Comprehensive statewide study tracks rapid spread of SARS-CoV-2 variants

Study reveals omicron benchmark for COVID-19 variants

January 31, 2023

Having carved a path of destruction around the globe, the novel coronavirus SARS-CoV-2 continues to recur in ever-changing disguises. Understanding the dynamics of viral transmission is crucial for ongoing and future public health preparedness.

In a first-of-its-kind, comprehensive statewide survey, Efrem Lim and his colleagues at Arizona State University’s Biodesign Institute teamed up with three regional hospitals to study the spread of SARS-CoV-2 variants. Portrait of ASU Associate Professor Efrem Lim. Efrem Lim is a researcher in the Biodesign Center for Fundamental and Applied Microbiomics and an associate professor with the ASU School of Life Sciences. Download Full Image

The study will help researchers, clinicians and public health officials better understand how quickly variants of the virus rise in prevalence throughout Arizona. The lightning-fast spread of the omicron variant is explored in detail through surveillance of community testing, hospital data and sequencing of viral variants found in community wastewater.

The findings highlight the fact that SARS-CoV-2 underwent a substantial alteration of its genomic profile in its transformation to omicron, a phenomenon known as antigenic shift. The emergence rate of omicron BA.1 (17.02 days) was over 2.3 times faster than the previous delta variant and the subsequent omicron lineages BA.2 and BA.5.

Lim is a researcher in the Biodesign Center for Fundamental and Applied Microbiomics and an associate professor with the ASU School of Life Sciences. The research incorporates community sequencing information from public clinics as well as from three hospitals located in the Phoenix metropolitan area: Valleywise Health, Phoenix Children’s and Dignity Health.

The study follows the omicron variant, observing its impact on hospital admissions and comparing this data with viral strains extracted from wastewater. Having analyzed the rapid ascent of omicron BA.1, “we now have a benchmark for all these other variants that are coming up,” Lim says. “Are they rising as fast as the superstar, the omicron BA.1? If they are, then that's a red flag that we need to start preparing for a very large surge, like the omicron wave.”

The research appears in the current issue of the American Society for Microbiology journal mBIO.

Shift in the viral strains

An antigenic shift is a sudden change in the genetic makeup of a virus or other pathogen, which leads to the creation of a new strain that is significantly different from previous strains. This can occur through mutation or through the reassortment of genetic material from different strains of the virus.

Such a shift in viral character can have consequential implications for public health, as the new strain may be able to evade the immunity developed by individuals who have been previously infected or vaccinated against the original strain of the virus, leading to more widespread outbreaks.

“There’s a difference between what we call antigenic shift versus antigenic drift,” Lim says.

A good example is the influenza virus, which typically undergoes small, incremental changes from year to year, requiring the production of new annual vaccines.

“But occasionally, the virus undergoes very large changes such as recombination with other influenza viruses like avian influenza or swine influenza. This is what we call an antigenic shift, and whenever a virus undergoes antigenic shift, it always leads to a large pandemic,” Lim says.

Graphic illustration depicting a hand holding a thermometer and people in a hospital.

The emergence rate of of SARS-CoV-2 variant omicron BA.1 was over 2.3 times faster than the previous delta variant and the subsequent omicron lineages BA.2 and BA.5. Fewer than 11 days elapsed from the BA.1 variant's first community appearance to subsequent hospitalizations. The BA.1 variant can now act as a benchmark for tracking the appearance and spread of new variants, giving public health officials and hospitals advanced warning of emergent variants posing the highest risk to the community. Graphic by Shireen Dooling/ASU

Influenza pandemics like the 2009 H1N1 outbreak were the result of antigenic shifts. The same rules apply for the SARS-CoV-2 virus.

The study explored the genomic epidemiology of SARS-CoV-2 at the state level by conducting baseline genomic sequencing surveillance of more than 27,000 samples from public testing and 1,125 samples from hospitalized patients, which were diagnosed between Nov. 1, 2021, and Jan. 31, 2022, in Arizona. Results indicate that omicron cases were identified in hospitals just 10.51 days after the variant’s first emergence in the community.

