Application of metagenomic next-generation sequencing (mNGS) approaches to characterize the whole-genome sequence of EVs has become a valuable tool for detecting multiple EVs that may be present during co-infection, especially caused by two EV types of same species. Since new recombinant EVs may present different properties (variations in virulence or transmissibility), it is essential to capture complete genomes to detect the occurrence of these recombination events for surveillance and public health purposes. Genetic recombination is a major process in EVs evolution 3. EVs are associated with a wide spectrum of clinical symptoms ranging from nonspecific febrile illness or upper respiratory illness to severe neurological conditions, including meningitis, encephalitis or acute flaccid paralysis 1. There are more than 100 types of EVs infecting humans which are classified into four species A to D 2.

The 5РІР‚в„ў part of the ORF encodes the structural proteins that form the capsid (among them the VP1 which is the most external), while the 3РІР‚в„ў part of the ORF encodes the non-structural proteins. Their positive single-strand RNA genome is about 7,500 nucleotides (nt), and is composed of a large open reading frame (ORF) flanked by 5РІР‚в„ў and 3РІР‚в„ў untranslated regions (UTRs) 1. The detection of a novel, disease-associated, recombinant form emphasizes the importance of genomic surveillance to monitor spread and evolution of EVs.Р”В®nteroviruses (EVs) belong to the family Picornaviridae, genus Enterovirus. Metagenomic sequencing provides an effective approach for the analysis of EV genomes directly from PCR-positive CSF samples. We observed a genetic turnover where emergent lineages (C1 for E6 and I for E30) replaced previous lineages circulating in Spain, some concomitant with outbreaks in other parts of Europe. Our analyses reveal the co-circulation of multiple Enterovirus B (EV-B) types (E6, E11, E13 and E30), including a novel E13 recombinant form. We have used metagenomic (untargeted) NGS to generate full-length EV genomes from CSF samples of EV-positive aseptic meningitis cases in Southern Spain between 20.

Only a few complete genomes of EVs circulating in Spain are available in public databases, making it difficult to address the emergence of recombinant EVs, understand their evolutionary relatedness and the possible implication in human disease. Upsurges of recombinant non-polio enteroviruses (NPEVs) associated with neurologic manifestations such as EVA71 or Echovirus 30 (E30) are a growing public health concern in Europe. New circulating Enterovirus (EV) strains often emerge through recombination.

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