Epidemiological surveillance and genomic analysis of imported chikungunya virus at Shenzhen Port, China, 2014-2025

This study aimed to characterize the epidemiological features of imported chikungunya virus (CHIKV) cases at Shenzhen Port during 2014-2025 and to investigate the genomic evolution of isolates from key years (2018, 2024, and 2025).

Surveillance was conducted at Shenzhen Port from 2014 to 2025, among travelers presenting with fever or arthralgia. Serum specimens were tested by real-time RT-PCR; whole-genome sequencing (WGS) was performed on a subset of RT-PCR-positive samples from selected years (2018, 2024, and 2025), chosen based on sample quality and availability, while archived specimens from other periods did not meet sequencing requirements. Phylogenetic and mutational analyses were conducted on these sequenced isolates to characterize viral genotypes and genetic variations.

Among 16,577 suspected cases, 52 were positive for CHIKV (0.31%). Most originated from Southeast Asia (50.0%, mainly Myanmar, India, Thailand) and East Asia (40.4%, mainly Hong Kong SAR and mainland China). Genomic analysis of 29 sequenced isolates (from 2018, 2024, and 2025) showed that most isolates belonged to the East/Central/South African (ECSA) lineage, with one isolate from 2018 clustering within the Asian lineage. The E1-A226V mutation was observed in multiple ECSA strains.

These findings suggest ongoing importation of CHIKV at Shenzhen Port and indicate that incorporating genomic analysis into routine surveillance may improve risk assessment at international ports of entry.