After omicron emergence and a brief lag of around 10 days, it caused a surge in hospital admissions, as the study verified. Researchers also identified mutations in three omicron genes that were significantly more common in cases of COVID-19 requiring hospitalization, compared with positive COVID-19 cases from community testing.

First-time sequencing of SARS-CoV-2 variants from wastewater

Wastewater-based epidemiology is a new and effective public health approach to monitoring communitywide infectious diseases occurrence. The advantages of wastewater monitoring during the COVID-19 pandemic include estimating disease burden despite decreased testing rates in the community over time. Presymptomatic and asymptomatic infections that may not normally be tested can also be evaluated through wastewater sequencing, identifying the viral lineages circulating within a community.

The study marks the first-time sequence data pertaining to variants of SARS-CoV-2 have been extracted from wastewater, significancy extending the power of the technique for public health surveillance. Wastewater monitoring and clinical surveillance are complementary approaches to public health efforts. In recent months, community and wastewater data on viral presence have diverged, suggesting that while cases of the virus are still rising, reduced testing habits in the community may be failing to register many of these.

One important lesson from studying the rise of omicron BA.1 is the tiny available window between the emergence of new variants and the first hospital cases. As omicron BA.1 demonstrates, this can occur in as little as 10 days, with the possibility of overwhelming underprepared hospitals. While most viral alterations will be minor and incremental, the chance of antigenic shift and sudden, heightened disease incidence remain a serious challenge for public health. Integrative, cooperative efforts, leveraging the resources of hospitals, community data and new sequencing methods will be essential as humanity continues to grapple with SARS-CoV-2 and other infectious threats.

Richard Harth

Science writer, Biodesign Institute at ASU


ASU microelectronics workshop addresses national effort to develop workforce

Leaders in industry, government and higher education discuss shared vision for advancing microelectronics talent pipeline

January 31, 2023

Last week, microelectronics leaders from across the nation came together for the 2023 Microelectronics Education and Workforce Development, or MEWD, Workshop, which highlighted the importance of improving semiconductor research, development and training across Arizona.

The workshop was organized by the Secure, Trusted, and Assured Microelectronics, or STAM, Center in the School of Computing and Augmented Intelligence, part of the Ira A. Fulton Schools of Engineering at Arizona State University. A close-up view of a semiconductor chip. Organized by the Secure, Trusted, and Assured Microelectronics Center in the School of Computing and Augmented Intelligence, part of the Ira A. Fulton Schools of Engineering at ASU, the 2023 Microelectronics Education and Workforce Development Workshop highlights the importance of improving semiconductor research, development and training across Arizona. Photo courtesy Pixabay Download Full Image

Michel Kinsy, director of the STAM Center and an associate professor of computer engineering, identified a crucial need for discussion and cooperation among stakeholders from various fields amid a national resurgence in microelectronics research and manufacturing.

“I wanted an intimate setting for folks to freely share ideas, not just of what they are doing themselves but what vision we should embark on collectively,” Kinsy says. “Hopefully the connections and the networking that started here can lead to more collaboration and overall greater outcomes for the nation and ASU as we move microelectronics forward.”

The event brought together multiple sectors involved in microelectronics efforts, including government departments, industry representatives, national labs, universities and military entities.

Speakers presented on specific facets of microelectronics that their organizations specialize in — including security, manufacturing, translational research, workforce development efforts, reskilling initiatives, curriculum development and more — and addressed how each of their teams is addressing workforce challenges.

“At ASU, we’re focused on building new infrastructure, growing the pipeline, providing and anticipating opportunities and looking for translational outcomes,” says Kyle Squires, the ASU vice provost for engineering, computing and technology and dean of the Fulton Schools. “Being able to scale programs to reach a large number of learners is key, in addition to expanding access to get more workers in the pipeline and delivering flexibility in our programs to meet learners where they are.”

Other efforts at ASU include a regionally collaborative proposal to establish the Microelectronics Commons, a national network funded by the CHIPS and Science Act of 2022, to close the innovation “lab-to-fab” capabilities gap in the United States.

