# Mechanism of Flavivirus RNA Capping

> **NIH NIH R01** · COLORADO STATE UNIVERSITY · 2020 · $374,993

## Abstract

Approximately 2/3rd of the world population is at risk of infection by at least one of the 35 insect-borne
flaviviruses known to cause disease in humans. There are currently few vaccines and no therapeutics available
to treat patients infected by flaviviruses such as Dengue, Zika, and West Nile viruses despite the severe
morbidity and mortality they cause globally each year. The development of improved vaccines and therapeutics
to prevent and treat flavivirus infections requires improved knowledge of the molecular mechanisms these
serious human pathogens use to replicate their genomes. RNA capping of flavivirus genomes has received
increasing attention over the last decade as an antiviral drug target due to its critical roles in maintaining viral
RNA stability, controlling viral protein translation, and innate immune evasion. There is, however, not much
known about how flavivirus RNAs are capped during infection. Therefore, this proposal will define how
flaviviruses cap their RNA genomes during infection and evaluate how capping affects innate immune evasion.
1) The NS5 RNA guanylyltransferase is a novel flavivirus enzyme with no structural or sequence similarities to
any other known nucleotidyltransferase enzyme. It is currently unknown how this important viral enzyme
functions, which is a critical gap in our understanding of flavivirus RNA replication. We are using a
combination mutagenesis and viral replication experiments to define the active site of the flavivirus NS5
guanylyltransferase, providing the first in-depth characterization of this unique viral replication enzyme.
2) The 5' untranslated region (UTR) of the flavivirus genome contains conserved sequence and structural
elements known to be involved in RNA replication, but their role in RNA capping has never been assessed. We
will use a series of mutated 5' UTR RNAs to test the specificity of NS5-mediated RNA capping to define how 5'
UTR terminal sequences and the stem-loop A structure affect binding and capping efficiency. 3) Degradation
of flavivirus genomes by the cellular RNA decay pathway results in the inhibition of RNA decay and RNAi
pathways, altering the immune response to infection. We wish to test the intriguing hypothesis that viral
capping efficiency may be strategically regulated by viruses to produce non-coding RNAs that alter infection
dynamics. Interestingly, we have recently found that uncapped viral RNAs are incorporated into virus particles
and may comprise up to a third of viral RNAs in an infected cell. This surprisingly high level of uncapped RNA
is likely processed by RNA decay factors and leads to high levels of a small sfRNA which has been shown
previously to antagonize RNAi and interferon responses (among other things). We will examine, therefore,
how NS5 capping efficiency affects viral RNA production, the fate of uncapped viral RNAs in cells, and how the
products of these uncapped RNAs influence the dynamics of a flavivirus infection. Overall, this project ...

## Key facts

- **NIH application ID:** 9838148
- **Project number:** 5R01AI132668-03
- **Recipient organization:** COLORADO STATE UNIVERSITY
- **Principal Investigator:** Brian Geiss
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $374,993
- **Award type:** 5
- **Project period:** 2018-01-01 → 2022-12-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9838148

## Citation

> US National Institutes of Health, RePORTER application 9838148, Mechanism of Flavivirus RNA Capping (5R01AI132668-03). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9838148. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*