Abstract
Objectives: The molecular characteristics of enterovirus (EV) circulating in Linyi remain unclear following the relaxation of COVID-19 control policies in December 2022. This study aims to clarify the EV spectrum and genetic features in Linyi during 2023–2024, providing a reference for future surveillance and prevention of EV infections. Methods: Pediatric patients with suspected EV infection were enrolled, and throat swabs were collected. RT-qPCR was used to detect EV, and positive samples were further typed by semi-nested PCR. The genomes of each EV-A serotype were amplified and sequenced for molecular characteristic analysis. Phylogenetic trees were constructed based on the VP1 gene, whole genome, P1, P2, and P3 regions using the Neighbor-Joining method. Recombination events among the strains identified in Linyi were analyzed using RDP4 and SimPlot. Results: Among 806 suspected cases of enterovirus infection, 565 (70.1%) were positive. Of these positive cases, 427 (75.6%) were identified as EV-A. Five EV-A serotypes were identified, including coxsackievirus A4 (CVA4), A5 (CVA5), A6 (CVA6), A10 (CVA10), and A16 (CVA16). The predominant serotype shifted from CVA6 in 2023 to CVA4 and CVA16 in 2024. The CVA4, CVA5, CVA6, and CVA10 strains identified in Linyi belonged to genotypes (subgenotypes or clades) C2, D, D3a, and C2, respectively. The CVA16 strains identified in Linyi were assigned to clades B1b and B1c. Additionally, a local recombination event between CVA5 and CVA6 was identified. Conclusions: After the relaxation of COVID-19 control policies, multiple EV-A serotypes, including CVA4, CVA5, CVA6, CVA10, and CVA16, have been circulating in Linyi. The B1c clade of CVA16 was identified in Shandong Province for the first time. A local recombination event was detected among some strains in Linyi. The epidemiology of EV in Linyi has changed, and it is necessary to monitor these strains for their potential to cause outbreaks or severe disease. Supplementary Information: The online version contains supplementary material available at 10.1186/s12879-026-12710-2.