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

Julie W Hirschhorn; N Esther Babady; Allen Bateman; Heather M Blankenship; Jennifer Dien Bard; Kelsey Florek; Paige M K Larkin; Marie-Claire Rowlinson; Kelly Wroblewski; Donna M Wolk

doi:10.1016/j.jmoldx.2024.09.005

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

J Mol Diagn. 2025 Jan;27(1):12-24. doi: 10.1016/j.jmoldx.2024.09.005. Epub 2024 Oct 21.

Affiliations

¹ The SARS-CoV-2 Whole Genome Sequencing Working Group of the Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina; Diagnostic Medicine Institute, Geisinger, Danville, Pennsylvania; Geisinger Commonwealth School of Medicine, Scranton, Pennsylvania. Electronic address: [email protected].
² The SARS-CoV-2 Whole Genome Sequencing Working Group of the Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
³ The SARS-CoV-2 Whole Genome Sequencing Working Group of the Association for Molecular Pathology, Rockville, Maryland; Wisconsin State Laboratory of Hygiene, Madison, Wisconsin.
⁴ The SARS-CoV-2 Whole Genome Sequencing Working Group of the Association for Molecular Pathology, Rockville, Maryland; Genomics Section, Division of Infectious Disease, Michigan Department of Health and Human Services, Lansing, Michigan.
⁵ The SARS-CoV-2 Whole Genome Sequencing Working Group of the Association for Molecular Pathology, Rockville, Maryland; Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California.
⁶ The SARS-CoV-2 Whole Genome Sequencing Working Group of the Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, NorthShore University HealthSystem, Evanston, Illinois.
⁷ The SARS-CoV-2 Whole Genome Sequencing Working Group of the Association for Molecular Pathology, Rockville, Maryland; Wadsworth Center Bacterial Diseases Laboratory, New York State Department of Health, Albany, New York; Bureau of Public Health Laboratories, Florida Department of Health, Jacksonville, Florida.
⁸ The SARS-CoV-2 Whole Genome Sequencing Working Group of the Association for Molecular Pathology, Rockville, Maryland; Association of Public Health Laboratories, Silver Spring, Maryland.
⁹ The SARS-CoV-2 Whole Genome Sequencing Working Group of the Association for Molecular Pathology, Rockville, Maryland; Diagnostic Medicine Institute, Geisinger, Danville, Pennsylvania; Geisinger Commonwealth School of Medicine, Scranton, Pennsylvania.

PMID: 39442753
PMCID: PMC11702284 (available on 2026-01-01)
DOI: 10.1016/j.jmoldx.2024.09.005

Abstract

Next-generation sequencing (NGS) has applications in research, epidemiology, oncology, and infectious disease diagnostics. Wide variability exists in NGS wet laboratory techniques and dry laboratory analytical considerations. Thus, many questions remain unanswered when NGS methods are implemented in laboratories for infectious disease testing. Although this review is not intended to answer all questions, the most pressing questions from a public health and clinical hospital-based laboratory perspective will be addressed. The authors of this review are laboratory professionals who perform and interpret severe acute respiratory syndrome coronavirus 2 NGS results. Considerations for pre-analytical, analytical, and postanalytical NGS will be explored. This review highlights challenges for molecular laboratory professionals considering adopting or expanding NGS methods.

Publication types

Review

MeSH terms

COVID-19* / diagnosis
COVID-19* / epidemiology
COVID-19* / virology
Consensus
Genome, Viral
Genomics / methods
High-Throughput Nucleotide Sequencing* / methods
Humans
Laboratories
Pathology, Molecular / methods
Public Health / methods
SARS-CoV-2* / genetics
SARS-CoV-2* / isolation & purification