Structural and phenotypic analysis of Chikungunya virus RNA replication elements

Kendall, C., Khalid, H., Müller, M., Banda, D. H., Kohl, A. , Merits, A., Stonehouse, N. J. and Tuplin, A. (2019) Structural and phenotypic analysis of Chikungunya virus RNA replication elements. Nucleic Acids Research, 47(17), pp. 9396-9312. (doi: 10.1093/nar/gkz640) (PMID:31350895) (PMCID:PMC6753490)

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Chikungunya virus (CHIKV) is a re-emerging, pathogenic Alphavirus transmitted to humans by Aedes spp. mosquitoes. We have mapped the RNA structure of the 5′ region of the CHIKV genome using selective 2′-hydroxyl acylation analysed by primer extension (SHAPE) to investigate intramolecular base-pairing at single-nucleotide resolution. Taking a structure-led reverse genetic approach, in both infectious virus and sub-genomic replicon systems, we identified six RNA replication elements essential to efficient CHIKV genome replication - including novel elements, either not previously analysed in other alphaviruses or specific to CHIKV. Importantly, through a reverse genetic approach we demonstrate that the replication elements function within the positive-strand genomic copy of the virus genome, in predominantly structure-dependent mechanisms during efficient replication of the CHIKV genome. Comparative analysis in human and mosquito-derived cell lines reveal that a novel element within the 5′UTR is essential for efficient replication in both host systems, while those in the adjacent nsP1 encoding region are specific to either vertebrate or invertebrate host cells. In addition to furthering our knowledge of fundamental aspects of the molecular virology of this important human pathogen, we foresee that results from this study will be important for rational design of a genetically stable attenuated vaccine.

Item Type:Articles
Additional Information:Royal Society [RG140704] and MRC [MR/N01054X/1] to AT; CK supported by BBSRC White Rose Doctoral Training Partnership PhD studentship [BB/M011151/1].
Glasgow Author(s) Enlighten ID:Kohl, Professor Alain
Authors: Kendall, C., Khalid, H., Müller, M., Banda, D. H., Kohl, A., Merits, A., Stonehouse, N. J., and Tuplin, A.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:Nucleic Acids Research
Publisher:Oxford University Press
ISSN (Online):1362-4962
Published Online:27 July 2019
Copyright Holders:Copyright © 2019 The Authors
First Published:First published in Nucleic Acids Research 47(17):9396-9312
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
656551Arbovirus interactions with arthropod hostsAlain KohlMedical Research Council (MRC)MC_UU_12014/8MVLS III - CENTRE FOR VIRUS RESEARCH