Mosaic genome structure of echovirus type 30 that circulated in Taiwan in 2001

Investigating the etiologic agents of aseptic meningitis outbreak in Iranian children

Introduction:

This study aimed to determine the viral agent (s) and their genome burden associated with an aseptic meningitis outbreak that occurred in Yasuj, Iran.

Materials and Methods:

During April to August 2015, 104 CSF samples from 104 patients under 14 years old admitted to the hospital of Yasuj, Iran, with aseptic meningitis associated clinical signs were collected. 200 μl CSF specimens was prepared for DNA and RNA viral genome extraction each and then subjected to diagnostic Taq-man real time PCR assays for the present of Enteroviruses, HSV, VZV, mumps, measles and rubella in the samples.

Results:

The majority of them had experienced clinical meningitis sign. Primary laboratory differentiated tests were in favor of viral meningitis. Among a total of 104 patients diagnosed with clinically aseptic meningitis, enterovirus as the most significant viral agent was detected in 53 subjects. However, mumps, HSV and VZV, as the endemic causes of viral meningitis, were detected in 6, 6 and 2 of the affected patients. It was revealed that two HSV and one VZV affected patients were co-infected with enteroviruses. All affected children with relatively variable viral load recovered without any sequels.

Conclusion:

The present study revealed enterovirus as the main predominant cause of pediatric aseptic meningitis that broke out in Yasuj-Iran. Also, the co-circulation of mumps, HSV and VZV, as the endemic cause during the same aseptic meningitis outbreak, was demonstrated in some cases.

Use of the 5' untranslated region and VP1 region to examine the molecular diversity in enterovirus B species

Human enteroviruses evolve quickly. The 5' untranslated region (UTR) is fundamentally important for efficient viral replication and for virulence; the VP1 region correlates well with antigenic typing by neutralization, and can be used for virus identification and evolutionary studies. In order to investigate the molecular diversity in EV-B species, the 5' UTR and VP1 regions were analysed for 208 clinical isolates from a single public-health laboratory (serving New South Wales, Australia), representing 28 EV-B types. Sequences were compared with the 5' UTR and VP1 regions of 98 strains available in GenBank, representing the same 28 types. The genetic relationships were analysed using two types of software (mega and BioNumerics). The sequence analyses of the 5' UTR and VP1 regions of 306 EV-B strains demonstrated that: (i) comparing the two regions gives strong evidence of epidemiological linkage of strains in some serotypes; (ii) the intraserotypic genetic variation within each gene reveals that they evolve distinctly largely due to their different functions; and (iii) mutation and possible recombination in the two regions play significant roles in the molecular diversity of EV-B. Understanding the tempo and pattern of molecular diversity and evolution is of great importance in the pathogenesis of EV-B enteroviruses, information which will assist in disease prevention and control.

Complete genome sequence analysis of human echovirus 30 isolated during a large outbreak in Guangdong Province of China, in 2012

In May and June 2012, an outbreak of aseptic meningitis caused by Echovirus 30 (E30) occurred on a large scale in Luoding, Guangdong Province, China. Our team successfully isolated one subtype, strain 2012EM161, and its complete genome was sequenced. The phylogenetic tree of viral protein (VP) 1 gene sequences showed that the viral isolate was similar to the E30 strain prevalent in Fujian (2011), with identity of 98.05–99.32 % and 98.63–99.32 % for nucleotides and amino acids respectively. Whole genome-based phylogenetic analysis indicated that 2012EM161 contained the most proximate consensus to DQ246620 (Zhejiang, 2003) and FDJS03 (AY948442, Jiangsu, 2005), with nucleotide homogeneity of 87.09 % and 86.98 % respectively. The RDP4.16 and Simplot analysis showed that the newly discovered 2012EM161 was probably a recombinant, which was closely related to the strain of E30 (DQ246620) in the first half of the genome and the strain of E6 (JX976771) in genomic P3 region. The whole genome sequence of 2012EM161 will allow further study of the origin, evolution, and the molecular epidemiology of E30 strains.

