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Flaviviral RNA Structures and Their Role in Replication and Immunity

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Dengue and Zika: Control and Antiviral Treatment Strategies

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 1062))

Abstract

More than simple vectors of genetic information, flaviviral RNAs have emerged as critical regulators of the virus life cycle. Viral RNAs regulate interactions with viral and cellular proteins in both, mosquito and mammalian hosts to ultimately influence processes as diverse as RNA replication, translation, packaging or pathogenicity. In this chapter, we will review the current knowledge of the role of sequence and structures in the flaviviral RNA in viral propagation and interaction with the host cell. We will also cover the increasing body of evidence linking viral non-coding RNAs with pathogenicity, host immunity and epidemic potential.

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Abbreviations

(+)gRNA:

Positive-stranded genome RNA

(−)gRNA:

Negative-stranded antigenome RNA

3′DB:

3′ untranslated region dumbbell region

3′HP:

3′ hairpin

3′SL:

3′ terminal stem loop

3′VR:

3′ untranslated region variable region

3′xrRNA:

3′ exonuclease-resistant RNA structure

5′cHP:

5′ capsid hairpin

5′ and 3′CS:

5′ and 3′ complementary cyclization sequences

5′ and 3′UAR:

5′ and 3′ complementary upstream of A regions

5′SLA/SLB:

5′ terminal stem loop A/B

DENV:

Dengue virus

DIG:

Defective interfering genome

dsRNA:

Double-stranded RNA

HCV:

Hepatitis C virus

IFN:

Interferon type I (IFN-α and IFN-β)

ISG:

Interferon-stimulated genes

JEV:

Japanese encephalitis virus

KUNV:

Kunjin virus

MTase:

Methyltransferase

m6A:

N-6 methyladenosine

ncRNA:

Non-coding RNA

NTPase:

Nucleoside triphosphatase

ORF:

Open reading frame

PRR:

Pathogen recognition receptor

RdRp:

RNA-dependent RNA-polymerase

RNAi:

RNA interference

sfRNA:

Subgenomic flaviviral RNA

UTR:

Untranslated region

vsRNA:

Viral small RNA

WNV:

West Nile virus

YFV:

Yellow fever virus

ZIKV:

Zika virus

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Authors and Affiliations

  1. Infectious Diseases IRG, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore

    Katell Bidet

  2. Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore

    Mariano A. Garcia-Blanco

  3. Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA

    Mariano A. Garcia-Blanco

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  1. Institute of Biochemistry, University of Lübeck, Lübeck, Germany

    Rolf Hilgenfeld

  2. Emerging Infectious Diseases Program, Duke-NUS Medical School Singapore, Singapore, Singapore

    Subhash G. Vasudevan

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Bidet, K., Garcia-Blanco, M.A. (2018). Flaviviral RNA Structures and Their Role in Replication and Immunity. In: Hilgenfeld, R., Vasudevan, S. (eds) Dengue and Zika: Control and Antiviral Treatment Strategies. Advances in Experimental Medicine and Biology, vol 1062. Springer, Singapore. https://doi.org/10.1007/978-981-10-8727-1_4

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