Clinical diagnostic laboratory professionals who perform and interpret next-generation sequencing (NGS) testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) will be interested in a new report from the Association for Molecular Pathology (AMP).
AMP has published a joint consensus document offering key pre-analytical, analytical, and post-analytical considerations to help improve NGS-based surveillance programs.
"Many questions remain unanswered when NGS methods are implemented in laboratories for infectious disease testing," wrote the authors of the special article available online November 14 in the Journal of Molecular Diagnostics.
In the report, Julie Hirschhorn, PhD, from the SARS-CoV-2 Whole Genome Sequencing Working Group of the AMP, Donna Wolk, PhD, division chief of molecular and microbial diagnostics and development at Geisinger in Danville, PA, and others, noted that the information is important as NGS methods are helping to document the prevalence of viral strains from different locations and demographics.
"This review is not meant to be comprehensive, but rather to address some of the infrastructure and planning needed to execute NGS, different NGS workflows, and how these different workflows can impact the turnaround time of results, which are important considerations for a surveillance program," wrote Hirschhorn and colleagues.
Further, AMP suggested the following:
- 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.
"Regardless of specimen source, one of the most critical requirements for successful sequencing is high-quality nucleic acid input material," Hirschhorn and colleagues noted. "To date, there are no quantitative viral load assays for SARS-CoV-2, standardized CT, or relative light unit value cutoffs, or standard SARS-CoV-2 gene target(s) for molecular methods."
Moreover, "nonmolecular tests, such as antigen tests or viral cultures, do not provide semiquantitative information that can be used to determine the samples that can be sequenced," the authors wrote. "In these cases, real-time PCR can be used as a screening test to identify specimens with a sufficiently high viral load before NGS."
Some public health and commercial laboratories are contributing to the National SARS-CoV-2 Strain Surveillance program in the U.S. as Omicron lineages continue to evolve since the virus emerged five years ago, according to the Centers for Disease Control and Prevention (CDC) in a SARS-CoV-2 update. Data from national surveillance helped guide the selection of XBB.1.5 and JN.1 lineages as the target antigens for 2023–2024 and 2024–2025 COVID-19 vaccines, respectively.
However, SARS-CoV-2 genomic results are only part of the surveillance picture, according to experts. Read AMP's SARS-CoV-2 NGS consensus report here.
