# Molecular mechanisms and ramifications of horizontal gene transfer into poxviruses

> **NIH NIH R01** · UNIVERSITY OF CALIFORNIA AT DAVIS · 2022 · $372,107

## Abstract

PROJECT SUMMARY/ABSTRACT: There is substantial phylogenetic evidence that horizontal gene transfer
(HGT) of host genes into large DNA viruses is a major driver of virus evolution. The status quo understanding of
HGT in viruses is based exclusively on bioinformatic and phylogenetic data; however, these approaches cannot
determine the molecular or evolutionary mechanisms underlying HGT. There is a critical need to develop an
experimental system to directly model HGT. The long-term goal is to define how host genes are acquired by
viruses and determine how these newly acquired genes evolve to provide a selective advantage to the virus. As
a step towards this goal, the objective of this project is to optimize novel in vitro and in vivo experimental models
to define mechanisms of HGT into poxviruses. The central hypothesis is that poxvirus HGT is facilitated through
RNA intermediates. This hypothesis is based on preliminary data using our novel cell culture-based experimental
model that demonstrated multiple independent long interspersed nuclear elements (LINE)-mediated HGT events
into vaccinia virus (VACV). The rationale for this proposed research is that developing a robust experimental
model of HGT into viruses will permit direct experimental approaches to address questions about the initial ac-
quisition and subsequent evolution of captured genes that cannot be addressed by bioinformatics. For example,
our preliminary data identified an unexpected evolutionary cascade that enabled transgenes to be acquired in
essential genes through a process of HGT, complementation via co-infection, and subsequent recombination.
The central hypothesis will be tested by three specific aims. 1) Characterize the molecular mechanisms of, and
factors influencing HGT into VACV. Long-read sequencing will map the genes and surrounding genomic archi-
tecture to define the mechanism(s) of HGT in cells. Cells either expressing different levels of LINE-1 or coinfected
with retroviruses will be used to determine if these conditions influence HGT. 2) Analyze the evolution of hori-
zontally transferred genes. HGT viruses will be serially passaged and subjected to long-read and Illumina-based
deep sequencing to determine how captured genes evolve, and if there are any adaptations driven by disruption
of different VACV genes due to the gene insertion event. 3) Define the mechanisms of horizontal gene transfer
in vivo. A transgenic mouse line will be generated to study HGT into VACV during infection. Moreover, mouse
infection studies will be performed to investigate the newly identified mechanism for sequential virus evolution
following HGT into an essential gene and to assess the fitness of viruses that acquired transgenes. The proposed
research is significant because it will establish and test novel experimental systems of HGT into viruses that will
facilitate a detailed understanding of HGT into poxviruses that will close a fundamental gap in our knowledge of
the evolution of th...

## Key facts

- **NIH application ID:** 10327724
- **Project number:** 5R01AI146915-03
- **Recipient organization:** UNIVERSITY OF CALIFORNIA AT DAVIS
- **Principal Investigator:** Stefan Rothenburg
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $372,107
- **Award type:** 5
- **Project period:** 2020-02-18 → 2025-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10327724

## Citation

> US National Institutes of Health, RePORTER application 10327724, Molecular mechanisms and ramifications of horizontal gene transfer into poxviruses (5R01AI146915-03). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10327724. Licensed CC0.

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