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Background Few congenital Zika syndrome (CZS) cases have been notified in Ecuador and, to our knowledge, there are no significant published studies dealing with their clinical evolution. We present a detailed clinical characterization of 21 children with congenital Zika virus (ZIKV) infection born in Ecuador who were followed up until September 2019. Methods We did a retrospective longitudinal study of children attended by the infectious disease specialists of Francisco Icaza Bustamante Children’s Hospital (Guayaquil) due to congenital ZIKV infection suspicion. The inclusion criteria consisted of laboratory confirmed diagnosis of congenital ZIKV infection. Results Sixteen of these 21 cases of congenital ZIKV infection showed clinical, neuroimaging and laboratory findings strongly suggestive of CZS and 5 children showed laboratory findings compatible with congenital ZIKV infection without congenital manifestations associated to CZS. All children with CZS showed neurodevelopmental delay, spasticity and hyperreflexia during follow-up, whereas the majority of them (14/15) experienced recurrent epileptic seizures and dysphagia (12/13). Two CZS cases died during follow-up. Visual evoked potential and hearing screening with acoustically evoked auditory brainstem response were abnormal in 50% and 37.5% of CZS cases, respectively. Congenital ZIKV infection without findings consistent with CZS at birth was not clinically relevant at 23 months of age in the five cases of our cohort. Conclusions Severe neurodevelopmental delay, severe microcephaly, epileptic seizures and dysphagia were present at 2 years of age in most CZS cases of our cohort.

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