Molecular characterization of Enterovirus in children hospitalized with severe acute respiratory infection in Northern Italy (2014-2017)

Background: The emergence of several Enterovirus (EV) types, such as EV-D68, EVC105 and Coxsackievirus (CV) A21, in severe illnesses – including severe acute respiratory infections (SARI) - is a major public health concern. This study aimed at investigating the EV types in children hospitalized with SARI in Northern Italy Methods: Between 2014 and 2017, respiratory samples were collected from 2,468 children <15 years hospitalized with SARI at University hospital in Milan. Specimens were tested for EV-RNA presence by multiplex real-time PCR (AnyplexTMII, RV16-Detection, Seegene). EV-positive samples were then analysed by real-time RT-PCR assay specific for EV-D68; EV- D68 negative specimens were molecularly characterized by partial sequencing (~400 nt.) of VP1/2A gene. Results: EV-RNA was detected in 9% (222/2468) of SARIs and mainly (80%; 171/222) in children <3 years. 142 EV- strains were molecularly analysed. EV-D68 was the predominant types detected in 15.5% of SARIs, almost exclusively in 2016. Overall, 22 EV types were recognized with a remarkable heterogeneity in distribution; EVs species B (49.3%) circulated more frequently than EV-D (28%), EV-A (20%) and EV-C (2.7%). EV-A (including 7 EV types) were more frequently detected in children <3 years while EV-B (including 12 EV types) in those aged 4-15 years. Species D and C included only one (EV-D68) and two (EV-A71, CV-A21) types, respectively. Emerging EVs were identified: six cases of CV- A6 (from Oct-2014 to June-2015), one case of EV-C105 (March-2015), one of EV-A71 (June-2016) and one of CV-A21 (Feb-2017). Conclusions: Molecular characterization of EVs from children with SARIs allowed drawing up the epidemiological picture of circulating EVs in Italy, identifying an outbreak of EV-D68 in 2016 as well as the circulation of several emerging EV types with epidemic potential.