Arizona COVID-19 Genomics Union Tracks SARS-CoV-2 Strain

The first findings reported by the Arizona COVID-19 Genomics Union (ACGU) show that the state has not experienced any undiscovered cases, following the first COVID-19 case reported in Arizona in late January. Mid-February and early April, suggesting that they were COVID-free until at least 11 different intrusions occurred between them.

Published results will be published in scientific journals mBio..

Hope City of Affiliate Translational Genomics Institute (TGen) faculty members, Northern Arizona University (NAU), University of Arizona (UArizona), and Arizona State University (ASU) launched ACGU in April. Causes of COVID-19, SARS-CoV-2: How it evolves and how it spreads inside and outside Arizona.

ACGU sequences the SARS-CoV-2 genome in as many virus-positive patient samples as possible in Arizona and works with Arizona public health personnel to apply the results for state-wide patient testing and follow-up. And provided guidance to Arizona as a public policy maker.

ACGU scientists said a swift response by ASU and public health authorities in Maricopa County was the first confirmed COVID-19 patient in Arizona, a student who had just returned from Hubei Province, China, where the disease originated. ) Is likely to have been protected from the ignition of the outbreak. Prevented Arizona from becoming an early epidemic of the epidemic.

“This is a good example of how a quick and thorough public health response can succeed in preventing the spread of the disease,” said ACAU’s Board of Directors, Professor of Biological Sciences at Regents, and NAU’s Microbiology. Dr. Paul Keim, Cowden Endowed Chair, said. Secretary-General of the NAU Institute for Pathogens and Microbiota.

Keem, a prominent professor and co-director of TGen’s Pathogens and Microbiota department, also said, “Future efforts to reopen businesses and schools even if the virus continues to spread and people are still susceptible to infection. A similar procedure can be followed when shaping the virus. “

Dr. Michael Warobbie, co-founder of ACGU and head of the Department of Ecology and Evolutionary Biology at the University of Arizona, agrees.

“It’s a combination of patients who are doing the right thing to isolate the patient and recognize that they may have this disease. Health authorities I’m doing everything right. Stopping the invasion of COVID-19 was a victory for Arizona, “Dr. Wrorobey said.

This has spent valuable time preparing for Arizona. The first reported case of a “community” outbreak occurred in Arizona in early March, resulting from an outbreak in Washington that was discovered in February. More than 80% of the SARS-CoV-2 genomic sequence of Arizona COVID-19 cases originated from at least 11 strains that were initially widely circulated in Europe, and the clusters that dominate development throughout the United States by travel Epidemiologically related to the original travel-related case in Arizona, suggesting early isolation and successful quarantine.

ACGU uses state-of-the-art sequencers, custom computational analysis workflows, and supercomputers to sequence the viral RNA genome. In contrast, the human genome has about 3 billion bases, which are as simple as eye and hair color and determine properties as complex as an individual’s tendency towards cancer and other diseases.

To date, TGen has sequenced the SARS-CoV-2 genome from approximately 3,000 COVID-19-positive samples from ACGU, with additional sequencing at ASU and U Alizona from over 200,000 positive cases in Arizona. Such a robust effort in Japan has become one of the most common. ACGU receives Arizona samples collected by state, county, tribal, and private health systems.

ACGU scientists use small changes and mutations in the virus’s genome that occur naturally as the virus propagates to track the spread of the virus. By comparing the mutations observed in Arizona with those found in strains circulating around the world, you can determine when and where the virus was introduced into Arizona.

Using molecular clock analysis, researchers have found that the majority of Arizona sequences are represented by two strains and several sub-strains. Most of these are believed to have been introduced through domestic travel, but there is some evidence of international imports.

“Through ACGU, we are leveraging our expertise in virology, genomics, evolution, and bioinformatics across Arizona to quickly extract these genomic data into actionable insights that can complement the state’s public health response.” Said Dr. Keem. “These results show the power of public health contact tracking and self-isolation following positive tests to stop the epidemic.”

Dr. David Engelthaler, Head of Flagstaff’s T Gen North, including the Institute’s Infectious Diseases Division, said the first ACGU findings were a unique story about what’s happening in each community and state in the COVID-19 pandemic. Said that it indicates that you are writing.

Dr. Engelthaler, one of the co-founders of ACGU, said: “When the disease was detected in Arizona on January 26, the public health department contacted immediately, all contacts were identified, samples were collected, and patients were very carefully monitored for the next two weeks. , More cases. “

Over the next few months, COVID-19 outbreaks need to be tracked and epidemiological barriers built around each case, especially for those at highest risk (65+, long-term care facilities, prisons, and those people). There are existing health problems that I mentioned.

“If this isn’t the focus, and if there’s no contact tracing, it’s easy to move from person to person,” said Dr. Engeltaler. “It is really useful for public policy makers to make informed decisions.”

Dr. Ephrem Lim, a virologist who leads the ASU team, said SARS-CoV-2 genomic sequence data can give healthcare providers and public policy makers an edge in the fight against pandemics.

“By tracking the transmission of the virus and its mutations, we can see that the treatments and vaccines under development are moving in the right direction,” said Dr. Lim, an assistant professor at ASU’s Biodesign Institute. “We now know what the SARS-CoV-2 virus in our community looks like at the sequence level.”