Development and evaluation of a next-generation sequencing methodology for measles virus using Oxford Nanopore Technology

We report the development of a bench protocol and evaluation of bioinformatics pipelines for the whole genome sequence (WGS) of measles virus (MeV) genotype D8. We established a bench protocol using 1 kb amplicons tiling the MeV WGS. Four different pipeline parameters were assessed based on two basecallers and two quality thresholds: Guppy simplex with Q-score thresholds of 20 and 25 (G20 and G25), and Dorado duplex with Q-score thresholds of 20 and 25 (D20 and D25). Using a reference genome, we determined that complete genomes were obtained down to 10 copies/µL with all four parameters; however, errors began to be detected in the consensus sequence at 100 copies/µL. A panel of specimens from 32 measles cases, for which measles WGS had been obtained by other methods (reference sequences), was used to assess the utility and accuracy of the Oxford Nanopore Technologies (ONT) for the purposes of measles surveillance. We found that a crossing point (Cp) value of 31 (corresponding to approximately 100 copies/µL) or less could be considered a predictor for the generation of accurate and complete WGS. The GQ20 parameter achieved the most complete genomes (75%) and had the most identical sequences (84.4%). Error rates compared with the reference sequences for all parameters were below one nucleotide per whole genome. After assessing the reproducibility, GQ20 had the most identical sequences (97.4%). Finally, we inserted ONT-generated WGS and reference sequences into outbreaks with known epidemiological links, and our results show that the ONT WGS matches the epidemiological data. This evaluation establishes that NGS generated by ONT produces accurate and reliable MeV WGS.IMPORTANCEThe use of ONT-sequencing platforms has the potential to expand the availability of measles sequencing as a result of its relatively lower cost and portability. This study establishes that measles sequences generated by ONT are accurate and reliable. This will enable sequencing in global regions where there is a lack of sequence data (which also tend to be the measles exporting regions) and more timely sequencing in low incidence settings, due also to the lower number of samples needed for the ONT platform. More timely generation of these data enables better investigation of cases, which informs public health response and outbreak management in measles-eliminated countries.