MedCity Influencers, Diagnostics

The power of Next Generation Sequencing in management of the pandemic and future outbreaks

The Covid-19 pandemic has brought a laser focus to the critical and immediate need for next-generation sequencing tools that can generate invaluable data for not only identifying emerging variants but for understanding the functional and epidemiological consequences of variant-specific mutations.

The Human Genome Project began over thirty years ago, taking more than thirteen years and 2.7 billion dollars to complete. Much of that hefty price tag came in the form of a genomics-inspired revolution in research and medicine. Today, sequencing technology itself has also been revolutionized, allowing for the simultaneous sequencing of an entire human genome in one day.

NGS technologies have been around since the early 2000s and have reached the point where they can cost-effectively and rapidly generate millions of data points simultaneously. However, primary applications for NGS have been mostly limited to research, applied sciences, and in public health, laboratories to characterize outbreaks of foodborne pathogens.

Along with the Covid-19 pandemic has come an increased awareness of the power and utility of NGS as the driving force behind genomic epidemiology and as a critical tool for combatting a global biothreat. Genomic advances achieved as part of this increased awareness will serve us as we seek to address current challenges and plan for prevention of and response to future pandemics.

Whole genome sequencing plays a critical role in the pandemic.

The ability to capture critical information about the genome is the methodology that helped identify SARS-CoV-2 as the pathogen responsible for Covid-19. And as a result, researchers were able to study and characterize the molecules of the pathogen to determine not only that SARS-CoV-2 was present but to evaluate how the virus affected human health in a particular environment and track its genetic sequencing as the virus spread and mutated. This is especially important for a rapidly mutating and transmissible virus, like SARS-CoV-2. The Delta variant, which is causing all the infections in the United States is two times more transmissible than the version of the virus that surfaced in Wuhan, China. And now we have Omicron, which is proving to be even more contagious than Delta.

The importance of genome sequencing in the battle against Covid-19 didn’t stop with disease identification; NGS technologies that allow rapid sequencing of millions of base pairs of RNA provided the precise genome sequence that led to the development of nucleic acid diagnostic tests and an mRNA vaccine. As the virus spreads and mutates, WGS continues to be the go-to method of tracking outbreaks, transmissions, and monitoring variants.

Continued sequencing is essential for better management of the virus.

The Covid-19 pandemic has brought a laser focus to the critical and immediate need for next-generation sequencing tools that can generate invaluable data for not only identifying emerging variants but for understanding the functional and epidemiological consequences of variant-specific mutations. SARS-CoV-2 has been nothing, if not unpredictable. The continued emergence and spread of new variants reinforce the critical role that genomic sequencing plays in the enhanced surveillance of Covid-19. To keep up with an ever-evolving virus, we need to employ rapid and reliable genomic surveillance tools equal to the task.

Thanks to the cloud, connectivity and advances in high-throughput, next-generation sequencing, scientists worldwide can observe this virus evolve, literally in real-time, as mutations weaken the virus, or in the case of Delta, strengthen the virus and speed up its spread.

With the impact of Covid-19, strong interest in the widespread adoption of NGS technologies is gaining momentum, including in clinical laboratories. The best platforms will feature turnkey automation, with little to no human intervention required. Results will be available in hours instead of days. Rapid workflow solutions will be end-to-end, with options for sourcing reagent kits and consumables in times of global supply limitations.

The future of sequencing impacts the future of pandemics

After a brutal summer with peaks of 2,000 people dying a day, we had a brief lull before the emergence of Omicron. It appears to evade vaccines though may cause mild disease compared with Delta.

Even when Covid-19 is behind us and we don’t know when, the reality is that this pandemic will not be the last. This is especially true as we enter flu season and anticipate many hidden pathogens to re-emerge. So we must invest appropriately in sequencing efforts so that labs, clinicians, and global health officials can better track, understand and mitigate current and future pathogens.

Continued surveillance is critical for the ongoing understanding of SARS-CoV-2 and its mutations. Any change in the caseload of Covid-19 only further validates the need for continued testing so the world can keep up with the pandemic and future variants.

Covid-19 isn’t going to disappear anytime soon. Scientists predict it will continue to circulate for years to come. While the vaccine can transform Covid-19 from a global threat into a manageable disease (like the flu or common cold), it is vital to stay ahead of it by continuing through surveillance and sequencing to conduct the most critical epidemiological analysis in the most timely manner possible.

Photo: santima.studio, Getty Images

Ramin leads the vision and strategy for teams of dedicated scientists across five divisions at Clear Labs. He brings extensive experience from the industry, government and academia. Previously, he was CEO of Dapco, a Biotech R&D company and served as Sr Advisor to the Ministry of Health. Ramin was Associate Professor and Chair of Food Science at SBMU. He has published over 80 papers in peer-reviewed journals.

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