AMP Publishes Joint Consensus Report on SARS-CoV-2 Genomic Surveillance for Hospitals and Public Health Laboratories

ROCKVILLE, MD — November 13, 2024 — The Association for Molecular Pathology (AMP), the premier global molecular diagnostic professional society, today 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, “Considerations for Severe Acute Respiratory Syndrome Coronavirus 2 Genomic Surveillance: A Joint Consensus Recommendation of the Association for Molecular Pathology and Association of Public Health Laboratories,” was released online ahead of publication in The Journal of Molecular Diagnostics.

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:

1. 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.
2. A proposed cycle threshold value for viral abundance could help laboratories assess sample quality and potentially improve early variant detection.
3. 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,” said 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 preanalytical, analytical, and postanalytical considerations to help improve critical NGS-based surveillance programs.”

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

To read the full manuscript, please visit https://doi.org/10.1016/j.jmoldx.2024.09.005.