# High-content optical pooled genome-wide screens of SARS-CoV-2 infection

> **NIH NIH R01** · BROAD INSTITUTE, INC. · 2020 · $357,840

## Abstract

PROJECT SUMMARY
Identifying gene function and impact on disease biology are overarching aims of life science research in the post-
genomic era. Functional genomics also underpins our ability to understand the meaning of genetic variation in
human populations. However, crucial gaps remain in the functional genomics tool set that will slow our progress
in applying genomics to unravel disease biology. Currently, efficiently pooled methods for genome-wide
screening require either selection of cells based on growth advantage or physical purification (e.g. by FACS or
for single-cell analysis). Many disease processes are characterized by complex cellular phenotypes including
defects in cell or organelle morphology, subcellular localization of molecular components, or cell motility. Other
key phenotypes of interest may involve transient states (eg mitosis), cell-cell interactions, or require dynamic
assays in live cells (eg, optical recording of electrophysiological activity of cardiac or neural cells). Image-based,
high-content screens using overexpression and RNA interference have uncovered novel genes involved in
complex phenotypes, including mitosis, synaptogenesis, and embryogenesis. However, such microplate-based
screens of clonal cell populations are not regularly conducted at the genomic scale due to the expense, labor,
and automation expertise required. In this program, we developed a new genomic perturbation and screening
concept that combines major advantages of pooled perturbation with imaging assays for single-cell arrayed
readout of complex phenotypes. Specifically, we screen pooled genomic perturbations (with CRISPR-Cas9
single-guide RNAs) using microscopy to read out phenotypes AND to identify perturbed genes at the single-cell
level via in situ sequencing with a sequencing by synthesis approach. This approach is highly scalable because
reagent and instrumentation costs are modest (now a few tens of thousands of dollars for a genome-wide
screen). Here we request an administrative supplement to apply the technology developed in our existing award
to screens for SARS-CoV-2 infection of cell lines with Rob Davey’s group at the Boston University Northeast
Emerging Infectious Disease Laboratory that is equipped and actively working with high-containment viral
pathogens including SARS-CoV-2. This work on antiviral host cell programs is within the scientific scope of the
original grant. We will tightly coordinate the rapid execution of optical pooled screens in multiple biological models
with Dr. Davey’s ongoing conventional CRISPR genomic screening activity. The data-rich genome-wide optical
screening data will identify new aspects of the SARS-CoV-2-host interface across the viral life cycle and advance
our understanding of candidate therapeutics as well as support the generation of new therapeutic hypotheses to
address the COVID-19 pandemic.

## Key facts

- **NIH application ID:** 10166221
- **Project number:** 3R01HG009283-04S1
- **Recipient organization:** BROAD INSTITUTE, INC.
- **Principal Investigator:** Paul Clark Blainey
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $357,840
- **Award type:** 3
- **Project period:** 2017-09-01 → 2022-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10166221

## Citation

> US National Institutes of Health, RePORTER application 10166221, High-content optical pooled genome-wide screens of SARS-CoV-2 infection (3R01HG009283-04S1). Retrieved via AI Analytics 2026-05-28 from https://api.ai-analytics.org/grant/nih/10166221. Licensed CC0.

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