Flaviviral RNA Structures and Their Role in Replication and Immunity

  • Katell Bidet
  • Mariano A. Garcia-Blanco
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 1062)


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.


Flavivirus RNA Structures Replication Pathogenesis 



Positive-stranded genome RNA


Negative-stranded antigenome RNA


3′ untranslated region dumbbell region


3′ hairpin


3′ terminal stem loop


3′ untranslated region variable region


3′ exonuclease-resistant RNA structure


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′ terminal stem loop A/B


Dengue virus


Defective interfering genome


Double-stranded RNA


Hepatitis C virus


Interferon type I (IFN-α and IFN-β)


Interferon-stimulated genes


Japanese encephalitis virus


Kunjin virus




N-6 methyladenosine


Non-coding RNA


Nucleoside triphosphatase


Open reading frame


Pathogen recognition receptor


RNA-dependent RNA-polymerase


RNA interference


Subgenomic flaviviral RNA


Untranslated region


Viral small RNA


West Nile virus


Yellow fever virus


Zika virus


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Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  • Katell Bidet
    • 1
  • Mariano A. Garcia-Blanco
    • 2
    • 3
  1. 1.Infectious Diseases IRG, Singapore-MIT Alliance for Research and TechnologySingaporeSingapore
  2. 2.Programme in Emerging Infectious DiseasesDuke-NUS Medical SchoolSingaporeSingapore
  3. 3.Department of Biochemistry and Molecular BiologyUniversity of Texas Medical BranchGalvestonUSA

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