Molecular evolution of types in non-polio enteroviruses

Area of Science:

• Virology
• Molecular Evolution
• Genetics

Background:

• Non-polio enteroviruses are diverse RNA viruses with over 100 known types, and new ones emerge regularly.
• The evolutionary mechanisms driving the emergence of novel enterovirus types remain poorly understood.
• Understanding enterovirus evolution is critical for public health and diagnostics.

Purpose of the Study:

• To investigate common evolutionary trends among non-polio enterovirus types using molecular clock analysis.
• To determine the approximate emergence times of contemporary enterovirus types.
• To evaluate the validity of current criteria for enterovirus type and genotype identification.

Main Methods:

• Bayesian coalescent molecular clock analysis of 35,629 partial VP1 sequences from 33 enterovirus types.
• Phylogenetic analysis to infer evolutionary history and population dynamics.
• Analysis of 2,657 complete VP1 sequences from 24 types to assess sequence identity thresholds for classification.

Main Results:

• Inferred substitution rates varied from 0.41x10^-2 to 3.07x10^-2 substitutions per site per year.
• The most recent common ancestors for known isolates of each type likely existed 55-200 years ago.
• Contemporary enterovirus types appear to have emerged within the last millennium, with evidence of population bottlenecks.

Conclusions:

• The 75% nucleotide sequence identity criterion for enterovirus type identification is generally valid but may need refinement.
• Amino acid sequence analysis, alongside nucleotide data, is recommended for accurate type identification due to potential drift beyond thresholds.
• Genotype identification using sequence identity is rational for some types, but distinct cut-offs (9-20%) are necessary for different types.