Building a global genome surveillance network

In recent studies, Cell hosts and microorganisms The journal has published a modular framework for a global sustainable network of viral genome surveillance.

study: Towards a global viral genome surveillance network. Image credit: PopTika/Shutterstock.com

Background

Virus genetic diversity and evolution can influence control efforts and dynamics of the spread of infection. Monitoring evolutionary processes may provide more answers than conventional epidemiology.

Genomic data are facilitating the development of diagnostic assays, therapeutics and vaccines, and can improve disease prediction models.

Viral genome sequencing can therefore help to better formulate and evaluate strategies to prevent disease and infection. The authors discussed viral genome sequencing and surveillance efforts in this study and presented a modular framework for a global viral genome surveillance network.

Genome sequencing and surveillance

Over the past two decades, viral genome surveillance has moved from retrospective assessment to near real-time assessment. Real-time analytics provide results that help guide interventions. This shift to real-time analysis has been made possible by methodological advances, computational techniques, and the demand for faster results.

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

The first outbreak of the century was recorded in rural China in 2002 and was caused by a novel coronavirus called severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1).

The first sequences of this virus became available in April 2003. Next-generation sequencing was not available at the time. Therefore, rapid sequencing was not possible.

However, technological advances enabled rapid sequencing six years later during the H1N1 influenza A pandemic in 2009, and genomic studies revealed its animal origin while the pandemic was still underway. became.

There is systematic genomic surveillance of influenza, and the World Health Organization (WHO) uses these data to predict influenza. antigen Improved vaccine strain evolution and selection.of Ebola virus disease The EVD (EVD) epidemic in West Africa from 2013 to 2016 marked a turning point for near real-time surveillance of viral genomes.

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

Within two months of China’s release of the first SARS-CoV-2 sequence in January 2020, 25 additional countries provided sequence data.

Many countries, especially the Caribbean and Africa, have taken advantage of this urgency to build or improve their sequencing capacities. Substantial funding has 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 capabilities, increasing to 39 by mid-2022. A similar trend was observed in the Caribbean.

Sequencing efforts stepped up during the surge caused by the SARS-CoV-2 variant. However, as pandemic control efforts are curtailed in some regions, fewer countries are providing sequence data.

A global goal, therefore, should be to preserve the training and financial investment accumulated during the COVID-19 period, and invest some of it in rapid response systems for future pandemics. .

A modular framework for viral genome sequencing

COVID-19 presents an opportunity to build a global surveillance network against other clinically important viruses by diverting rather than closing existing (sequencing) pipelines.

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

However, transitioning between different sequencing strategies can be challenging, and protocol continuity is critical to repurposing sequencing capacity.

Core components of a SARS-CoV-2 sequencing laboratory include access to residual samples and metadata, sample selection, target amplification, library preparation, sequencing, data processing, quality control, storage and sharing .

For new viruses, these steps may differ.For example, sequencing of monkeypox virus involves a variety of protocols and reagent It has a unique bioinformatics pipeline for amplification and library preparation, and data processing.

A simpler solution involves adapting the SARS-CoV-2 pipeline to monkeypox virus with minimal protocol changes. The same library preparation kit can be used by exchanging the primer set for amplification.

Therefore, only the bioinformatics pipeline needs to be updated. This modular approach allows laboratories to maintain a single base set of dry and wet virus testing protocols.

Conclusion

Genomic surveillance remains critical in the public health response to endemic and epidemic viruses. Years of infrastructure building and technological advances have resulted in large-scale sequencing efforts during the COVID-19 pandemic. Transforming this and developing strategies against endemic viruses that have been historically ignored is critical.

A global sustainable genome surveillance network could potentially be established using a modular framework. Simply sequencing viruses from human clinical samples may not be informative and efficient.

Therefore, building new approaches that complement clinical sequences by monitoring air, wastewater, and travelers may provide early indications of outbreaks, which is of great importance when resources are scarce. may become.