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This document is a summary of a special issue of the journal "Viruses" focused on advances in research on alphaviruses and flaviviruses. The special issue includes research articles, review articles, and brief reports covering various aspects of these viruses. The research articles explore topics such as the susceptibility of chickens to Zika virus, serological misdiagnosis of certain viruses in Australia, the evolutionary history of dengue virus in Brazil, and the pathogenesis of Tembusu virus in mammals. The review articles discuss the mechanisms and environmental factors of yellow fever virus and the immune responses to chikungunya virus. The brief reports present a phylogenetic analysis of dengue virus serotypes and the development of a mouse infection model for vaccine testing. Overall, this special issue provides new insights into alphavirus and flavivirus research. [Extracted from the article]