As the response to SARS-CoV-2 pandemic has evolved, next generation sequencing efforts have been scaled up to support the public health response to COVID-19. There are currently multiple effort​s ongoing in public and private sectors to sequence SARS-CoV-2 genomes. In support of this effort, APHL has compiled a number of resources for use by public health laboratories.

Wet Lab Protocols​​​​

​Below is a compilation of publicly available protocols and resources:

​Genome Submissions to Public Repositories

The APHL SARS-CoV-2 Sequencing Recommendations​ aim to provide standardization and improve data utility across public health laboratories by outlining key recommendations related to:

  • Data quality and sharing parameters
  • Minimum metadata requirements
  • Frequency of data reporting to public repositories
  • Troubleshooting sequences rejected from public repositories

Below are publicly available protocols to assist with uploading data to public access repositories.


Below are bioinformatics resources, including workflows developed on commercial platforms such as CLCbio:

NextStrain provides data visualization builds for each state using publicly available datasets. To view state specific builds, please visit the SPHERES NextStrain page.​

Example reports summarizing genomic surveillance data for jurisdications are provided below:

​​Training Resources​

Northeast Region SARS-CoV-2 Training
Training covering sequencing methods for SARS-CoV-2, Linux, and data visualization and sharing with public databases.

May 2020 Demystifying Webinar Series-SARS-CoV-2 Resources
Webinar discussing the multitude of resources available for SARS-CoV-2 sequencing and data sharing with an emphasis on resources most applicable to state PHLs.

COVID-19 Genomic Epidemiology Toolkit
From the Office of Advanced Molecular Detection (AMD), this toolkit addresses topics related to the application of genomics to epidemiological investigations and public health responses to SARS-CoV-2.

Nextstrain Tutorials-SARS-CoV-2
This documentation covers topics related to SARS-COV-2 and Nextstrain​ including preparing your data, running and customizing your analysis and data visualization and sharing.

QMS Tools and Resources
CDC and APHL adopted the CLSI 12 QSEs as building blocks for developing a QMS for clinical and public health laboratories performing NGS-based tests. 


The National SARS-CoV-2 Strain Surveillance (NS3)​ program was established to provide baseline surveillance information as well as information on currently circulating variants of concern. Guidance documents, FAQs and program contact information can be found on our NS3​ webpage.