Targeted sequence capture of coxsackievirus A6 using Nanopore sequencing directly from clinical specimens

We developed a tiling amplicon-based Nanopore sequencing protocol for CVA6 using primers designed from the prototype strain Gulda. Twenty-four clinical samples with a broad range of viral loads Ct values 15.54-32.7) were sequenced on both PromethION and GridION platforms. Sensitivity was assessed via serial tenfold dilutions, and accuracy was rigorously compared to Illumina sequencing.