Metagenomic and Targeted Sequencing of Imported Chikungunya Virus Cases

Objective: To verify the technical feasibility of metagenomic next-generation sequencing (mNGS) and targeted Oxford Nanopore Technology (ONT) sequencing for the genomic surveillance of imported Chikungunya virus (CHIKV), and to evaluate the complementary value of these two strategies in small-sample application scenarios. Methods: Three serum samples confirmed positive for imported CHIKV by RT-qPCR were selected. Viral genomic sequences were obtained using unbiased mNGS and argeted-amplicon-based ONT sequencing. Technical verification and assessment of the two sequencing strategies were conducted focusing on genomic coverage, sequence identity, assembly continuity, and the consistency of phylogenetic genotyping results. Results: After consensus sequence correction, near-complete CHIKV genomes were recovered from all samples. Phylogenetic analysis demonstrated that both sequencing strategies yielded consistent results in genotype determination and phylogenetic placement. Under targeted enrichment, ONT achieved continuous genomic coverage, while mNGS maintained stable sequence accuracy within an unbiased detection context. Conclusion: In small-sample case series, both mNGS and targeted ONT sequencing can support the molecular epidemiological analysis of imported CHIKV. The two strategies exhibit complementary characteristics in practical surveillance, and their result consistency can be ensured through appropriate bioinformatics correction strategies. This study aims at technical verification and does not involve a generalized performance comparison of different sequencing platforms.