# In situ functional genomics to understand transcriptional regulation

> **NIH NIH DP2** · NEW YORK GENOME CENTER · 2020 · $518,550

## Abstract

PROJECT SUMMARY
 The COVID-19 pandemic has taken the lives of nearly 500,000 people worldwide in the span of a few months.
Recently, a novel isolate of the SARS-CoV-2 virus carrying a point mutation in the Spike protein (D614G) has
emerged and rapidly surpassed others in prevalence, including the original SARS-CoV-2 isolate from Wuhan,
China. This Spike variant is a defining feature of the most prevalent clade (A2a) of SARS-CoV-2 genomes
worldwide and, recently, we and others have demonstrated this variant leads to virions with an ~8-fold increase
in human cell transduction. This is the first experimental evidence of a SARS-CoV-2 population variant acting in
a gain-of-function manner.
 Although there are hundreds of Spike variants now in circulation, we lack tools for high-throughput
characterization of these variants and their virulence. Here, we propose to develop a massively-parallel, high-
throughput approach to test all Spike variants using a pooled forward genetic screen, examine the impact of
these mutations on proteolytic cleavage of Spike and on ACE2 receptor binding kinetics, and validate changes
in viral transduction with live SARS-CoV-2 via an innovative trans-complementation assay.
 Our proposed studies aim to understand the interactions between Spike protein variants and host (human)
cell infection and their underlying biochemical mechanisms. This research will enable us to predict whether
particular Spike variants can drive more serious COVID-19 outbreaks.

## Key facts

- **NIH application ID:** 10199425
- **Project number:** 3DP2HG010099-01S2
- **Recipient organization:** NEW YORK GENOME CENTER
- **Principal Investigator:** Neville Sanjana
- **Activity code:** DP2 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $518,550
- **Award type:** 3
- **Project period:** 2020-09-01 → 2021-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10199425

## Citation

> US National Institutes of Health, RePORTER application 10199425, In situ functional genomics to understand transcriptional regulation (3DP2HG010099-01S2). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10199425. Licensed CC0.

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