# Host response-based screening for unexpected or emerging respiratory viruses

> **NIH NIH R21** · YALE UNIVERSITY · 2021 · $209,375

## Abstract

PROJECT SUMMARY
In the past two decades, in addition to the expected annual viral infections, several emerging respiratory
viruses have had a global impact including the SARS coronavirus, the 2009 swine flu, and currently the
emerging 2019 coronavirus (2019-nCoV). The ability to screen for potential emerging viral pathogens would
enable better preparation for such events. Current diagnostic tests for respiratory viruses readily detect known
viruses, but do not detect unexpected viruses. However, prior work shows that many respiratory viruses induce
a common pattern of gene and protein expression in the nasopharynx. This project will measure this host
antiviral response in samples from symptomatic patients which have tested negative for common respiratory
viruses. The central hypothesis of this project is that unexpected or emerging viruses will be found in patient
samples in which a nasal antiviral response is evident, but no known viruses have been detected. The long-
term objective of this work is to define an efficient strategy to identify unexpected or emerging viral respiratory
pathogens, in order to aid in efforts to anticipate and prepare for the spread of illnesses caused by these
viruses.
In the proposed project, we will investigate our central hypothesis by screening samples from symptomatic
patients to look for samples testing negative for known viruses, but positive for a biomarker of the antiviral
response that we defined in previous work. In Aim 1, we will perform a detailed evaluation of these “screen-
positive” samples to look for unexpected or novel viruses using a range of techniques which include next
generation sequencing and advanced bioinformatics analysis, and classic virus discovery techniques such as
viral culture and isolation and electron microscopy. In Aim 2, we will generate reference nasopharyngeal
transcriptomes from patients with known viral infections including coronaviruses, a group which includes
several high-impact emerging viruses but which has not yet been studied in this way. These reference
transcriptomes will serve as a resource for evaluating samples with suspected novel viral infections and will
also inform further refinements of the screening strategy. Together, these aims will advance a promising new
strategy for detecting unrecognized viruses able to cause illness in humans.

## Key facts

- **NIH application ID:** 10109282
- **Project number:** 1R21AI156208-01
- **Recipient organization:** YALE UNIVERSITY
- **Principal Investigator:** Ellen Flescher Foxman
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $209,375
- **Award type:** 1
- **Project period:** 2021-03-15 → 2023-02-28

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10109282

## Citation

> US National Institutes of Health, RePORTER application 10109282, Host response-based screening for unexpected or emerging respiratory viruses (1R21AI156208-01). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10109282. Licensed CC0.

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