Host Response to Respiratory Infections

In this study, we describe a strategy to identify undiagnosed respiratory viral infections through screening nasopharyngeal (NP) swabs for the chemokine CXCL10, which is highly induced in the nasopharynx as part of the host antiviral response. Using this strategy, we conducted two screens: first, we screened NP swabs collected at Yale New Haven Hospital (YNHH) in January 2017 from patients with undiagnosed respiratory viral infections and identified patients infected with seasonal coronaviruses and the relatively uncommon influenza C virus. Second, we screened samples from the beginning of March 2020 in the weeks before YNHH tested for SARS-CoV-2 and identified four patients that had undiagnosed SARS-CoV-2 infections. Sequences uploaded as part of this study include samples with rhinovirus, human coronavirus NL63, and 8 samples as part of the January 2017 screen for undiagnosed respiratory viral infections.]]> Patient samples included in this RNA-sequencing analysis are split into the following groups: Rhinovirus (both rhinovirus A and C) Human coronavirus NL63 Unknown (suspected viral infection) Samples in the unknown group were previously determined to be negative for viruses tested at YNHH in 2017 which includes the following tests: adenovirus, human metapneumovirus, influenza A and B, parainfluenza 1-3, RSV A and B, and rhinovirus. The 8 unknown samples included in this analysis were positive for the CXCL10 screen which suggested an undiagnosed viral infection.]]>