# Investigating the Formation and Function of Subgenomic Flavivirus RNAs During Flavivirus Infection of the Mosquito Vector

> **NIH NIH F31** · UNIVERSITY OF COLORADO DENVER · 2023 · $36,476

## Abstract

Project Summary:
During infection by arthropod borne flaviviruses such as Dengue (DV) and Zika (ZV), infected cells accumulate
non-coding RNAs termed Subgenomic Flaviviral RNAs (sfRNAs) that consist of the viral genomic RNA’s 3
untranslated region (UTR). sfRNAs are generated when the host 5 to 3 exoribonuclease Xrn1 encounters
exoribonuclease-resistant RNA (xrRNAs) structures in the genome’s 3 UTR that halt its progress. Analysis of
flaviviral genomes has revealed that the majority of mosquito-borne flaviviruses have multiple xrRNAs “in
tandem”. It was hypothesized that these structures were functionally redundant and working independently to
generate sfRNA. However, data in our lab has revealed that within certain flaviviruses the structural integrity of
one xrRNA is sensed by the other, affecting its function. We hypothesize that this “coupling” or “coordination” is
due to tandem xrRNAs interacting through intervening sequences and/or structures. To test this hypothesis, we
developed a surrogate reporter system that allows us to test the functional effects of mutations in the intervening
sequence of the Dengue virus tandem xrRNAs. Specifically, our assay reports on changes in the patterns of
produced sfRNAs, which have been well characterized for the wild type sequences. For aim 1 we will use this
system to explore the mechanism of this coupling between xrRNAs in multiple flaviviruses. In addition, this
research will also include uncovering the mechanism in which sfRNAs interfere with the mosquito immune
response. Specifically, it has been shown that sfRNAs are capable of interacting with the mammalian Dicer
protein, reducing the amount of small interfering RNA (siRNA) formed in vitro. Since mosquitos rely on RNA
interference (RNAi) as their primary defense against viral infection, and mammalian and mosquito Dicer proteins
are well conserved, we hypothesize that sfRNAs dampen the RNAi response in mosquitos by interacting with
the Dicer-2 (Dcr2) protein of the mosquito RNAi pathway. Under aim 2 we will utilize a series of in vitro
biochemical assays to test how this interaction between sfRNA and Dcr2 is taking place and elucidate on how
sfRNAs work to dampen the immune response of the mosquito vector. Uncovering the dynamics of these host
pathogen interactions could lead to new strategies for attenuating sfRNA production in mosquitos to curb the
spread of flaviviruses.

## Key facts

- **NIH application ID:** 10677398
- **Project number:** 1F31AI176728-01
- **Recipient organization:** UNIVERSITY OF COLORADO DENVER
- **Principal Investigator:** Elizabeth Spear
- **Activity code:** F31 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $36,476
- **Award type:** 1
- **Project period:** 2023-09-01 → 2026-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10677398

## Citation

> US National Institutes of Health, RePORTER application 10677398, Investigating the Formation and Function of Subgenomic Flavivirus RNAs During Flavivirus Infection of the Mosquito Vector (1F31AI176728-01). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10677398. Licensed CC0.

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