# System Biological Analyses of Adaptive Responses to vaccination

> **NIH NIH U19** · EMORY UNIVERSITY · 2020 · $2,300,069

## Abstract

The recent emergence of the novel, pathogenic SARS-coronavirus 2 (SARS-CoV-2) pandemic
poses a major global health challenge. Coronavirus disease (COVID-19) is caused by SARSCoV-2 and represents the causative agent of a potentially fatal disease. Science has moved very
rapidly in isolating, sequencing, and cloning the virus, and developing diagnostic kits, within a
matter of weeks. However, major knowledge gaps remain about the dynamic interaction between
the human immune system and the SARS-CoV-2. In particular, several fundamental questions
regarding its pathogenesis, and the mechanisms of protective immunity that need to be induced
by vaccination, remain unanswered. Learning how the immune system senses SARS-CoV-2
infection and orchestrates protective immunity is critical for designing effective vaccines and
therapeutics. Our previous work using systems biology, multi-omics approaches to analyze
immune responses to vaccination in humans has delineated molecular signatures of innate
immunity to vaccination and infection and have provided rich mechanistic insights into the immune
response1-7
. In this proposal, we propose a site-specific study to analyze samples from the
IMPACC sub-study performed at Emory. We will use an integrated multi-omics approach (single
cell transcriptomics, metabolomics, single cell epigenomics) to study innate immunity to COVID19 infection in humans. We will obtain PBMCs and tracheal aspirate samples from the IMPACC
sub-study that will be conducted at Emory. We will address the following questions: What are the
molecular and cellular signatures of the immune response to COVID-19 infection in the blood and
tracheal aspirates of infected subjects? Does COVID-19 infection exert an epigenetic imprint of
innate immunity? What is the molecular landscape and function of myeloid cell subsets and airway
epithelial cells in the healthy lung, and following COVID-19 infection? These questions will be
addressed in the following specific aims: 1) Determine the single cell transcriptional and
epigenetic landscape of the immune response to COVID-19 infection in blood and tracheal
aspirates, and 2) Determine the molecular identity and functions of myeloid cell subsets and
epithelial cells in human lung and their response to COVID-19 infection. These studies will provide
significant insight into the human immune response to COVID-19 infection that can be leveraged
for designing vaccines and therapeutics to prevent or treat the infection.

## Key facts

- **NIH application ID:** 10201503
- **Project number:** 3U19AI090023-11S1
- **Recipient organization:** EMORY UNIVERSITY
- **Principal Investigator:** Rafi Ahmed
- **Activity code:** U19 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $2,300,069
- **Award type:** 3
- **Project period:** 2020-07-13 → 2022-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10201503

## Citation

> US National Institutes of Health, RePORTER application 10201503, System Biological Analyses of Adaptive Responses to vaccination (3U19AI090023-11S1). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10201503. Licensed CC0.

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