Coxsackievirus A6 was the Predominant Pathogen of Hand, Foot, and Mouth Disease with Frequent Recombination and Mutations in Shandong Province, 2023

Abstract Background The pathogens of hand, foot, and mouth disease are changing, with CV-A6 becoming the predominant one and evolving rapidly. Methods We collected data on monthly HFMD infections per county and related demographic variables in Shandong Province, China, during 2023. Viruses were isolated and sequenced for further bioinformatics analysis. An epidemiological follow-up study in Jinan city was conducted to explore the relationship between onychomadesis and CV-A6. The risk factors of atypical skin lesions were analyzed using binary logistic regression models. Results Totally 47, 396 cases were clinically diagnosed as HFMD, among which 9543 samples were collected and 7133(74.75%) were laboratory-confirmed EV-positive cases. CV-A6 became the predominant pathogen (5993, 84.02%). Forty-six representative CV-A6 strains were successfully isolated, by successfully constructing a novel amplicon-based NGS method, fully genome of the 46 strains were sequenced. All strains belonged to the D3c sub-genotype. A new recombination lineage emerged with 3 specific amino acid mutations in P3 region. Fourteen amino acid sites in P3 coding region and three in VP1 coding region were identified as highly variable amino acid sites. On the whole, viral evolution was predominantly driven by negative selection. Three amino acid sites in VP1 coding region and one in P3 coding region were under positive selection. Among which P3-551 was both the highly variable amino acid site as well as underwent positive selection pressure. CV-A6 strains in Shandong, 2023 may have originated from Southwest China lineages, which emerged from Vietnam. CV-A6 was the primary pathogen of onychomadesis and atypical skin lesions. The increase in age, male individuals, living in suburban areas, with fever and respiratory symptoms were significant risk factors for atypical skin lesions. Conclusion In 2023, CV-A6 was the predominant pathogen of HFMD in Shandong and underwent rapid evolution with frequent recombination and mutations. Therefore, surveillance for disease prevention and control should be strengthened.