Key result
Native barcoding yields ~2.3-fold more reads and higher reproducibility than rapid barcoding despite identical consensus sequences.
Why the study?
The relative performance of ligation-based (Native Barcoding) and transposase-based (Rapid Barcoding) Oxford Nanopore Technologies library preparation methods for poliovirus sequencing had not been systematically evaluated.
Rapid barcoding is a cost-effective and efficient approach for routine poliovirus surveillance, producing identical consensus sequences to native barcoding despite lower sequencing yield.
Native barcoding may be prioritized for higher yield in viral sequencing workflows; leaves open optimal method selection balancing output and practicality.
Accurate and timely sequencing of poliovirus is critical for global eradication efforts, particularly for molecular epidemiology based on the typing region of the genome, viral protein 1 (VP1). While Oxford Nanopore Technologies (ONT) sequencing has expanded capabilities for poliovirus surveillance, the relative performance of different ONT library preparation methods, including ligation-based (Native Barcoding) and transposase-based (Rapid Barcoding) approaches, has not been systematically evaluated. In this study, we compared rapid barcoding and native barcoding workflows for sequencing VP1 amplicons from 17 type 2 poliovirus-positive samples, each processed in triplicate. Native barcoding generated significantly more sequencing output, producing approximately 2.3-fold greater total read yield than rapid barcoding, and demonstrated higher run-to-run reproducibility (R 2 = 0.979-0.998 vs. 0.847-0.929, respectively; p < 0.001). In addition, native barcoding generated 80% of the total yield achieved by rapid barcoding within approximately 7 hours, whereas rapid barcoding required approximately 40 hours to reach the same output. Despite these differences, both methods produced identical VP1 consensus sequences across all samples, with comparable read quality (median per-base Q-scores of approximately Q17-Q18). Rapid barcoding provided substantial practical advantages, reducing hands-on library preparation time (55 vs. 200 minutes) and per-sample cost ($12.82 vs. $16.54), while simplifying workflow and reducing technical complexity. These findings indicate that sequencing yield may not be a determinant of downstream analytical outcomes for poliovirus VP1 ONT sequencing. Rapid barcoding therefore represents a cost-effective and efficient approach for routine poliovirus surveillance, whereas native barcoding remains advantageous in applications requiring rapid data generation or maximal sequencing depth.
No takes yet. Share an insight, caveat, or question.
Bullows et al. (2026) studied Poliovirus (n=17). Rapid barcoding vs. Native barcoding was evaluated on Total read yield and run-to-run reproducibility (p=<0.001). Native barcoding produced 2.3-fold greater total read yield and higher reproducibility than rapid barcoding (p<0.001), though both methods produced identical VP1 consensus sequences.
Synapse has enriched 5 closely related papers on similar clinical questions. Consider them for comparative context: