Genetic variation and evolutionary characteristics of Echovirus 11: new variant within genotype D5 associated with neonatal death found in China

Abstract

Echovirus 11 (E11) has gained attention owing to its association with severe neonatal infections. From 2018 to 2023, a surge in severe neonatal cases and fatalities linked to a novel variant of genotype D5 was documented in China, France, and Italy. However, the prevention and control of E11 variants have been hampered by limited background data on the virus circulation and genetic variance. Therefore, the present study investigated the circulating dynamics of E11 and the genetic variation and molecular evolution of genotype D5 through the collection of strains from the national acute flaccid paralysis (AFP) and hand, foot, and mouth disease (HFMD) surveillance system in China during 2000-2022 and genetic sequences published in the GenBank database. The results of this study revealed a prevalent dynamic of E11 circulation, with D5 being the predominant genotype worldwide. Further phylogenetic analysis of genotype D5 indicated that it could be subdivided into three important geographic clusters (D5-CHN1: 2014-2019, D5-CHN2: 2016-2022, and D5-EUR: 2022-2023). Additionally, variant-specific (144) amino acid mutation sites and positive-selection pressure sites (132, 262) were identified in the VP1 region. Cluster-specific recombination patterns were also identified, with CVB5, E6, and CVB4 as the major recombinant viruses. These findings provide a preliminary landscape of E11 circulation worldwide and basic scientific data for further study of the pathogenicity of E11 variants.

Keywords: Echovirus 11; Enterovirus; gene recombination; molecular epidemiology; variants; virus evolution; virus transmission.

Figure 1.

Phylogenetic tree constructed using the maximum likelihood method based on datasets of echovirus 11 (E11) VP1 region sequences. The circle is segmented into four layers to represent distinct information. The innermost layer uses leaf colours to denote the region of strain origin. The second layer primarily contains strain labels. Strain names highlighted in red signify their origin from China. The third layer displays the collection year of strains, while the outermost layer presents genotype distribution.

Figure 2.

Chronological, geographical, and genotypic distribution of globally circulating echovirus 11 (E11) strains. (A) Pie chart showing the genotypic distribution of E11 across regions, with the size of the pie chart proportional to the number of detected E11 strains. (B) Histogram illustrating the detection years and genotype distribution of globally prevalent E11 strains. Below the histogram, the graph depicts the span of detection years within each genotype, with the numbers within the circles indicating the number of countries per year and the total number (purple circles) of each genotype.

Figure 3.

Maximum clade credibility tree with temporal phylogenies and evolutionary characteristics for echovirus 11 (E11) genotype D5 based on the VP1 region of representative strains. (A) The scatter plot on the left side displays the outcomes of root-to-tip regression analysis. The trend diagram below the picture represents the Bayesian skyline plot (BSP) output. The height of the curve within the diagram indicates genetic diversity. Significant time to the most recent common ancestor (TMRCA) points are highlighted for reference. (B) Spatial transmission routes of genotype D5 based on Bayesian phylogeographic inference. The line thickness indicates the migration rate, while the line colour represents the support rate of the Bayes factor. The colours at both ends of the line symbolize the direction of transmission.

Figure 4.

Analysis of the genetic variance of the VP1 sequence of genotype D5. (A) Gene diversity at single amino acid sites. (B) Left: site of positive selection pressure (blue) and high variation (red), determined via entropy value analysis with a threshold value of 0.6. Right: significant amino acid mutation sites involved in clusters. (C) Left: 6LA6 as a model to illustrate the distribution of each amino acid site in E11 virus particles. VP1 protein is represented in purple and VP2 protein in orange. Right: a model showing the potential interaction between amino acid site 262 and the FcRn receptor.

Figure 5.

Recombination patterns among different clusters of genotype D5. (A) Left: phylogenetic tree constructed based on the whole genome. Right: recombination pattern of D5-CHN1 and D5-CHN2. (B) Similar results generated using Simplot software.