Molecular diagnostics have superseded cell culture and neutralisation as the gold standard for enterovirus (EV) diagnosis and serotyping in resource rich countries. EV positive isolates from Nottingham University Hospitals NHS Trust are referred to the Enteric Virus Unit (EVU) for typing; performed through amplification and sequencing of viral capsid protein-1 (VP1). An audit of local EVU typing data (2013–2017 showed a significant (P<0.005) increase in untypable EV strains isolated from clinical specimens. Following a literature review of published EV typing assays and in silico analyses of 2201 EV genomes, an end point RT-snPCR VP1-typing assay was derived from a widely cited protocol and successfully employed to produce a simple, reliable and cost-effective typing assay. Twenty-three previously untypable isolates were identified, with phylogenetic analyses of the VP1 region showing broad distribution across EV-A and B species. This assay detected serotypes across EV species A-D, including EV-D68, responsible for severe neurological and respiratory disease. Following an increase in severe EV infections, including six cases of suspected acute flaccid myelitis, this RT-snPCR was employed locally as a rapid typing assay. In combination with 5’UTR PCR and an EV-D68 specific PCR, designed to amplify the complete VP1 region, EV-D68 was detected in respiratory and neurological specimens, including the CSF of a patient with brainstem encephalitis.

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