Recombination strategies and evolutionary dynamics of the Human enterovirus A global gene pool

Abstract

We analysed natural recombination in 79 Human enterovirus A strains representing 13 serotypes by sequencing of VP1, 2C and 3D genome regions. The half-life of a non-recombinant tree node in coxsackieviruses 2, 4 and 10 was only 3.5 years, and never more than 9 years. All coxsackieviruses that differed by more than 7 % of the nucleotide sequence in any genome region were recombinants relative to each other. Enterovirus 71 (EV71), on the contrary, displayed remarkable genetic stability. Three major EV71 clades were stable for 19-29 years, with a half-life of non-recombinant viruses between 13 and 18.5 years in different clades. Only five EV71 strains out of over 150 recently acquired non-structural genome regions from coxsackieviruses, while none of 80 contemporary coxsackieviruses had non-structural genes transferred from the three EV71 clades. In contrast to earlier observations, recombination between VP1 and 2C genome regions was not more frequent than between 2C and 3D regions.

Two Genotypes of Coxsackievirus A2 Associated with Hand, Foot, and Mouth Disease Circulating in China since 2008

“…Recombination is a well-known phenomenon among EVs [24–26], and our finding reaffirmed this conclusion. Previous studies have indicated that recombination between different serotypes may occur when different viruses infect and replicate in the same cell, and that recombination usually occurs among EV serotypes within a species [5, 27].…”

“…Recombination plays an important role in the emergence of the genetic diversity of EVs, including CV-A2 [24, 25]. Some clinical observations showed that infection with the recombinant CV-A6 virus was associated with different clinical features from on generalized rash [28, 29].…”

Circulation of two Enterovirus C105 (EV-C105) lineages in Europe and Africa

“…2c). As observed previously for EV-D111 (Harvala et al, 2011), EV-71 (Lukashev et al, 2014;McWilliam Leitch et al, 2012) and for HEV-B (Lindberg et al, 2003), phylogenetic incongruences in the VP1 and 3Dpol regions are indicative of recombination events. Minor inconsistencies in the clustering pattern of EV-C105 in the capsid region (P1) and noncapsid region (P3) suggest that a recombination event may have occurred in EV-C105 group B viruses.…”

Analysis of an echovirus 18 outbreak in Thuringia, Germany: insights into the molecular epidemiology and evolution of several enterovirus species B members

“…Lukashev et al published a similar study for human enterovirus species A including various EV-A71 isolates. Thereby, the existence of three stable groups of EV-A71 was demonstrated [31]. Here, we define an EV recombination group (recogroup) by co-clustering of VP1 and 3D sequences in the respective phylogenetic trees.…”