National Genomic Surveillance Dashboard

A new virus variant of SARS-CoV-2 has one or more mutations that differentiate it from predominant variants already circulating among the general population. As the pandemic progresses and new variants of SARS-CoV-2 have emerged, it is critical for the United States and other countries to sequence and analyze virus samples. This sequence data will provide us with real-time information about the genetic diversity, spread, and evolution of the virus to assess the impact on current efforts to control the pandemic, including vaccines. Laboratories in the United States and across the world have generated hundreds of thousands of viral genetic sequences from SARS-CoV-2 positive patient specimens. Through ongoing variant surveillance, CDC can improve our public health response to COVID-19. Since late 2020, CDC’s sequencing efforts have increased; even so, considerable gaps exist. CDC is enhancing these efforts by collaborating with state and local public health laboratories and partners, such as the Association of Public Health Laboratoriesexternal icon, to increase the number of specimens that are sequenced as part of the National SARS-CoV-2 Strain Surveillance (NS3) program. CDC is also increasing sequencing capacity through contracts with commercial diagnostic laboratories.

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• SARS-CoV-2 Variants Surveillance
• SARS-CoV-2 Variants
• How CDC is responding to SARS-CoV-2 variants globally

Starting in November 2020, state health departments and other public health agencies began sending SARS-CoV-2 specimens to CDC for sequencing and further characterization as part of NS3. This system was scaled up to process 750 requested specimens from states and jurisdictions per week beginning January 25, 2021. CDC has also contracted with commercial diagnostic laboratories and obtained commitments to sequence an additional 6,000 samples per week, with plans for further expansion. The SARS-CoV-2 genetic sequence data obtained from these sources, as well as the sequence data generated by state and local public health laboratories and academic partners, inform public health decision-making and is available to scientists globally via publicly accessible databases maintained by the National Center for Biotechnology Information (NCBI) and GISAID.

As laboratories scale up sequencing capacity, CDC is meeting this need by improving our infrastructure and workflow to ensure efficient sequence data submission to public repositories. Next generation sequencing is a multi-step process that involves both laboratory and bioinformatic workflows. The time from sample receipt at CDC to assembled sequence ready for submission into public databases is approximately 10 days. A similar timeline often applies to state, local, academic, and commercial partners. These collaborative sequencing efforts will provide a real-time understanding of what SARS-CoV-2 variants exist in the US.