Emergence and spread of multirecombinant enterovirus A71 lineages C1.3/RF5 and C1.3/RF6 associated with neurological diseases in Europe, 2016–2022, ENPEN multicentre study

Since its re-emergence in Europe in 2015, enterovirus A71 (EV-A71) has been associated with sporadic cases of severe infections and outbreaks. Currently, there is no treatment but a few Asian countries have implemented vaccination programmes. The aim of our study was to characterize the EV-A71 cases in Europe and track the evolution of the virus between 2016 and 2022. For this retrospective study, we compiled the data of confirmed EV-A71 infections collected by 19 institutes participating in the European Non-Polio Enterovirus Network between 2016 and 2022. We also sequenced whole EV-A71 genomes to follow the viral evolutionary history of the virus and its molecular changes. Between 1 January 2016 and 31 December 2022, 627 EV-A71 cases were reported in 14 European countries. Most cases (59.3%) occurred in children under two years of age. Of the 537 subjects for whom clinical information was available, 52.7% were diagnosed with neurological signs, and 10.6% presented with acute flaccid paralysis or acute flaccid myelitis. EV-A71 infections were linked to two subclades, C1.2 and C1.3, within the C1 subgenogroup. Two marked epidemic waves, in 2016 and 2019, were characterized by the predominance of C1.3 viruses. Comparisons of 153 whole genomes revealed nine recombinant forms (RFs), each arising from multiple recombination events affecting different genomic regions. Only C1.3/RF5 and C1.3/RF6 lineages achieved widespread geographic dissemination initially in Europe and subsequently in Asia and the Americas, and long-term circulation. Phylodynamic analyses indicated that C1.3 viruses emerged around 2013-2014, displacing earlier C1.1 viruses, and the effective population size closely parallels the timing of clinical cases. Molecular analyses of the capsid revealed several amino acid changes, few of which occurred within known antigenic sites. These findings document the role of the C1.3/RF5 and C1.3/RF6 multi-recombinant lineages of EV-A71 as frequent causes of neurological disease in young children in Europe. The study highlights the need for sustained genome-informed surveillance to anticipate the emergence and spread of novel epidemic lineages, and to inform the evaluation of future EV-A71 vaccination strategies.