From COVID-19 to future threats: building a global genomic surveillance network

By Tarun Sai LomteJun 16 2023Reviewed by Lily Ramsey, LLM

A recent study published in the Cell Host and Microbe Journal presented a modular framework for global sustainable networks of viral genomic surveillance.

Study: Toward a global virus genomic surveillance network. Image Credit: PopTika/Shutterstock.com

Background

Virus genetic diversity and evolution can impact control efforts and dynamics of an outbreak. Monitoring evolutionary processes can provide more answers than conventional epidemiology.

Genomic data have been instrumental in developing diagnostic assays, therapeutics, and vaccines and can improve disease forecasting models.

Therefore, viral genomic sequencing can help better formulate and evaluate strategies to prevent disease and transmission. The authors discussed viral genomic sequencing and surveillance efforts in the present study and presented a modular framework for global virus genomic surveillance networks.

Genomic sequencing and surveillance

Viral genomic surveillance has transitioned from retrospective to near real-time assessments over the past two decades. Real-time analyses offer actionable results for interventions. This shift to real-time analyses was made possible due to methodological advances, computational technology, and the demand for faster results.

The response to the ongoing human immunodeficiency virus (HIV) pandemic led to many methodological advances in viral genomic surveillance and infrastructure.

The first epidemic of the present century was recorded in rural China in 2002, caused by a novel coronavirus named severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1).

The first sequences of this virus were available in April 2003. Next-generation sequencing was unavailable then; thus, rapid sequencing was not possible.

However, technological advances enabled rapid sequencing six years later, in 2009, during the H1N1 influenza A pandemic, and genomic studies uncovered its animal origins while the pandemic was still developing.

Systematic genomic surveillance was implemented for influenza, and the World Health Organization (WHO) leverages these data to forecast antigen evolution and improve the selection of vaccine strains. The Ebola virus disease (EVD) epidemic during 2013-16 in West Africa represented a watershed moment for near real-time surveillance of viral genomes.

Around 5% of the cases were sequenced during the epidemic, constituting the largest dataset until the pandemic of coronavirus disease 2019 (COVID-19). Sequencing efforts have been unprecedented and monumental during COVID-19.

Twenty-five additional countries provided sequence data within two months after China released the first SARS-CoV-2 sequence in January 2020.

Many countries, especially in the Caribbean and Africa, leveraged this urgency and built or improved sequencing capacity. Substantial funding enabled the African Centers for Disease Control and Prevention (CDC) to support or establish sequencing hubs.

By April 2020, 20 African countries had SARS-CoV-2 sequencing capacity, increasing to 39 by mid-2022. The trend in the Caribbean was also similar.

Sequencing efforts amplified during the surges caused by the SARS-CoV-2 variants. However, as the pandemic control efforts are being scaled down across several regions, fewer countries provide sequence data.

Therefore, global goals should be to maintain the training and financial investment accrued during COVID-19 and invest some of this into rapid response systems for future pandemics.

Modular framework for viral genome sequencing

COVID-19 provides an opportunity to build global surveillance networks for other clinically important viruses by diverting the existing (sequencing) pipelines rather than closing them.

This ensures the maintenance of equipment functionality, database management, supply stocks, access to diagnostic samples, the rationale for funding, and employment of trained personnel.

However, the transition between different sequencing strategies could be difficult, but protocol continuity will be crucial to divert sequencing capacity.

The core components of SARS-CoV-2 sequencing laboratories include access to remnant samples and metadata, sample selection, targeted amplification, library preparation, sequencing, data processing, quality control, and storage and sharing.

These steps could differ for a new virus. For instance, monkeypox virus sequencing involves an untargeted DNA metagenomic approach that requires different protocols and reagents for amplification and library preparation and a distinct bioinformatic pipeline for data processing. 

A simpler solution would require adaptation of the SARS-CoV-2 pipeline for the monkeypox virus with minimal changes in the protocol. The same library preparation kits can be used by swapping out primer sets for amplification.

Consequently, only bioinformatic pipelines would require to be updated. This modular approach enables laboratories to maintain a single base set of dry and wet virus lab protocols.

Concluding remarks

Genomic surveillance remains pivotal for public health response to endemic and epidemic viruses. Years of infrastructure building and technological advances have culminated in a colossal sequencing effort during COVID-19. It is critical to transform this to create strategies for historically neglected and endemic viruses.

Global sustainable genomic surveillance networks could be established using a modular framework. Sequencing viruses from human clinical samples alone might not be informative and efficient.

As such, building new approaches to supplement clinical sequencing by surveilling air, wastewater, and travelers might provide early indications of an outbreak and could be critical when low on resources.