Swab-Free Transport as an Optimized Preanalytical Workflow for SARS-CoV-2 Molecular Testing

Abstract

The emergence of SARS-CoV-2 (COVID-19) and the global ramp up of molecular diagnostic testing has resulted in an enormous strain on both testing supply and personnel resources. Early into the pandemic, consumables such as swabs, pipette tips, and transport media became challenging to obtain, thereby necessitating changes in test protocols and laboratory workflows. Clinical laboratories and diagnostic companies have stepped up to the challenge by validating alternative transport media and devices, developing alternative types of swab, evaluating unique specimen types and pooling methods, and utilizing nontraditional automation systems to meet the enormous need for testing (1–3). While these efforts have allowed for testing to expand, the methods in place are not always those most optimal for laboratory workflows. In this issue of The Journal of Applied Laboratory Medicine, Lockwood et al. describe the requirement for manual preanalytical specimen processing steps that are typical of many molecular SARSCoV-2 assays with Emergency Use Authorization (EUA) (4). Manual processing requirements demand extreme care to avoid cross-contamination and specimen errors and involve repetitive motions, generally within a restrictive biosafety cabinet. While not individually time consuming ( 1minute per sample), for laboratories performing large-scale testing these manual activities can increase personnel requirements considerably. Lockwood et al. estimate that this extra processing adds 1 FTE per 500 samples tested. If a laboratory is fully utilizing some of the common high-capacity molecular instruments, this could result in up to 3 additional people needed per instrument per day. High-capacity molecular instruments with automated liquid handling systems have decreased hands-on time and streamlined workflows of traditional swab-based molecular assays for pathogens such as Neisseria and Chlamydia. However, manual specimen processing requirements exist for many EUA SARS-CoV-2 assays run on the same test instruments. Depending on specimen type, these requirements include removal of collection swabs from transport media (Abbott m2000, Abbott Alinity m) or aliquot of specimen into a swab-free assay tube (Hologic Panther Fusion, Hologic Aptima, Roche 6800) before placement on the instrument (5). These requirements are included because the presence of a swab, and the size or shape of a transport container may create an obstruction to the automated systems. This interference may result in mechanical damage to the instrument, loss of sample, or inaccurate test results. As an example, the Roche