Date of Award

1-1-2019

Document Type

Open Access Thesis

Degree Name

Master of Public Health (MPH)

Department

School of Public Health

First Advisor

Melinda Pettigrew

Second Advisor

Ellen Foxman

Abstract

INTRODUCTION: In 2015 lower respiratory infections (LRI) were the fifth leading cause of

death and the leading cause of death for children under five years old. Despite increasing advances in viral detection technology, etiology is never established for a large portion of viral respiratory infections. The most recent of such advancements- next-generation sequencing (NGS)- has greatly improved the ability to discover and/or identify rare or novel viruses. However, NGS platforms are still not feasible in a clinical laboratory due to cost, complexity, personnel, etc. The ability to screen for unknown viruses using technology that is already present in most clinical laboratories would offer an efficient, cost-effective way to determine which samples may benefit from further testing with NGS.

OBJECTIVES: Establish a methodology for general screening of clinical respiratory samples for unknown or unidentified viruses.

METHODS: Clinical nasopharyngeal swabs collected in January 2017 were examined based on the results of the hospital’s virus PCR panel; samples testing negative for all viruses on the panel were screened for the inflammatory host biomarker for viral infection CXCL10 using an ELISA. CXCL10-positive samples were tested for viruses not included on the panel to ensure the presence of a “true unknown” virus. Potential NGS approaches were concurrently investigated using rhinovirus-positive samples from the same population.

RESULTS: Out of 251 patients with negative viral results from the clinical laboratory, 60 were found to express a high level of CXCL10 in their sample, indicating a likely viral infection. Twenty-eight of these were found to contain coronaviruses, and the remaining 32 were declared “unknown.” These unknown samples will undergo further testing through a variety of techniques to determine the identity of any virus present in the sample.

CONCLUSION: Protein host biomarker CXCL10 is produced in human respiratory epithelial cells in the presence of viral infection. Screening of respiratory samples for CXCL10 provides a pan-viral test that does not require knowledge of a specific pathogen; this study demonstrated a feasible workflow that could be used to screen large numbers of clinical respiratory samples for the presence of unknown viruses using technology that is already widely used in clinical laboratories. This screening assay could serve as a low-cost way to identify samples containing viral pathogens that otherwise would not be detected; such samples could then be sequenced to identify the infectious agent.

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