Enterovirus Migration Patterns between France and Tunisia

International audienceThe enterovirus (EV) types echovirus (E-) 5, E-9, and E-18, and coxsackievirus (CV-) A9 are infrequently reported in human diseases and their epidemiologic features are poorly defined. Virus transmission patterns between countries have been estimated with phyloge-netic data derived from the 1D/VP1 and 3CD gene sequences of a sample of 74 strains obtained in France (2000-2012) and Tunisia (2011-2013) and from the publicly available sequences. The EV types (E-5, E-9, and E-18) exhibited a lower worldwide genetic diversity (respective number of genogroups: 4, 5, and 3) in comparison to CV-A9 (n = 10). The phylo-genetic trees estimated with both 1D/VP1 and 3CD sequence data showed variations in the number of co-circulating lineages over the last 20 years among the four EV types. Despite the low number of genogroups in E-18, the virus exhibited the highest number of recombi-nant 3CD lineages (n = 10) versus 4 (E-5) to 8 (E-9). The phylogenies provided evidence of multiple transportation events between France and Tunisia involving E-5, E-9, E-18, and CV-A9 strains. Virus spread events between France and 17 other countries in five continents had high probabilities of occurrence as those between Tunisia and two European countries other than France. All transportation events were supported by BF values > 10. Inferring the source of virus transmission from phylogenetic data may provide insights into the patterns of sporadic and epidemic diseases caused by EVs

Spatial diffusion events supported with BF values > 3 for echovirus 5 (A), echovirus 9 (B), echovirus 18 (C), and coxsackievirus A9 (D).

<p>The phylogenetic analyses were performed with the samples of complete or near-complete 1D/VP1 gene sequences. The countries inferred to explain the probable diffusion events and the BF values are indicated within the inset tables. The countries are listed alphabetically; the order of country names does not indicate the direction of the spatial migration. The sampling countries are indicated by full white circles. The probable spatial migration events T1 to T9 are shown. The lines connecting countries are colored according to the intensity scale (shown in panel A), which indicates increasing BF values (range from 3 to 500).</p

Genetic diversity and phylogenetic patterns of temporal and spatial distribution of coxsackievirus A9.

<p>See the legend to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145674#pone.0145674.g001" target="_blank">Fig 1</a> for detailed description. Abbreviations used: AUS, Australia; CAN, Canada; CHN, China; CUB, Cuba; FRA, France; GBR, Great Britain; IND, India; TUN, Tunisia; USA, United States of America.</p

Genetic diversity and phylogenetic patterns of temporal and spatial distribution of echovirus 5.

<p>(A) The phylogenetic tree was estimated with the complete VP1 gene sequences and used to identify genetic clusters among the E-5 sequences. Only bootstrap values of greater than 70% are shown. The genogroups were differentiated at a divergence threshold of 15% nt differences (red bar) and designated by lower case letters in grey circles. (B) The maximum clade credibility tree was inferred with a Bayesian Markov chain Monte Carlo analysis and a discrete phylogeographic model. The tree branches are colored according to the geographic location estimated with the highest probability; the color code for geographic locations is indicated in the figure. The tree nodes are colored according to the most probable geographic location and the circle size is proportional to posterior probability (pp). A node shown with an open dark circle (and letter T followed by a number) indicates transportation of a virus strain between two countries. The time to the most recent common ancestor (TMRCA) and the highest posterior probability density (HPD) intervals are indicated for the main nodes in the tree and the table. The scale at the bottom of the figure indicates calendar years. Abbreviations used: AUS, Australia; DEU, Germany; FRA, France; IND, India; KOR, Korea; TUN, Tunisia; USA, United States of America.</p

Spatial diffusion patterns assessed for echovirus 5 (A), echovirus 9 (B), echovirus 18 (C), and coxsackievirus A9 (D).

<p>The diffusion patterns were inferred through phylogenetic analyses of sequence samples derived from the 5’ part of the 1D/VP1 gene. The sampling countries are indicated with full white circles. The lines connecting countries were colored according to the intensity scales indicating increasing BF values shown within each panels. The complete lists of spatial migration events with BF values > 10 are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145674#pone.0145674.s007" target="_blank">S4 Table</a>.</p

Genetic diversity and phylogenetic patterns of temporal and spatial distribution of echovirus 18.

<p>See the legend to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145674#pone.0145674.g001" target="_blank">Fig 1</a> for detailed description. Abbreviations used: AUS, Australia; CHN, China; FRA, France; KOR, Korea; TUN, Tunisia; USA, United States of America.</p

Schematic representation of the connections between France, Tunisia, and other countries assessed with BF > 10 from the phylogenetic patterns of echovirus 5(A), echovirus 9(B), echovirus 18 (C), and coxsackievirus A9 (D).

<p>The figure summarizes the data shown in Figs <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145674#pone.0145674.g005" target="_blank">5</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145674#pone.0145674.g006" target="_blank">6</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145674#pone.0145674.s003" target="_blank">S3 Fig</a>. The connections were estimated from the complete or near-complete 1D/VP1 gene sequences (green lines) and the partial sequences derived from the 5’ (blue lines) and 3’ (red lines) part of the 1D/VP1 gene. The solid lines indicate connections between France and other countries and dashed lines those between Tunisia and other countries.</p