Repeated genomic transfers from echovirus 30 to echovirus 6 lineages indicate co-divergence between co-circulating populations of the two human enterovirus serotypes.
Human echovirus types 6 (E-6) and 30 (E-30) cause seasonal epidemics of aseptic meningitis. These two enteroviruses are frequently observed in co-circulation, an epidemiological pattern that is prerequisite for the occurrence of dual infections, which can lead to recombination between co-infecting virus strains. Viral sequences were determined at loci 1D (VP1 capsid protein) and 3CD (non structural proteins) in 49 E-6 strains recovered in a single geographical region in France from 1999 to 2007, during the epidemiological survey of enterovirus infections. They were compared with previously recorded sequences of E-30 strains to investigate their evolutionary histories and possible recombination patterns. Phylogenetic analyses identified two distinct E-6 populations and different subpopulations. Assuming a relaxed molecular clock model and a Bayesian skyline demographic model in coalescent analyses with the BEAST program, the substitution rate in E-6 was estimated at 8.597×10(-3) and 6.252×10(-3) substitution/site/year for loci 1D and 3CD respectively. Consistent estimates of divergence times (t(MRCA)) were obtained for loci 1D and 3CD indicating that two distinct E-6 populations originated in 1997 and 1999. Incongruent phylogenetic patterns inferred for the two loci were indicative of recombination events between the two populations. Phylogenies including the E-30 3CD sequences showed close genetic relationships between E-6 and discrete E-30 subpopulations. Recombination breakpoints were located with statistical significance in E-6 and E-30 genomes. Estimates of t(MRCA) of phylogenetic recombinant clades indicated directional genetic transfers from E-30 to E-6 populations and their co-divergence over the time period studied.
Bailly
J-L
JL
Clermont Université, Université d'Auvergne, EA 3843, BP 10448, F-63000 Clermont-Ferrand, France. j-luc.bailly@u-clermont1.fr
Mirand
A
A
Henquell
C
C
Archimbaud
C
C
Chambon
M
M
Regagnon
C
C
Charbonné
F
F
Peigue-Lafeuille
H
H
D001483:Base Sequence; D001499:Bayes Theorem; D036022:Capsid Proteins / Q000235:genetics; D004458:Echovirus 6, Human / Q000235:genetics*; D004457:Echovirus Infections / Q000453:epidemiology / Q000635:transmission / Q000821:virology*; D029822:Enterovirus B, Human / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D005602:France; D022761:Gene Transfer, Horizontal; D016679:Genome, Viral; D005838:Genotype; D006801:Humans; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D010447:Peptide Hydrolases / Q000235:genetics; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D012703:Serotyping
D036022:Capsid Proteins; D010447:Peptide Hydrolases