Through the course of the COVID-19 pandemic, genomic surveillance of variants of concern has become a critical tool in managing public health. Identification of variants as they emerge and spread across geographic regions can help inform policy and public health decisions, as well as solutions such as vaccine development. But the process of collecting and sequencing samples is not yet universally available across all regions or for all pathogens, which have the potential to seed the next pandemic.
In March 2022, the World Health Organization released its strategy to “strengthen and scale genomic surveillance around the world” and acknowledged that “improving global disease surveillance means improving local disease surveillance.” Experience learned from the pandemic can be leveraged strategically to help establish uniform genomic surveillance programs for multiple pathogens — such as influenza, monkeypox and respiratory syncytial virus — economically and efficiently.
Aggregation of genomic samples
Collaborative networks within the healthcare system can serve to expand the reach of genomic surveillance to regions that may not have the infrastructure, technology, financial resources or workforce to implement it. A centralized sequencing facility can offer enough capacity to serve a number of organizations and hospital systems that can uniformly collect samples for diagnostic and epidemiological surveillance programs. This allows for the aggregation of genomic samples from a broad geographic area, which is key to scaling the process economically and being able to identify potential pandemic outbreaks in real time, even if they occur in less densely populated areas.
Optimization of workflow process
Optimization of a high-throughput genome sequencing process can significantly decrease the cost and time to test, while increasing scalability and performance. For example, the Pandemic Response Lab — New York City’s primary SARS-CoV-2 testing partner and provider of 37% of SARS-CoV-2 surveillance sequencing for the state of New York as of September 2022 — developed a robust strategy to optimize its process for efficiency and speed, including implementing laboratory methods that reduce the time for sequencing library preparation from a full work-day to under an hour. These optimizations ultimately allow daily processing and sequencing of samples at a rate of up to 15,000 per week with a small laboratory footprint.
PRL’s unique process to maximize genomic surveillance capabilities may prove insightful for others as the nation works toward uniform genomic surveillance programs. PRL has optimized the logistics of sample handling to maintain the integrity of viral genomic RNA before it enters the sequencing pipeline. PRL has also optimized the reaction mixture and primer set to amplify RNA and convert it to DNA, providing even coverage of the genome and accounting for mutations that have evolved in the virus over the course of the pandemic. Finally, the process of sequencing library preparation and barcoding was also optimized to allow economical use of reaction mixture, rapid processing and optimal coverage of all samples in the sequencing run.
Securing the necessary funding
While PRL and other public and private sequencing labs have made great strides in developing increased capacity for viral genome sequencing, the vision of geographically widespread genomic surveillance across all pathogens that could cause the next pandemic is not yet established. One of the largest barriers is the lack of a centralized push for sources of funding, particularly federal funding to incentivize the private sector to build the infrastructure, develop a skilled workforce, and innovate and commercialize the necessary technology efficiently at scale.
To secure the necessary funding, what will be required is a shift in political will and policy, as well as alleviation of public concerns over the perceived infringement of people’s privacy. Education campaigns will be imperative to secure public buy-in to implement these programs. Campaigns must educate people on what information is gathered — for example, sequencing facilities testing for infectious diseases such as SARS-CoV-2 sequence only viral genetic information, not the patient’s — and how this information is used.
Increasing equitable access
One of the most efficient ways to gather epidemiologic information across populations and ensure equal representation — even among those who are hesitant or are unable to get tested — is through wastewater collection. Targeting wastewater allows pathogen surveillance without linking data to individuals. In the future, wastewater sequencing and other public sources of information on circulating strains will prove invaluable to establishing comprehensive genome surveillance of pathogens.
Leveraging pipeline capabilities
The pandemic highlighted the need for innovative diagnostic solutions, such as rapid, low-cost tests based on multiplexed polymerase chain reaction technology. Coupling multiplexed diagnostics to a generalized, streamlined and automated sequencing pipeline can allow genomic surveillance of a multitude of pathogens with minor adaptations to the existing workflow. This universal surveillance is vital, as no one knows which pathogen might cause the next pandemic.
While a uniform, widespread genome surveillance program is not yet in place, the most important message to communicate to the government, the private sector, academia, public health officials and the public is that despite the price tag of genomic surveillance, preventing a pandemic will always be less expensive than fighting one.
For more information, visit the Pandemic Response Lab website.
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Pandemic Response Lab launched in 2020 in response to the COVID-19 pandemic to make rapid, accurate and low-cost testing equitably accessible. By applying our revolutionary PCR testing and surveillance-based whole genome sequencing methodology beyond COVID-19, we're expanding access to infectious disease testing to better inform disease management and health outcomes.