and the head of Department of Ecology and Evolutionary Biology in the UArizona College of Science, agrees.

“It’s a combination of the patient doing the right things to isolate himself and be aware that he possibly had this disease, and public health officials doing all the right things. Stopping an incursion of COVID-19 was a victory for the state of Arizona,” said Dr. Worobey, who also is a member of the UArizona BIO5 Institute.

This bought Arizona valuable time for preparedness efforts. The first reported case of community transmission occurred in Arizona in early March and descended from the Washington state outbreak that was discovered in February. More than 80% of the SARS-CoV-2 genome sequences from Arizona COVID-19 cases descended from at least 11 separate lineages that were initially circulating widely in Europe, and by travel have since dominated the outbreak throughout the U.S. None of the observed transmission clusters are epidemiologically linked to the original travel-related case in the Arizona, suggesting successful early isolation and quarantine.

The ACGU uses state-of-the-art sequencers, custom computational analysis workflows and supercomputers to determine the sequence of the virus’s RNA genome, which is just under 30,000 bases long. In contrast, there are nearly 3 billion bases in the human genome, which determine traits as simple as eye and hair color, and as complex as an individual’s propensity for cancer and other disease.

TGen has so far sequenced SARS-CoV-2 genomes from almost 3,000 COVID-19 positive samples for the ACGU. Additional sequencing was performed at ASU and UArizona, from among the more than 200,000 positive cases in Arizona, making it one of the most robust such efforts in the nation. ACGU receives Arizona samples collected by state, county, tribal and private health care systems.

ACGU scientists take advantage of small changes or mutations in the virus’s genome, which naturally occur over time as the virus reproduces, to track the spread of the virus. By comparing mutations observed in Arizona to those present in strains circulating across the globe, they can determine when and from where the virus has been introduced to Arizona.

“On average, the SARS-CoV-2 genome accrues a new change in its genetic code every two weeks that is passed on to its descendants. These genomic signatures allow us to track where different lineages come from,” said Brendan Larsen, a doctoral student in Dr. Worobey’s lab and one of the lead authors of the study.

Using molecular clock analyses, which allows researchers to gather clues about the evolutionary history of the virus based on the rate of genetic variances accumulating over time, the authors found that the majority of Arizona sequences are represented by two lineages and several sub-lineages, most of which were likely introduced through domestic travel, but with some evidence for international importation.

“Through the ACGU, we are harnessing expertise in virology, genomics, evolution and bioinformatics from throughout Arizona in order to rapidly distill these genomic data into actionable insights that can complement the state’s public health response,” Dr. Keim said. “These results demonstrate the power of public health contact tracing and self-isolation following a positive test for stemming the tide of infections moving forward.”

David Engelthaler, PhD, director of TGen North in Flagstaff, which includes the institute’s infectious disease branch, said the initial ACGU findings show how each community and each state is writing its own story for what is happening in the COVID-19 pandemic.

“We need to understand all of those plot lines that have led to where we are now,” said Dr. Engelthaler, another of the ACGU co-founders. “Once this disease was detected in Arizona on Jan. 26, public health immediately jumped in to make sure that all contacts were identified, samples were collected and the patient was watched very closely for the next couple of weeks to make sure there were not any more cases.”

In the coming months, he said, it will be necessary to track COVID-19 outbreaks and build epidemiological walls around each case, especially for those most at risk: persons older than 65, those in long-term care facilities or prisons, and those with preexisting health problems.

“When you don’t have eyes on this, when you don’t have contact tracing, then it can really easily move from person to person,” Dr. Engelthaler said. “It’s really useful for public policy makers to be making locally informed decisions.”

Efrem Lim, PhD, a virologist who leads the ASU team, said the SARS-CoV-2 genome sequence data can give health care providers and public policy makers an edge in fighting the pandemic.

“Tracking the transmission of the virus and its mutations ensures that therapeutics and vaccines being developed are on the right course,” said Dr. Lim, an assistant professor at the ASU Biodesign Institute. “We now have a handle on what the SARS-CoV-2 virus in our communities looks like at the sequence level.”

The researchers’ study – “An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona” – was supported by The NARBHA Institute, Flinn Foundation, The Virginia G. Piper Charitable Trust, Blue Cross and Blue Shield of Arizona, the National Institutes of Health, the David and Lucile Packard Foundation, the University of Arizona College of Science and Office of Research Innovation and Impact, and the BIO5 Institute.

The authors acknowledge the critical role the Arizona Department of Health Services and multiple county and tribal health departments play in directing samples to the ACGU to be sequenced. Computational analyses were run on Northern Arizona University’s Monsoon computing cluster, funded by Arizona’s Technology and Research Initiative Fund. Software development efforts were funded in part by the Chan-Zuckerberg Initiative and the Alfred P. Sloan Foundation. Additional analysis effort was funded under the State of Arizona Technology and Research Initiative Fund, administered by the Arizona Board of Regents, through NAU. The Cowden Endowment for Microbiology provided funds to support salaries.

The UArizona Health Sciences COVID-19 Research webpage can be found here.

For the latest on the University of Arizona response to the novel coronavirus, visit the university’s COVID-19 webpage.

For UANews coverage of COVID-19, visit https://news.arizona.edu/news/covid19.

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A version of this article appeared originally on the UANews website.

NOTE: Images available upon request.

About the University of Arizona Health Sciences
The University of Arizona Health Sciences is the statewide leader in biomedical research and health professions training. UArizona Health Sciences includes the Colleges of Medicine (Tucson and Phoenix), Nursing, Pharmacy, and the Mel and Enid Zuckerman College of Public Health, with main campus locations in Tucson and the Phoenix Biomedical Campus in downtown Phoenix. From these vantage points, Health Sciences reaches across the state of Arizona, the greater Southwest and around the world to provide next-generation education, research and outreach. A major economic engine, Health Sciences employs nearly 5,000 people, has approximately 4,000 students and 900 faculty members, and garners $200 million in research grants and contracts annually. For more information: uahs.arizona.edu (Follow us: Facebook | Twitter | YouTube | LinkedIn | Instagram).

About the University of Arizona
The University of Arizona, a land-grant university with two independently accredited medical schools, is one of the nation's top public universities, according to U.S. News & World Report. Established in 1885, the university is widely recognized as a student-centric university and has been designated as a Hispanic Serving Institution by the U.S. Department of Education. The university ranked in the top 20 in 2018 in research expenditures among all public universities, according to the National Science Foundation, and is a leading Research 1 institution with $687 million in annual research expenditures. The university advances the frontiers of interdisciplinary scholarship and entrepreneurial partnerships as a member of the Association of American Universities, the 65 leading public and private research universities in the U.S. It benefits the state with an estimated economic impact of $4.1 billion annually. For more information: arizona.edu (Follow us: Facebook | Twitter | YouTube | LinkedIn | Instagram).

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