Characterizing enterovirus C96 genome and phylodynamics analysis.

Area of Science:

• Virology
• Molecular Epidemiology
• Genomics

Background:

• Enterovirus C96 (EV-C96) is a recently identified serotype within the Enterovirus C species.
• EV-C96 has been detected in diverse clinical and environmental samples, including those from patients with acute flaccid paralysis and hand, foot, and mouth disease.
• Limited full-length genome data has hindered comprehensive molecular epidemiological studies of EV-C96.

Purpose of the Study:

• To conduct comprehensive molecular epidemiological analyses of EV-C96 using newly collected and existing genomic data.
• To investigate the genetic diversity, evolutionary rate, and potential recombination events of EV-C96.
• To provide valuable genomic data for future global EV-C96 research.

Main Methods:

• Whole genome sequencing and analysis of rare EV-C96 strains collected in China (1997-2020).
• Comparative sequence analysis with existing EV-C96 genomes from GenBank.
• Phylogenetic analysis to determine genetic variation, evolutionary rate, and the most recent common ancestor (MRCA).
• Recombination analysis to identify potential origins of EV-C96.

Main Results:

• EV-C96 exhibits significant genetic variation, with nucleotide and amino acid similarities to the prototype strain ranging from 75%-81.8% and 85%-94.9%, respectively.
• Fifteen distinct genogroups were identified within EV-C96.
• The mean evolutionary rate was estimated at 5.16 × 10^-3 substitutions/site/year, with an MRCA dated to 1925.
• Recombination analysis suggests EV-C96 may be a recombinant strain within the EV-C group, particularly in the nonstructural protein coding region.

Conclusions:

• EV-C96 possesses high genetic diversity and a complex evolutionary history.
• The findings indicate a potential recombinant origin for EV-C96, likely involving other Enterovirus C serotypes.
• This study significantly expands the genomic database for EV-C96, offering critical insights for global molecular epidemiology and public health surveillance.