Abstract
Human enteroviruses (EVs) comprise more than 100 types of coxsackievirus, echovirus, poliovirus and numbered enteroviruses, which are mainly transmitted by the faecal-oral route leading to diverse diseases such as aseptic meningitis, encephalitis, and acute flaccid paralysis, among others. Since enteroviruses are excreted in faeces, wastewater-based epidemiology approaches are useful to describe EV diversity in a community. In Uruguay, knowledge about enteroviruses is extremely limited. This study assessed the diversity of enteroviruses through Illumina next-generation sequencing of VP1-amplicons obtained by RT-PCR directly applied to viral concentrates of 84 wastewater samples collected in Uruguay during 2011–2012 and 2017–2018. Fifty out of the 84 samples were positive for enteroviruses. There were detected 27 different types belonging to Enterovirus A species (CVA2-A6, A10, A16, EV-A71, A90), Enterovirus B species (CVA9, B1-B5, E1, E6, E11, E14, E21, E30) and Enterovirus C species (CVA1, A13, A19, A22, A24, EV-C99). Enterovirus A71 (EV-A71) and echovirus 30 (E30) strains were studied more in depth through phylogenetic analysis, together with some strains previously detected by us in Argentina. Results unveiled that EV-A71 sub-genogroup C2 circulates in both countries at least since 2011–2012, and that the C1-like emerging variant recently entered in Argentina. We also confirmed the circulation of echovirus 30 genotypes E and F in Argentina, and reported the detection of genotype E in Uruguay. To the best of our knowledge this is the first report of the EV-A71 C1-like emerging variant in South-America, and the first report of EV-A71 and E30 in Uruguay.
Highlights
Human enteroviruses (EVs) are ubiquitous viruses mainly transmitted among all age groups in a community by the faecal-oral route [1]
Human enteroviruses (EVs) comprise more than 100 types of coxsackievirus, echovirus, poliovirus and numbered enteroviruses, which are mainly transmitted by the faecal-oral route leading to diverse diseases such as aseptic meningitis, encephalitis, and acute flaccid paralysis, among others
There were detected 27 different types belonging to Enterovirus A species (CVA2-A6, A10, A16, Enterovirus A71 (EV-A71), A90), Enterovirus B species (CVA9, B1-B5, E1, E6, E11, E14, E21, echovirus 30 (E30)) and Enterovirus C species (CVA1, A13, A19, A22, A24, EV-C99)
Summary
Human enteroviruses (EVs) are ubiquitous viruses mainly transmitted among all age groups in a community by the faecal-oral route [1] They are associated with a large number of clinical conditions, ranging from nonspecific symptoms as fever and malaise, mild conditions as herpangina, gastroenteritis or hand-foot-and-mouth disease (HFMD), up to severe diseases as aseptic meningitis (AM), encephalitis, pancreatitis, myocarditis, or acute flaccid paralysis (AFP), among others [2]. Wastewater Based Epidemiology (WBE) approaches are useful for describing the molecular diversity of EVs either as a complement of clinical surveillance, or as a tool to obtain information regarding enteroviruses when clinical surveillance is not done in a community. Enterovirus diversity in wastewater assessed by next-generation sequencing the possibility of detecting emerging types in wastewater, before the appearance of clinical cases, makes WBE of EVs, a fundamental tool for epidemiological surveillance. As part of a project to characterize the diversity of EVs in the South American region, two EV types detected in this project (EV-A71 and E30) were subjected to phylogenetic analysis along with sequences of strains previously detected in wastewater from Cordoba, Argentina [29], to evaluate viral dynamics within a regional context and to identify viral introductions and country-specific transmission clusters
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