Highlights
• A decade of CV-A16 molecular epidemiology in Shenzhen was analyzed.
• Bayesian methods estimated the molecular evolutionary rate of CV-A16.
• Transmission risk and evolutionary dynamics of CV-A16 in Shenzhen were assessed.
Abstract
Objectives
To investigate the epidemiological and genetic characteristics of coxsackievirus A16 (CVA16) associated with hand, foot and mouth disease (HFMD) in Shenzhen, China.
Methods
CVA16 was examined by a real-time RT-PCR method. Complete VP1 gene sequences of CVA16 strains were determined, and sequence analyses were performed using a series of bioinformatics programs.
Results
Of 6436 mild HFMD specimens collected between 2012 and 2022, 1395 (21.7%) were CVA16-positive, with annual detection rates ranging from 4.1% to 45.4% and peaking in 2018. Molecular phylogenetic analysis revealed the circulation of three CVA16 sub-genotypes (B1a, B1b and B3) in Shenzhen, China. The major sub-genotype was B1b from 2013 to 2019, while the sub-genotype B1a predominated in 2020-2022. Phylogenetic and sequence homology analyses suggested that re-emerging CVA16 B1a strains in Shenzhen originated from Vietnam and Thailand. The mean evolutionary rate of CVA16 strains circulating in Shenzhen was estimated at 3.604×10-3 substitutions per site per year. Distinct amino acid mutations in VP1 correlated with temporal shifts in Shenzhen's dominant CVA16 sub-genotypes: N14S/L23M for B1b, and T164K/V251I for the 2017–2022 re-emergent B1a.
Conclusion
In the post-EV-A71 vaccine era, CVA16 remains one of the major pathogens of HFMD in Shenzhen. Over the study period, the CVA16 sub-genotype in Shenzhen underwent a B1a→B1b→B1a turnover, which was associated with both imported lineages and local adaptive evolution. This study underscores the critical importance of continuous molecular surveillance for CVA16.
Source:
Link: https://doi.org/10.1016/j.jcv.2026.105998
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