Phylogenetic analysis of complete VP1 sequences of echoviruses 11 and 6: high genetic diversity and circulation of genotypes with a wide geographical and temporal range

Abstract

Echovirus 6 (E6) and echovirus 11 (E11) are common causes of meningitis and other human diseases; they are among the most frequently isolated enteroviruses worldwide. In the present work we have studied genetic variability over the entire VP1 gene of selected isolates representing a wide geographical and temporal range. Fifty new sequences from North Africa were included, together with previously published sequences from different countries. The sequence diversity between strains of the same type was high: 22 and 30 % for E6 and E11, respectively. Phylogenetic analysis revealed five genogroups within each type, the genetic diversity within a genogroup generally being ,20 %. Some genogroups were further subdivided into genotypes, most containing isolates that had circulated over a wide geographical (several countries from different continents) and temporal (up to two decades) range. Several genotypes were also shown to co-circulate in a region during the same period of time. These features differ from other enteroviruses that divide into temporal or geographical clusters. This study reports new sequences from North Africa, updates the molecular epidemiology of E6 and E11, and proposes a new genogroup in each type. INTRODUCTIONHuman enteroviruses (HEVs) are small non-enveloped viruses with a worldwide distribution. Laboratory diagnosis of related infections currently is based on virus detection by isolation in cell culture or by direct PCR amplification from clinical samples. HEV types are identified by seroneutralization or partial sequencing of the VP1 region (Caro et al., 2001;Norder et al., 2001;Oberste et al., 1999a Oberste et al., , b, 2000Palacios et al., 2002). Similar to other RNA viruses, HEVs have a high capacity to evolve genetically. Genotypes are identified based on the genetic variability and phylogenetic relationships among isolates. The circulation of these genotypes throughout the world and over time has been studied to increase our understanding of the dynamics of their transmission, to evaluate their endemicity and to explain the extent of epidemics when they occur. Beyond type identification, sequencing of the VP1 region has also proved to be a reliable method for such molecular epidemiological studies.Echovirus 6 (E6) and echovirus 11 (E11) are among the most commonly isolated HEVs worldwide, and are frequently associated with outbreaks and sporadic cases of aseptic meningitis, as well as with several diseases ranging from mild non-specific illness to encephalitis, paralysis, myocarditis and severe systemic infections in neonates (Abe et al., 2000;Ashwell et al., 1996;Atkinson et al., 1998;Bahri et al., 2005;Belguith et al., 2007a;Boyd et al., 1987;Cabrerizo et al., 2008;Chomel et al., 2003;Druyts-Voets, 1997;El-Sageyer et al., 1998;Joo et al., 2005;Khetsuriani et al., 2006;Mao et al., 2010;Mirand et al., 2008;Miwa & Sawatari, 1994;Somekh et al., 2001;Ventura et al., 2001). However, despite their important impact on human health, studies of the molecular epidemiology of E6 and E11 remain li...

Identification and molecular characterization of non-polio enteroviruses from children with acute flaccid paralysis in West Africa, 2013–2014

“…4). In sub-group C5, strains isolated in Senegal and Guinea clustered together with Algerian strains isolated from AFP cases in 2006 12 with a mean of 10.1% distance between each other and up to 24.4% divergence with the prototype E6 strain D’amori (group A). On the other hand, the nine E6 strains isolated in Niger clustered in sub-group C9 with strains from different countries and continents with a mean 10.8% divergence between each other and up to 23.6% divergence with the prototype (Fig.…”

Evolution of echovirus 11 in a chronically infected immunodeficient patient

“…On this and subsequent dendrograms the incremental number after the genogroup indicates the temporal order in which they were isolated. Attempts were made previously to classify EV11 isolates into genogroups [ 5 , 26 ]. The comparison of the newly sequenced isolates showed that the closest relative to our genogroup A was 1995 Tunisian isolate (HQ674714), which had 3.4–3.7% nucleotide differences with cEV11, and 5.8–8.3% with iEV11.…”

“…Previous studies found about 30% divergence between different isolates of EV11 [ 26 ]. Therefore close similarity between strains described in this study lends support to the notion that all the iEV11s isolated between 1995 and 1999 were sequentially related to four group A isolates from 1992 and 1993.…”

Molecular epidemiology of coxsackievirus type B1

“…The estimates of average evolutionary divergence of sequence pairs within genotypes varied from 0.08 % to 8.3 %, and between genotypes, from 12.1 % (between genotypes I and II) to 28.2 % (between genotypes I and V), which conformed to the generally accepted criterion for enterovirus genotype demarcation (less than 11 % nucleotide sequence variation in the VP1 region within an enterovirus genotype and more than 11 % nucleotide sequence variation in the same region between enterovirus genotypes) [22]. In the literature, different genotypes and clusters for echoviruses 3, 6, 11 and 30, coxsackievirus type B4 and B5 have been described [23][24][25][26][27][28][29].…”