Molecular Evolution and Epidemiology of Parechovirus-A3 in Japan, 1997–2019

Abstract Parechovirus-A3 (PeV-A3), first reported in 2004 in Japan, is an emerging pathogen that causes sepsis and meningoencephalitis in neonates and young infants. Although PeV-A3 has been identified worldwide, its epidemiological characteristics differ by region. To investigate the molecular evolution and epidemiology of PeV-A3, we performed genetic analyses of 131 PeV-A3 strains from the years 1997–2019 in Niigata, Japan. During 2016–2019, annual numbers remained steady, in contrast to the PeV-A3 epidemic interval of every 2–3 years that was observed in Japan from 2006. Bayesian evolutionary analysis of the complete viral protein 1 region revealed alternate dominant clusters during years of PeV-A3 epidemics. The branch including the oldest and first isolated PeV-A3 strains in Japan has been disrupted since 2001. The year of PeV-A3 emergence was estimated to be 1991. Continuous surveillance with genetic analyses of different regions will improve understanding of PeV-A3 epidemiology worldwide. Bayesian evolutionary analysis revealed alternate dominant clusters in the epidemic years of parechovirus-A3 infection, and disruption of the oldest and first isolated strains in Japan.