Improving Pandemic Preparedness Through Metagenomics-Based Detection and Genotyping of Respiratory Viruses in Self-Collected, Ambient Temperature-Preserved Nasal Swabs (Preprint)

Abstract

The SARS-CoV-2 pandemic has underscored the need for field specimen collection and transport to diagnostic and public health laboratories.

Self-collected nasal swabs transported without dependency on a cold chain have the potential to remove critical barriers to testing and expand testing capacity and, to reduce opportunities for exposure of health professionals in the context of a pandemic.

We compared nasal swab collection by study participants from themselves and their children at home to collection by trained research staff. Swabs were placed in temperature-stable preservative and respiratory viruses were detected by shotgun RNA sequencing, enabling viral genome analysis.

Study participants reported that self-collection was acceptable. Agreement between identified respiratory viruses in both swabs by sequencing demonstrated adequate collection technique was achieved by brief instructions.

Our results demonstrate the feasibility of scalable and convenient means for identification of respiratory viruses and implementation in pandemic preparedness for influenza virus and other respiratory pathogens.