Unlocking the power of NGS for pandemic preparedness and beyond

Dr Somesh Kumar, Country Director, Jhpiego – India, Senior Director, Technical Leadership & Innovations- US highlights that NGS, a powerful tool, unlocks the secrets hidden within a pathogen’s genetic code. It unveils the origins, maps the mutations, and anticipates potential variants, offering a compass through the uncharted territory of viral evolution

Disease surveillance acts as our vigilant guardian, providing us with the intelligence needed to respond with precision during pandemics and customise strategies to the distinctive traits of each outbreak. It serves as the wellspring of vital data, guiding our decision-making and the efficient allocation of resources, thereby bolstering our resilience against the ever-looming specter of public health threats. With the world’s concerted move towards unlocking the untold potential of genomics, our surveillance capabilities take a giant leap forward, offering us the swiftness required to spot emerging diseases on the horizon. This, in turn, grants us the invaluable time needed to deploy robust response measures with agility and effectiveness.

Amid the turbulent waves of the COVID-19 pandemic, the birth of the Indian SARS-CoV-2 Genomic Consortium (INSACOG) marked a transformative milestone. It swiftly expanded its network of Next-Generation Sequencing (NGS) sites across the nation, forming an omnipresent sentinel for scrutinising the genetic essence of the virus during this relentless battle. NGS, a powerful tool, unlocks the secrets hidden within a pathogen’s genetic code. It unveils the origins, maps the mutations, and anticipates potential variants, offering a compass through the uncharted territory of viral evolution.

The episodes of the highly contagious Delta and Omicron variants that unfurled in 2021 and 2022 serve as compelling testaments to NGS’s pivotal role. It played the role of a swift investigator, enabling timely identification and thorough understanding of these rapidly evolving viral strains. This achievement was made possible by the extensive network of INSACOG. In the face of these unpredictable twists in the viral saga, Indian health authorities were equipped with the knowledge needed to adapt public health measures and vaccination strategies, thus charting a more effective course for safeguarding public health.

NGS is a revolutionary technology that has the potential to transform pandemic preparedness and response through its astounding capabilities of detecting the range of pathogens, sequencing the genomes of pathogens, and tracking the spread of pathogens. NGS detects and sequences a wide range of pathogens, including viruses, bacteria, fungi, and parasites, with high accuracy and sensitivity. This information can be used to identify new and emerging pathogens, including Disease X. “Disease X” is a term used to refer to a hypothetical, unknown, or novel disease that could emerge in the future, potentially causing a global pandemic. It’s a placeholder term used by health authorities and experts to highlight the unpredictability of infectious diseases. In essence, Disease X represents the idea that new diseases can appear unexpectedly, with the potential for rapid transmission and severe health impacts. By acknowledging the existence of such an unknown or unexpected disease, the global health community aims to emphasise the importance of preparedness and the need for robust response strategies to address emerging health threats. By sequencing the genomes of pathogens from different patients and locations, NGS can help scientists to identify new pathogens, track their spread, and monitor their evolution. This information can be used to develop and implement effective prevention and control measures, thus guiding the development of diagnostic tests and treatments; track pathogen spread thus facilitating public health interventions such as contact tracing and quarantine; and monitor pathogen evolution thus aiding in the development of new vaccines and treatments.

NGS can also be used to sequence the genomes of pathogens from animals and the environment. This can help to identify new pathogens that may have the potential to spill over from animals to humans or from the environment to humans. One Health is an approach to health that recognises the interconnectedness of human, animal, and environmental health. NGS is a powerful tool for supporting the One Health approach to pandemic preparedness and response by enabling the detection and surveillance of pathogens in both animals and humans.

The emergence/re-emergence of newer pathogens/variants has been associated with the increase in Antimicrobial Resistance (AMR) and Multi-drug Resistant (MDR) pathogens. In India, the National Antimicrobial Resistance Research and Surveillance Network (NARS Net) is using NGS to identify and characterise AMR genes and mutations in pathogens from both human and animal sources, facilitating the tracking of AMR spread, identification of risk factors, and the formulation of strategies for AMR prevention and control.

Beyond its application in pandemic preparedness and response, NGS also has the potential to revolutionise disease detection and surveillance across the spectrum. For example, NGS can be used to identify the causative agents of rare and emerging diseases, detect pathogens in low-abundance clinical specimens, monitor the response of pathogens to treatment, track the spread of antimicrobial resistance, and develop personalised treatment plans for patients with communicable as well as non-communicable diseases.

While NGS is a groundbreaking advancement, several challenges must be addressed before it becomes universally accessible in public health settings. Cost remains a significant barrier, but the decreasing expense of NGS offers hope for wider adoption. Diversifying the use-cases for NGS in public health can potentially also decrease the cost for the manufacturers. Additionally, the need for trained personnel to operate and interpret NGS data underscores the importance of investing in staff training within public health laboratories.

Thus, despite these challenges, NGS is a beacon of hope in the fight against infectious diseases. Its potential to identify and track pathogens, unveil emerging variants, and monitor AMR is unparalleled. INSACOG and NARS Net’s utilisation of NGS in support of a One Health approach exemplifies the crucial role this technology plays in our collective endeavor to prevent and control future pandemics.

As NGS technology continues to evolve and become more accessible, its impact on public health is poised to be profound. NGS has the potential to enable earlier and more accurate diagnosis of infectious diseases, guide the development of more effective treatments, and inform targeted public health interventions, thereby increasing the responsiveness and resilience of our health systems.


data surveillancegenomicNext-Generation Sequencing (NGS)pandemic
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