# Comparative Analysis of Next- and Third-Generation Sequencing Platforms for Chikungunya Virus Whole-Genome Sequencing Using a Lineage-Inclusive Primer Set During the 2025 Foshan Outbreak

## TL;DR

This study compares sequencing technologies for tracking the Chikungunya virus during an outbreak and introduces a new primer set that works across virus lineages.

## Contribution

A lineage-inclusive primer set and direct comparison of NGS and TGS for CHIKV whole-genome sequencing during an outbreak.

## Key findings

- Illumina NGS showed higher raw read accuracy, while Nanopore TGS provided better UTR coverage and faster processing.
- After polishing, variant calls from both sequencing platforms were fully concordant.
- Phylogenetic analysis suggested a single introduction event linking the Foshan outbreak to strains from Réunion Island.

## Abstract

Chikungunya virus (CHIKV) poses an increasing global public health threat, as evidenced by the significant 2025 Foshan outbreak in China. Rapid, whole-genome sequencing (WGS) is critical for outbreak response but is challenged by primer mismatches across diverse lineages and a lack of direct sequencing platform comparisons. To address this, we developed a novel lineage-inclusive primer set and performed parallel WGS on 24 clinical samples from the outbreak using both Illumina (NGS) and Oxford Nanopore Technologies (TGS) platforms. Our lineage-inclusive primer set successfully amplified full-length CHIKV genomes across all samples. Comparisons revealed that Illumina NGS provided higher raw read accuracy, while Nanopore TGS achieved more complete coverage of terminal UTRs with a faster turnaround time. Crucially, after polishing, variant calls between the two platforms were 100% concordant. Phylogenetic analysis was consistent with a single introduction event, with all outbreak isolates forming a monophyletic clade within the ECSA lineage most closely related to contemporaneous strains from Réunion Island. This study validates a lineage-inclusive amplicon-based sequencing strategy and demonstrates that NGS and TGS offer complementary advantages. When integrated, they provide a robust framework for real-time genomic surveillance, enhancing preparedness and guiding public health interventions against CHIKV.