Population Structure of Yellow Fever Virus: Influence of Viral Diversity on Vaccine Attenuation

Abstract

Yellow fever virus (YFV) is the prototype of all arthropod-borne viruses, the study of which encompasses some of the landmark paradigm shifts in modern vaccinology. Recently, studies on the lifecycle of RNA viruses have indicated that population structure of these viruses is in many cases complex, which in itself may confer fitness within hosts or host ecologies. Thus, these dissertation studies were performed under a set of hypotheses that the YFV population structure is in itself complex, and that features of these populations define a signature that differentiates wild-type from serially passaged and attenuated vaccine strains. Using deep sequencing techniques, a comparison was made between the prototype West African YFV strain Asibi, and a commercial aliquot of the YFV 17D-204 vaccine. In silico methods revealed the vaccine to be of lower diversity than the parental strain, leading to subsequent hypotheses that the level of complexity in the vaccine populations would be related to phenotypic stabilities. A deep sequencing study was performed comparing a set of rare 17D vaccine seeds, which represent all main lineage (substrain) relationships in modern production of the vaccine, and millions of doses administered. The population structures of the vaccine seeds were found to be stable, showing both low diversity and repeatability of subpopulation content. A deep sequencing study was performed on a set of institutional collection strains representing the discontinued YFV French neurotropic vaccine (FNV), which was developed concurrently to 17D. FNV strains with high neurovirulence contained homogeneity in their population structures, showing that the neurotropic adverse events caused by FNV were the result of mouse brain adaptation to attenuate. A deep sequencing study of an adapted strain of Asibi which causes viscerotropy in hamsters was shown to be of low complexity, suggesting that YFV disease of the liver is rare due to low content of viscerotropic alleles. Finally as confirmation, the Japanese encephalitis vaccine strain SA14-14-2 was compared to its wild-type parental strain SA14 by deep sequencing, revealing that loss of diversity for the vaccine was localized to regions of the genome previously thought to influence pathogenicity. The combined results from both JEV and YFV suggest that population studies are useful in the control of empiric vaccine stability and monitoring of safety.