Amplification and next generation sequencing of near full-length human enteroviruses for identification and characterisation from clinical samples

More than 100 different enterovirus (EV) genotypes infect humans and contribute to substantial morbidity. However, current methods for characterisation of full-length genomes are based on Sanger sequencing of short genomic regions, which are labour-intensive and do not enable comprehensive characterisation of viral populations. We have developed a simple and sensitive protocol for the amplification and sequencing of near full-length genomes of human EV species using next-generation sequencing. We aim to characterise enteroviruses in the Viruses in the Genetically at Risk cohort study and to investigate the intra-host virus evolution of EVs, variations associated with at-risk populations and outbreaks.