Case report on the identification of whole genome sequence of chikungunya virus using probe-capture metagenomics sequencing from throat swab sample

Objective Exploring the feasibility of detecting chikungunya virus (CHIKV) from throat swab samples. Methods Blood and throat swab samples were collected from an imported case of Chikungunya virus infection at Beijing port in May 2025. Both samples were tested using quantitative real-time RT-PCR. Additionally, liquid-phase probe capture combined with high-throughput sequencing technology was employed for metagenomic sequencing. Bioinformatics methods were used for sequence assembly and comparison with public databases to analyze genetic characteristics. Results CHIKV nucleic acid was detected in both throat swab and blood samples by fluorescence quantitative RT-PCR, with CT values of 28 and 26 respectively. CHIKV nucleic acid sequences were also detected in both throat swab and blood samples through metagenomic sequencing..The throat swab sample yielded 6,757 CHIKV sequences with a genome coverage of 94.31%, while the blood sample yielded 9,558 CHIKV sequences with a genome coverage of 98.13%. Both samples showed nucleotide sequence homology greater than 99% with CHIKV metagenomic sequences from the National Center for Biotechnology Information (NCBI) database (accession numbers PP896918.1 and MH124579.1). Maximum likelihood phylogenetic tree analysis revealed that both samples clustered in the same branch as NCBI database sequences PP896921.1 and MW281311.1, belonging to the East/Central/South African genetic lineage (ESCA genotype). Conclusion The detection of the whole genome sequence of CHIKV in nasopharyngeal swab samples provides evidence for the laboratory diagnosis of suspected cases in populations where blood collection is challenging, such as infants and young children, using non-invasive sampling methods.