Molecular evolution of types in non-polio enteroviruses

Abstract

Non-polio enteroviruses are a ubiquitous and divergent group of non-enveloped RNA viruses. Novel types are reported regularly in addition to over 100 known types; however, mechanisms of emergence of novel types remain obscure. Here, the 33 most common types represented by 35-629 non-redundant partial VP1 sequences in GenBank were studied in parallel using Bayesian coalescent molecular clock analysis to investigate common evolutionary trends among enterovirus types. Inferred substitution rates were in the range of 0.41×10 to 3.07×10 substitutions per site per year. The most recent common ancestors of known isolates of each type presumably existed between 55 and 200 years ago. Phylogenetic analysis results suggested that global type populations underwent bottlenecks that could repeatedly reset the common ancestor dates. Nevertheless, species-level analysis suggested that the contemporary enterovirus types emerged within the last millennium. Analysis of 2657 complete VP1 sequences of the 24 most common types indicated that the type criterion based upon 75 % nucleotide sequence identity remains generally valid, despite exponential growth of the number of known sequences and a high rate of mutation fixation. However, in few types there was evidence that enteroviruses can drift slightly beyond the type threshold, up to 73 % identity, and both amino acid and nucleotide sequences should be considered for type identification. Analysis of sequence distances within types implied that sequence-identity-based identification of genotypes is rational within some, but not all, types and distinct genotype cut-offs (9-20 %) may be useful for different types.

Prisoners of war — host adaptation and its constraints on virus evolution

“…27 ), but could poliovirus have existed in the 14th century bc? By conventional extrapolation, the emergence of the Enterovirus C species (to which poliovirus belongs) would be dated to only a few hundred years ago 28 and not >3,000 years ago.…”

Metagenomic next-generation sequencing of samples from pediatric febrile illness in Tororo, Uganda

“…Within the species rhinovirus, we assembled de novo a total of 13 HRV-C (mean coverage: 39-fold) and 13 HRV-A (mean coverage: 268-fold) genomes (> 500 bp). Of these, 10 HRV-A and nine HRV-C genomes had complete coverage of the VP1 region, which is used to define enterovirus types [28]. Unique HRV types are defined by <73% similarity in the VP1 gene.…”

Molecular epidemiology and phylogenetics of human enteroviruses: Is there a forest behind the trees?

“…Non‐polio enteroviruses accumulate substitutions at a comparable rate, probably slightly slower. In most types, the rates (Table ) were in the range of 0.6 to 1.2 × 10 −2 substitutions per site per year (s/s/y) . The rate estimates are in general fairly reproducible between different studies but can vary between genotypes of a type .…”

“…In most types, the rates (Table 3) were in the range of 0.6 to 1.2 × 10 −2 substitutions per site per year (s/s/y). 38,50 The rate estimates are in general fairly reproducible between different studies but can vary between genotypes of a type. 59 It is important that the genetic distance (the number of substitutions) reflect the cumulative time between a common ancestor and each of two viruses.…”

“…60 Analysis of the most common types showed that many types probably underwent global population bottlenecks over the last 70 years. 38 Global enterovirus populations therefore exist as global gene pools and may regularly undergo near-complete extinction. On the other hand, there is no evidence that any EV type ever became completely extinct over the last 60 years, as even rare types are still found in circulation when thousands of virus samples are screened.…”