Genome analysis of yellow fever virus of the ongoing outbreak in Brazil reveals polymorphisms

The current yellow fever (YF) outbreak in Brazil is the most severe recently reported in the country. It has rapidly spread to areas where YF viral activity have not been observed for more than seventy years and vaccine coverage is almost null. Here, we sequenced the whole YF genome of two naturally infected howler-monkeys (Alouatta clamitans) from the Municipality of Domingos Martins, State of Espirito Santo, Brazil. The ongoing-outbreak genome sequences are identical. They clustered in 1E sub-clade (South America I genotype) together with recent Brazilian and Venezuelan strains characterized from infections in humans and non-humans primates. However, we detected eight unique amino acid changes in the viral proteins, which are located in the structural capsid protein (1 change), and the components of viral replicase complex, the NS3 (2 changes) and NS5 (5 changes) proteins, suggesting a potential role in the capacity of viral infection to vertebrate and/or invertebrate hosts and spreading in the ongoing outbreak.