Toward a global virus genomic surveillance network

Abstract

The COVID-19 pandemic galvanized the field of virus genomic surveillance, demonstrating its utility for public health. Now, we must harness the momentum that led to increased infrastructure, training, and political will to build a sustainable global genomic surveillance network for other epidemic and endemic viruses. We suggest a generalizable modular sequencing framework wherein users can easily switch between virus targets to maximize cost-effectiveness and maintain readiness for new threats. We also highlight challenges associated with genomic surveillance and when global inequalities persist. We propose solutions to mitigate some of these issues, including training and multilateral partnerships. Exploring alternatives to clinical sequencing can also reduce the cost of surveillance programs. Finally, we discuss how establishing genomic surveillance would aid control programs and potentially provide a warning system for outbreaks, using a global respiratory virus (RSV), an arbovirus (dengue virus), and a regional zoonotic virus (Lassa virus) as examples.

Figure 1

Timeline of public health emergencies since 2000 and associated technological advances White boxes indicate the timing of the start of epidemics, either based on when the spillover was inferred to happen, or when epidemics were reported or declared. Purple boxes indicate technological advancements. Countries are colored based on where the epidemic was first detected.

Figure 2

Global SARS-CoV-2 sequencing effort during the COVID-19 pandemic (A) The number of laboratories worldwide submitting genomes to GISAID, by week and cumulative. (B) The log number of genomes sampled in each country between 2020 and 2022.

Figure 3

Modular amplicon-based virus sequencing framework Steps where swapping of key elements make the framework generalizable to other viruses are highlighted in yellow. Created with BioRender.com.