Publications
B22. NEW FRONTIERS IN ENVIRONMENTAL AND OCCUPATIONAL LUNG DISEASE RESEARCHMay 2024 DOI:
10.1164/ajrccm-conference.2024.209.1_MeetingAbstracts.A3090

Virome Sequencing to Characterize Exposure to Respiratory Pathogens in Inner City Schools

Sun, Y.; Javornik Cregeen, S.J.; Allen, J.G.; Greninger, A.L.; Petrosino, J.; Phipatanakul, W.; Lai, P.S.
Product Used
Genes
Abstract
Rationale - The detection of respiratory viruses in children peaks after the school year starts. Schools have been identified as a major course of pandemic outbreaks such as SARS-CoV-2, but little is known about the diversity of exposure to respiratory viral pathogens in classrooms. Methods - Vacuumed dust samples were collected between 2015-2020 from eight different elementary school classrooms in four different schools in the Northeastern United States. Nucleic acid extraction was performed using the Maxwell HT Viral TNA Kit (Promega) on the Kingfisher Flex platform. We performed cDNA synthesis, libraries were constructed, and overnight hybridization-based capture enrichment for respiratory viral nucleic acids performed using the Respiratory Virus Research Panel (Twist Bioscience) prior to sequencing on the Illumina NovaSeq platform. After QC and removal of host reads, VirMAP was used for viral genome reconstruction and reference mapping. Result - From a median 1.13 million total high-quality viral reads per sample, we detected 25 distinct human respiratory virus strains. Respiratory viral genomes were recovered from all classroom samples with a median 10 [interquartile range 9 - 13] different viral strains detected per classroom. There were drastic differences in classroom respiratory virus composition in dust samples collected on the same day from different classrooms in same school (Figure 1). Both DNA and RNA viruses were detected in classroom samples, including viruses that typically cause mild upper respiratory symptoms such as rhinovirus as well as viruses that can cause more severe disease such as human adenovirus, respiratory syncytial virus, and influenza (including H1N1 influenza). Conclusions - Our study demonstrates that metagenomics sequencing targeted towards respiratory pathogens is possible on built environment samples using hybrid capture to enrich for viral nucleic acids; this approach may be used for surveillance monitoring of circulating respiratory viruses in schools. More research is needed to identify effective interventions to reduce student and teacher exposure to respiratory viral pathogens in schools.
Product Used
Genes

Related Publications