Summary: The AMP published a consensus report on best practices for SARS-CoV-2 genomic surveillance using next-generation sequencing (NGS), providing critical guidelines to enhance data accuracy and public health outcomes.

Takeaways:

  1. Standardization Enhances Data Accuracy: AMP’s report emphasizes standardizing NGS practices to improve data consistency across clinical and public health labs, facilitating a unified pandemic response.
  2. Improving Sample Quality: A recommended cycle threshold for viral abundance could help labs assess sample quality, aiding early variant detection and improving surveillance effectiveness.
  3. Stronger Surveillance Networks: AMP suggests a more integrated network between clinical diagnostic and public health labs to boost localized virus tracking and support timely public health interventions.

The Association for Molecular Pathology (AMP), the premier global molecular diagnostic professional society, has published a joint consensus report that reviews and summarizes standard concepts and best practices for next-generation sequencing (NGS) methods for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic surveillance. 

The manuscript was released online ahead of publication in The Journal of Molecular Diagnostics.

AMP and APHL Collaboration

AMP convened a SARS-CoV-2 Whole Genome Sequencing Working Group with organizational representation from the Association of Public Health Laboratories (APHL) to identify and describe current best practices for general NGS processes, limitations, variability, and potential impacts on sequencing data and turnaround times. 

The working group’s assessment was based on a directed review of the available scientific literature and the expertise and professional experience of the multidisciplinary subject matter experts. 

Key considerations included:

  • Greater standardization of NGS processes across clinical and public health laboratories could help improve data accuracy, facilitate comparison, and support a more unified global response to pandemics.
  • A proposed cycle threshold value for viral abundance could help laboratories assess sample quality and potentially improve early variant detection.
  • A more integrated surveillance network between community-based clinical diagnostic labs and public health labs could help improve public health outcomes by accelerating the ability to localize and personalize virus-tracking efforts.

“In response to the COVID-19 pandemic, NGS testing has advanced to be the recognized gold standard technology for genomic surveillance,” says Donna M. Wolk, PhD, division chief of microbial diagnostics and development at Geisinger. “The ability to monitor genetic changes in SARS-CoV-2 and other pathogens ultimately depends on the collaboration between public health and clinical laboratories. This report offers key pre-analytical, analytical and post-analytical considerations to help improve critical NGS-based surveillance programs.”

AMP plans to update these considerations as new data and reference materials become available.


Further reading