COVID-19 genomic surveillance

The COVID-19 pandemic has triggered the largest ever global expansion of genomic surveillance capacity and demonstrated the powerful potential of next-generation sequencing (NGS) technologies to transform disease surveillance and public health readiness for epidemics and pandemics.

However, this expansion has exposed existing inequities in disease surveillance systems marked by the uneven distribution and gaps in diagnostic testing and genome sequencing capacities in low- and middle-income countries (LMICS). Given the critical role of NGS technologies in rapid identification and monitoring of emerging viral variants to inform the global pandemic response, we present the SARS-CoV-2 Genomic Surveillance Capacity Map to offer a comprehensive understanding of the SARS-CoV-2 diagnostic and sequencing landscape and support the ongoing efforts of the global health community to strengthen genomic surveillance worldwide.

The dashboard describes the systematic approach used for mapping the global diagnostic testing and SARS-CoV-2 genomic surveillance landscape, including:

• The rationale for the metrics selected to understand existing capacity
• The methodology for establishing data-driven targets for these metrics
• The classification framework to group countries into distinct archetypes
• The archetype-specific recommendations for improving genomic surveillance capacity

In addition, the dashboard enables visualization of changes in volumes COVID-19 diagnostic testing and SARS-CoV-2 sequencing through the course of the pandemic and a summary of investments in genomics surveillance strengthening across LMICs from member organizations of the ACT-Accelerator diagnostics pillar.

We envision this dashboard and recommendations as important tools to help visualize information on SARS-CoV-2 sequencing and COVID-19 diagnostic surveillance. These tools can also catalyze potential partnerships and opportunities for NGS scale-up, and coordinate investments to support the design of country-focused action plans to operationalize and expand SARS‑CoV‑2 genomic surveillance. We plan for future versions of the dashboard to incorporate new data and metrics, such as facilities where sequencing was performed, sampling representativeness amongst reported cases, and ongoing usage of NGS in countries at sub-national levels. We encourage all users to share data to refine country‑specific information on COVID-19 diagnostics, NGS, and SARS-CoV-2 genomic surveillance. Feedback can be provided here.

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