Random Codon Re-encoding Induces Stable Reduction of Replicative Fitness of Chikungunya Virus in Primate and Mosquito Cells

PLoS Pathogens

Fabien Aubry¹  Ernest A. Gould¹  Antoine Nougairede¹  Lauriane De Fabritus¹  Xavier de Lamballerie²  Edward C. Holmes³ 

[1] Aix Marseille Univ, IRD French Institute of Research for Development, EHESP French School of Public Health, UMR_D 190 “Emergence des Pathologies Virales,” Marseille, France;Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America;Sydney Emerging Infections and Biosecurity Institute, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia

关键词: Viral replication;    Microbial mutation;    Chikungunya virus;    Vero cells;    Deletion mutation;    Mutation detection;    Primates;    RNA viruses;   

DOI  :  10.1371/journal.ppat.1003172

学科分类：生物科学（综合）

来源: Public Library of Science

【 摘 要 】

Large-scale codon re-encoding represents a powerful method of attenuating viruses to generate safe and cost-effective vaccines. In contrast to specific approaches of codon re-encoding which modify genome-scale properties, we evaluated the effects of random codon re-encoding on the re-emerging human pathogen Chikungunya virus (CHIKV), and assessed the stability of the resultant viruses during serial in cellulo passage. Using different combinations of three 1.4 kb randomly re-encoded regions located throughout the CHIKV genome six codon re-encoded viruses were obtained. Introducing a large number of slightly deleterious synonymous mutations reduced the replicative fitness of CHIKV in both primate and arthropod cells, demonstrating the impact of synonymous mutations on fitness. Decrease of replicative fitness correlated with the extent of re-encoding, an observation that may assist in the modulation of viral attenuation. The wild-type and two re-encoded viruses were passaged 50 times either in primate or insect cells, or in each cell line alternately. These viruses were analyzed using detailed fitness assays, complete genome sequences and the analysis of intra-population genetic diversity. The response to codon re-encoding and adaptation to culture conditions occurred simultaneously, resulting in significant replicative fitness increases for both re-encoded and wild type viruses. Importantly, however, the most re-encoded virus failed to recover its replicative fitness. Evolution of these viruses in response to codon re-encoding was largely characterized by the emergence of both synonymous and non-synonymous mutations, sometimes located in genomic regions other than those involving re-encoding, and multiple convergent and compensatory mutations. However, there was a striking absence of codon reversion (<0.4%). Finally, multiple mutations were rapidly fixed in primate cells, whereas mosquito cells acted as a brake on evolution. In conclusion, random codon re-encoding provides important information on the evolution and genetic stability of CHIKV viruses and could be exploited to develop a safe, live attenuated CHIKV vaccine.

【 授权许可】

CC BY