Newswise — 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 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,” said Donna M. Wolk, Ph.D., 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.
To read the full manuscript, "Considerations for Severe Acute Respiratory Syndrome Coronavirus 2 Genomic Surveillance," visit https://doi.org/10.1016/j.jmoldx.2024.09.005.
ABOUT THE ASSOCIATION FOR MOLECULAR PATHOLOGY
The Association for Molecular Pathology (AMP) was founded in 1995 to provide structure and leadership to the emerging field of molecular diagnostics. AMP’s more than 3,000 members practice in various disciplines of molecular diagnostics, including bioinformatics, infectious diseases, inherited conditions and oncology. Our members are pathologists, clinical laboratory directors, basic and translational scientists, technologists and trainees who work in a variety of settings, including academic and community medical centers, government and industry. Through the efforts of its board of directors, committees, working groups and members, AMP is the primary resource for expertise, education and collaboration in one of the fastest-growing fields in healthcare. AMP members influence policy and regulation on the national and international levels, ultimately serving to advance innovation in the field and protect patient access to high-quality, appropriate testing.
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