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Innate immunity and viral interference

Technological advances offer new opportunities to detect and understand respiratory infections in vivo using patient samples and data together with primary cell organoid models and new modalities for characterizing samples, including transcriptomics and proteomics.
Influenza infection in differentiated human airway epithelial cell cultures (green cells=influenza infected), without (left) or with (right) prior exposure in rhinovirus.

Through a combination of clinical data analysis of electronic medical record data coupled with experiments using primary cell organoids, we explored the idea that infection with the common cold virus, human rhinovirus, may protect against influenza, inspired by the observation that rhinovirus season appeared to delay the 2009 swine flu pandemic in Europe, and by the staggered timing of the annual seasonal rhinovirus and influenza virus epidemics. We found evidence that prior infection with rhinovirus can transiently protect against influenza virus by jump-starting antiviral defenses within virus target cells in the airway epithelium.

More recently, we showed that though a similar mechanism, rhinovirus blocks the replication of SARS-CoV-2

In collaboration with the Yale Clinical Virology Laboratory, showed that biomarkers of the antiviral response detected using respiratory swabs can serve as a pan-viral diagnostic test, accurately identifying patients with diverse respiratory virus infections.

SARS-CoV-2 viral RNA 24,48, and 72 hr post-infection in organoid cultures with (blue) or without (black) prior exposure to rhinovirus infection (Cheemarla et al, JEM, 2021).