PCR-based detection is still the most commonly used method for routine identification of viruses of clinical importance, and this approach is often complemented by Sanger sequencing for further genotype determination. Yet, point mutations and recombination events that occur frequently in the genomes of human viruses can potentially lead to false negative results when PCR-based techniques are uniquely used. Here, we developed a set of assays based on Oxford nanopore technologies to obtain whole genomes of enteroviruses (RNA viruses) from clinical samples. We will present our conclusions about direct RNA sequencing vs. indirect sequencing of RNA (via cDNA synthesis and sequencing), in terms of costs, turnaround time, accuracy, and types of foreseen applications in the clinical setting.
