# Viral genomics: comprehensive detection, transmission inference, and functional characterization

> **NIH NIH U19** · BROAD INSTITUTE, INC. · 2024 · $1,876,974

## Abstract

Viral infectious diseases remain a significant threat and, as demonstrated in recent years, can be particularly
disruptive and unpredictable in their impact on human lives, economies, and public health. Advances in
genomic science have enabled leaps in how to manage, respond to, and mitigate viral disease, but significant
gaps remain in what we know: we have a limited understanding of the pathogens that exist in our environment,
how they spread, and which of them have epidemic potential, leaving us vulnerable to the emergence of future
threats. Without more complete knowledge of the pathogens around us, it will be difficult or impossible to
develop countermeasures with sufficient speed to stop major outbreaks in the future.
Our long-term goal is to advance understanding and utility of viral genomics so that we are better able to
prepare for and respond to future outbreaks: we aim to comprehensively identify circulating viruses, infer viral
evolutionary signals and human transmission chains, and characterize the effect of consequential mutations on
the virus, its immunogenicity, and impact on humans. The Broad Institute’s GCID has led many technical,
analytical, and translational advances that have revolutionized the application of genomics to viral disease. The
experience, resources, and innovative capacity of this group will all be necessary to address the gaps that
remain, and new challenges that emerge, in our understanding of and our ability to respond to ongoing threats
posed by viral diseases. The premise of this proposal is improved insights from viral genomic data will
accelerate the design of viral diagnostics, therapeutics, and vaccines, and will inform public health strategies
and policy. We plan to do this by pursuing the following three specific aims: 1) Detect emerging viral threats
with robust metagenomics and diagnostic designs (this includes improving methods for metagenomic
surveillance and PCR diagnostic designs). 2) Genomic epidemiology and population genetics of viral outbreaks
and epidemics (this includes analytic methods for Bayesian phylogenetic inference of evolutionary signals and
of human transmission chains and clusters. 3) Identify and characterize viral genetic variation with phenotypic
impact (this includes identification and in vitro characterization of viral mutations). The expected outcomes of
this work are a systematic understanding of circulating viral threats with epidemic potential,
genomics-informed view of viral transmission during outbreaks, and a characterization of the viral genetic
adaptations that affect their spread and impact on society. This proposal will have a positive impact by
providing genomic data resources, insights into viral circulation, developing new analytic and interpretive
frameworks for epidemiological insights to influence public health practice, and creating public data sets to
enable the design of new interventions for viral disease. Our work will advance viral genomics by creating...

## Key facts

- **NIH application ID:** 10853971
- **Project number:** 2U19AI110818-11
- **Recipient organization:** BROAD INSTITUTE, INC.
- **Principal Investigator:** Pardis Christine Sabeti
- **Activity code:** U19 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $1,876,974
- **Award type:** 2
- **Project period:** 2014-04-10 → 2027-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10853971

## Citation

> US National Institutes of Health, RePORTER application 10853971, Viral genomics: comprehensive detection, transmission inference, and functional characterization (2U19AI110818-11). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10853971. Licensed CC0.

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