Many presentations addressed a shared goal of achieving scale, access and flexibility, with outcomes for the workshop including growing a diverse and highly skilled pipeline of microelectronics employees and developing a common infrastructure that enables more access to testing and implementing new semiconductor technologies for operational use as part of their training.

Keynote speaker Dev Shenoy, principal director for microelectronics for the Office of the Under Secretary of Defense for Research and Engineering in the U.S. Department of Defense, agrees that building the workforce is vital.

“Workforce development and an increased emphasis on microelectronics education is critical for the U.S. to be successful in onshoring semiconductor manufacturing,” Shenoy says. “The CHIPS and Science Act will foster the pipeline of talent through the Microelectronics Commons, for example, to strengthen the workforce where it is needed and bolster local economies where hubs and core facilities are located.”

In addition to the Department of Defense, other government entities present included the U.S. Department of Commerce and its National Institute of Standards and Technology, the CHIPS Act implementation team and the Defense Advanced Research Projects Agency, or DARPA.

“We want to return leading-edge manufacturing to the U.S.,” says Jessica R. Nicholson, workforce policy advisor for the CHIPS Act. “To do that, we need to create an ecosystem of manufacturers and suppliers, equipment materials researchers and designers in processes, and build a trained workforce. The availability of these resources will drive innovation across the technological and industrial sectors.”

Among the other attendees were industry groups including SynopsysRaytheon TechnologiesBoeingSiemens Government Technologies and BAE Systems. There was also representation from military organizations, including the DEVCOM Army Research Laboratory and the Air Force Research Laboratory.

National laboratories in attendance included Argonne National LaboratoryPacific Northwest National Laboratory and Sandia National Laboratories.

In his presentation, Rick McCormick, a representative from the Microsystems Engineering, Science and Application Center at Sandia National Laboratories, alluded to the strong correlation between manufacturing and innovation, and the impact of student collaboration.

“The way we execute our mission is heavy partnering within the government and all kinds of companies,” he says. “Three-quarters of the projects have university partners associated with them, with one of our partners being ASU.”

All event participants agreed that higher education institutions play a crucial role in bridging the workforce gap in microelectronics, with universities including ASU, Northern Arizona UniversityUniversity of ArizonaGeorge Washington University and Morgan State University in attendance to discuss how opportunities through each school are preparing students to enter the workforce. 

A key discussion surrounded how to engage more diverse populations, including members of minority groups, veterans and community college students. University participants also highlighted the importance of pathway programs and reaching students at a young age, with K–12 pipelines to guide students toward microelectronics during their early education, such as at engineering summer camps and at ASU Preparatory Academy.

Squires detailed current efforts including the Microelectronics and Nanomanufacturing Certificate Program — offered in partnership with Penn State, the University of California San DiegoGeorgia Institute of Technology and Norfolk State University — to reach active military personnel and veterans with stackable credential certifications at four strategically located regional partner sites.

The sites, which are located in Phoenix, Atlanta, San Diego and Norfolk, Virginia, will each offer the program in collaboration with one state university and one local community college. In Phoenix, this will include Rio Salado College and ASU.

“Students who go through this program can achieve the kind of certification that industry understands and values,” Squires says.

The workshop also featured an academic panel on microelectronics training needs and an industry panel on talent needs, in addition to a tour of ASU’s MacroTechnology Works in Tempe. Led by Zachary Holman, an associate professor of electrical engineering in the Fulton Schools, the tour explored the facility and its efforts in accelerating semiconductor, advanced materials and energy device research.

“The MacroTechnology Works facility is a very unique space that will be integral in building physical infrastructure and advancing research, in addition to providing opportunities for training, internships and partnerships,” Squires says.

Squires also noted that the recent launch of ASU’s School of Manufacturing Systems and Networks, part of the Fulton Schools, exemplifies the university’s efforts to address current and future challenges and provide a center of gravity across engineering disciplines to focus on efforts relating to manufacturing.

“This workshop and the engagement that it fostered highlight the sort of interactions that we want to be having on a regular basis around this important topic,” Kinsy says. “Our goal was to open the door for continued discussions, which I believe we have achieved.”

Annelise Krafft

Communications Specialist, Ira A. Fulton Schools of Engineering