by Sarah E. Glass

A higher viral load of SARS-CoV-2 in plasma is associated with increased COVID-19 disease severity. How viral load affects the expression of host (immune response) genes in the upper airway, however, has not been probed in the context of early symptomatic disease.  

Suman Das, PhD, and colleagues conducted metatranscriptomic (gene expression) analysis of nasopharyngeal swab samples collected from an overall young population diagnosed with COVID-19 within 24 hours of sample collection, allowing for early timepoint assessment. 

The researchers found that high viral load was associated with the upregulation of adaptive immune system, interferon signaling and chemokine signaling genes. Their method detected SARS-CoV-2 in almost all samples with high genome coverage, with few individuals having any other common respiratory viruses, highlighting the effectiveness of public health measures like masking.  

This study, published in the Journal of Virology, provides important insights into how SARS-CoV-2 viral load can affect upper airway mucosal gene expression at an early timepoint, which could impact disease progression.

Co-authors of the paper were Seesandra Rajagopala, PhD, Britton Strickland, Suman Pakala, Kyle Kimura, MD, Meghan Shilts, Christian Rosas-Salazar, MD, MPH, Hunter Brown, Michael Freeman, PhD, Bronson Wessinger, MD, Veerain Gupta, MD, Elizabeth Phillips, MD, Simon Mallal, MBBS, and Justin Turner, MD, PhD.

This work was supported in part by the Centers for Disease Control and Prevention, National Institutes of Health grants AI142321, AI142321, AI154016, AI149262, HL148638, and HL146401, and the Vanderbilt Technologies for Advanced Genomics Core.