Phylogeographic dynamics and molecular characteristics of

Area of Science:

• Virology
• Genomics
• Molecular Evolution

Background:

• Enterovirus 71 (EV71) and coxsackievirus (CV-A16) are primary causes of hand, foot, and mouth disease (HFMD).
• Understanding the genomic diversity and evolution of EV71 is crucial for disease control.

Purpose of the Study:

• To analyze the genomic evolution and genetic events of EV71 strains in China.
• To identify new EV71 genotypes and understand their emergence mechanisms.

Main Methods:

• Analysis of full-length genomic sequences of 312 EV71 strains from China (1998-2019) and 8 reference genomes.
• Phylogenetic and phylogeographic analyses.
• Identification of natural recombination events.

Main Results:

• The predominant EV71 genotype in China is C4, with co-circulation of A, B5, C1, and C2 subgenotypes.
• A novel B6 genotype emerged in China.
• Twenty-eight natural recombination events were identified, suggesting a role in new genotype emergence.
• Non-structural proteins, particularly 3C, P2A, and RNA-dependent RNA polymerase, showed high variability.

Conclusions:

• EV71 evolution in China is characterized by prevalent C4 genotypes and the emergence of new genotypes like B6.
• Intratypic and intertypic recombination events are key drivers for the emergence of new EV71 genotypes.
• Genomic variability in non-structural proteins may influence EV71 evolution and adaptation.