Molecular Epidemiology Analysis of Imported Chikungunya Virus Cases Based on Second- and Third-Generation Sequencing

Objective: This study aimed to analyze the molecular epidemiological characteristics of imported Chikungunya virus (CHIKV) infections identified during port surveillance and to evaluate the consistency and complementarity of second-generation metagenomic next-generation sequencing (mNGS) and third-generation Oxford Nanopore Technologies (ONT) sequencing in real-world monitoring scenarios. Methods: Three CHIKV-positive serum samples, confirmed by RT-qPCR, were selected as a case series. Viral genomic sequences were obtained using mNGS and amplicon-based ONT sequencing. Sequencing data were assessed for quality, genome coverage, variant distribution, and phylogenetic relationships. Cross-platform concordance was used as an internal validation for molecular epidemiological interpretation. Results: Both sequencing approaches successfully generated near-complete CHIKV genomes and produced highly consistent typing and source-tracing results in phylogenetic analyses. ONT sequencing demonstrated superior performance in genome continuity and coverage of complex regions, identifying more potential variant sites, whereas mNGS exhibited greater stability at the amino acid level. Despite differences in the number of detected variants between platforms, sample origin determination and phylogenetic placement remained highly concordant. Conclusion: This case-oriented study indicates that both second- and third-generation sequencing can reliably support molecular epidemiological investigations of imported CHIKV infections. mNGS and ONT each offer distinct advantages and can be strategically combined in practical applications to achieve efficient and precise molecular surveillance and source tracing of CHIKV.