Illumina Inc., a global leader in DNA sequencing and array-based technologies, today recognized the progress and impact of genomic technologies on pathogen preparedness and response. Following the boost in sequencing infrastructure and capabilities driven by the COVID-19 pandemic, today genomic technologies are enabling public health agencies and health care systems to better prepare for, and respond to, pathogenic threats.

From the onset of the pandemic in 2020, Illumina's pathogen genomic surveillance solutions were deployed to characterize the genome of SARS-CoV-2, catalyze development and updates to vaccines and diagnostics, identify virus variants of concern, and monitor the virus's evolution and spread. As the World Health Organization (WHO) and countries including the United States have begun declaring an end to their states of public health emergency, COVID-19 continues to present a complicated global public health challenge.

"Even with the end of the public health emergency, there are individuals, communities, and economies deeply impacted by the COVID-19 pandemic; continued vigilance by public health agencies and access to testing, genomic surveillance, vaccines, and treatments is required," said Dr. Phil Febbo, chief medical officer of Illumina. "While we all want to move past the pandemic, by building on the capabilities established during that time, we have the opportunity to keep COIVD-19 controlled and become better prepared for the predictable introduction of future pathogens."

Genomic surveillance

According to the WHO, genomic surveillance is "the process of constantly monitoring pathogens and analyzing their genetic similarities and differences." It has already been used in a focused way with relatively limited capacity to track pathogens, for example in 2013 by the Food and Drug Administration for its GenomeTrackr program, which gathered data from over 100 laboratories performing routine surveillance of the American food supply, many using Illumina technology. This program run in partnership with the US Centers for Disease Control and Prevention (CDC) and Department of Agriculture, enhanced monitoring for foodborne pathogens, and guided the response to foodborne disease outbreaks.

The COVID-19 pandemic accelerated the adoption of genomic surveillance at-scale to support the global response and reduced the barriers for sharing data internationally. This enabled the tracking of viral evolution and movement in the global population in a manner, scale and timeframe not previously possible. By sequencing the genomes of dangerous pathogens, today scientists can better understand how they spread and how to best control them to protect human and animal health as well as the environment.

Since 2020, these expanded capabilities have been applied to public health threats in the US, including mpox, highly pathogenic avian influenza, and other notable respiratory pathogens. Surveillance data provides scientists with a clearer picture from which public health officials can make recommendations and manage outbreaks.

For example, officials at the city, county, and state levels across the US have begun using Illumina technology to conduct wastewater surveillance for SARS-CoV-2, polio, and pathogens whose antimicrobial resistance poses an existential threat to human health.

This type of genomic surveillance is opening new doors to understanding the patterns of pathogen transmission at population scale. A recently published article in The Lancet, "A global aircraft-based wastewater genomic surveillance network for early warning of future pandemics," asserts that this type of surveillance could be a critical component of a comprehensive global pandemic early warning system.

Outside of United States, the genomic surveillance infrastructure and framework developed in response to COVID-19 has already been applied to respond to outbreaks of other viral threats, such as Marburg virus in Tanzania and Ebola virus in Uganda. In Brazil, Illumina genomic surveillance solutions played a critical role in the response to a major Dengue virus outbreak, supporting the public health response.

A proactive approach

"There is significant work underway globally to build capacity and capabilities to enable pandemic preparedness and response," said Vanessa Moeder, senior director of Global Health at Illumina. "We need to establish clear expectations for future pathogen surveillance—with defined targets to detect, investigate, and respond to potential threats. Genomics plays a profound role in robust surveillance efforts. By enabling comprehensive characterization of circulating pathogens, we can deeply understand them, rapidly respond with countermeasures, and ultimately save lives. It helps move public health officials from a reactive to more proactive position."

Beginning in 2021, a rise in reported outbreaks in hospitals and nursing homes of the dangerous fungus ?Candida auris called for quick genomic surveillance activation to identify where infections were occurring. In an article featured on Illumina.com, Andrew Gorzalski, PhD, Nevada State Health Lab molecular supervisor, commented on how the more robust sequencing infrastructure his lab established to monitor COVID-19 bolstered its readiness to respond to subsequent threats.

"We're getting sequencing results out faster than we're getting susceptibility results back from our regional laboratory, so that allows us to identify those infections that are genotypically drug resistant, and then pass that information along to epidemiologists," he said.

C. auris is just one of many multidrug-resistant, health-care-associated infections that American health systems are monitoring through genomics. The Enhanced Detection System for Healthcare-Associated Transmission, established by infectious disease experts at the University of Pittsburgh School of Medicine and funded by the National Institute of Health, combines routine genomic surveillance of bacterial pathogens with machine learning and data mining of electronic medical records to identify outbreaks not detected by traditional methods.

Expanding access to genomic technology globally

As Illumina celebrates its 25th anniversary in 2023, its mission of unlocking the power of the genome includes expanding access to genomic capabilities, to ensure their benefits are available to all.

The pandemic spurred an expansion of next-generation sequencing infrastructure in countries and regions that previously had little or no access to it.

In Africa, several programs, including the Pathogen Genomics Initiative, have rapidly expanded capacity and knowledge. Africa CDC has set the target for all 55 African Union member countries to establish next-generation sequencing capacity and pathogen genomics capabilities within the next two years. This will enable countries to better manage their own unique infectious disease threats, rather than having to ship samples to Europe or the US, which leads to prolonged response times.

In Central and South America, over 30 nations and territories now actively participate in the COVID-19 Genomics Surveillance Regional Network (COVIGEN). This represents a vital expansion of sequencing capacity in the region since the network's establishment in early 2020. Pan American Health Organization member states committed in 2022 to expanding pathogen genomics capacity in the region over the next five years.

"Maintaining focus on the importance of preparedness and response is critical," said Moeder. "We are committed to remaining at the forefront of leveraging genomics against infectious disease and partnering worldwide to share expertise to ensure that these capabilities are available everywhere, so that pathogens have nowhere to hide."

About Illumina

Illumina is improving human health by unlocking the power of the genome. In 2023 we celebrate 25 years of innovation, which has established us as a global leader in DNA sequencing and array-based technologies, serving customers in the research, clinical, and applied markets. Our products are used for applications in the life sciences, oncology, reproductive health, agriculture, and other emerging segments.