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Workflow for Long-Read Amplicon Sequencing of Chikungunya Virus Using Oxford Nanopore Technology.

Francesco Branda·Massimo Ciccozzi·Fabio Scarpa
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Abstract

This protocol provides a comprehensive, step-by-step workflow for whole-genome sequencing of Chikungunya virus (CHIKV) using an amplicon-based strategy optimized for Oxford Nanopore Technologies (ONT) platforms. The procedure includes detailed instructions for sample handling, viral RNA extraction, quality control, cDNA synthesis, multiplex PCR amplification, library preparation, sequencing, and primary bioinformatic processing. The protocol is designed to maximize reproducibility across laboratories and is suitable for genomic surveillance applications, including outbreak investigation and molecular epidemiology, even when working with low-to-moderate viral loads.

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Chikungunya virusWorkflowRNA, ViralHigh-Throughput Nucleotide SequencingHumansChikungunya FeverGenome, ViralMultiplex Polymerase Chain ReactionWhole Genome SequencingComputational BiologyAmplicon-based sequencingGenomic surveillanceMolecular epidemiologyMultiplex PCRNext-generation sequencingOxford Nanopore TechnologiesProtocolViral RNAWhole-genome sequencingJournal Article

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Francesco Branda, Massimo Ciccozzi, Fabio Scarpa. 2027. Workflow for Long-Read Amplicon Sequencing of Chikungunya Virus Using Oxford Nanopore Technology.. https://doi.org/10.1007/978-1-0716-5496-5_24

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