Molecular epidemiology of Echovirus 30 in Taiwan, 1988-2008

To investigate the molecular epidemiology of Taiwanese Echovirus 30 (E-30) strains, we analyzed the 876 bp sequence of the VP1 gene from 32 Taiwanese strains isolated in 1988-2008, 498 reference sequences, and one Echovirus 21 strain as the out-group. Phylogenetic analysis detected six E-30 genotypes (designated GI-GVI) that had circulated globally during the past five decades. The genotypes varied widely in geographic distribution and circulation half-life. The GI, GII, and GV were ancient genotypes in which the first strains emerged in the 1950s. The GIII was a reemerging genotype, in which strains had first appeared in Colombia in 1995 before reemerging in the New Independent States (NIS) in 2003. The GIV, an emerging genotype that recently appeared in Asia in 2003, was closely related to the ancient genotypes. The GVI was the circulating genotype, which included eight clusters (A-H) that had circulated since 1967. No GVI-A, C, D, or E strains have been identified during the past 10 years. The GVI-B first appeared in China in 1984 and later in Russia and Asia in the 2000s. The GVI-F, G, and H strains, which comprised the prevalent clusters, had been dominant in Asia Pacific area, globally, and Europe, respectively. Taiwanese strains were classified into GVI-D (1988-1989), GVI-F (1993-2004), and GVI-G (1993-2008). The quiescence period of E-30 is longer in Taiwan (5-8 years) than in other countries (3-5 years).

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.

Phylogenetic analysis of Echovirus 30 isolated during the 2005 outbreak in France reveals existence of multiple lineages and suggests frequent recombination events

BACKGROUND

Echovirus 30 (E-30) was responsible in France for a major aseptic meningitis outbreak during 2005 summer season. However, the virological mechanisms responsible for the periodic emergence of the epidemic strains remain to be investigated.

OBJECTIVES

To assess the genetic diversity of two genome regions, VP1 and 3Dpol, of echovirus 30 strains isolated during the 2005 aseptic meningitis outbreak in Champagne Ardenne (CA) area (France).

STUDY DESIGN

Partial VP1 genomic region of 23 E-30 strains isolated in CA was sequenced and compared with 73 E-30 strains originating from different French areas to estimate the number and the diversity of E-30 lineages. Partial sequences for 3D polymerase (3Dpol) were analyzed to detect potential recombination events within the non-structural (NS) region of the genome of EV neurotropic strains.

RESULTS

Phylogenetic analysis of the VP1 evidenced the co-circulation of 6 distinct E-30 lineages responsible for the 2005 aseptic meningitis outbreak in France of which three had co-circulated in CA. Partial sequencing of the 3Dpol coding region showed that all of the E-30 strains exhibited different phylogenetic links between VP1 and 3Dpol genomic regions, suggesting multiple intra- or inter-serotypic recombination events within the NS part of the genome.

CONCLUSIONS

Our findings revealed existence of multiple lineages and suggested frequent recombination events among E-30 strains having co-circulated in a restricted area during a short time outbreak period. Moreover, our data demonstrated that study of single VP1 genome region analysis could not accurately describe the phylogenetic origin of E-30 isolates.

Transmission networks and population turnover of echovirus 30

Globally, echovirus 30 (E30) is one of the most frequently identified enteroviruses and a major cause of meningitis. Despite its wide distribution, little is known about its transmission networks or the dynamics of its recombination and geographical spread. To address this, we have conducted an extensive molecular epidemiology and evolutionary study of E30 isolates collected over 8 years from a geographically wide sample base (11 European countries, Asia, and Australia). 3Dpol sequences fell into several distinct phylogenetic groups, interspersed with other species B serotypes, enabling E30 isolates to be classified into 38 recombinant forms (RFs). Substitutions in VP1 and 3Dpol regions occurred predominantly at synonymous sites (ratio of nonsynonymous to synonymous substitutions, 0.05) with VP1 showing a rapid substitution rate of 8.3 x 10(-3) substitutions per site per year. Recombination frequency was tightly correlated with VP1 divergence; viruses differing by evolutionary distances of >0.1 (or 6 years divergent evolution) almost invariably (>97%) had different 3Dpol groups. Frequencies of shared 3Dpol groups additionally correlated with geographical distances, with Europe and South Asia showing turnover of entirely distinct virus populations. Population turnover of E30 was characterized by repeated cycles of emergence, dominance, and disappearance of individual RFs over periods of 3 to 5 years, although the existence and nature of evolutionary selection underlying these population replacements remain unclear. The occurrence of frequent "sporadic" recombinants embedded within VP1 groupings of other RFs and the much greater number of 3Dpol groups than separately identifiable VP1 lineages suggest frequent recombination with an external diverse reservoir of non-E30 viruses.

Characterization of the genome of human enteroviruses: design of generic primers for amplification and sequencing of different regions of the viral genome

Human enteroviruses are among the most common viruses infecting humans and can cause diverse clinical syndromes ranging from minor febrile illness to severe and potentially fatal diseases. Biodiversity and evolution of human enterovirus genomes are shaped by frequent recombination events. Therefore, identification and characterization of circulating strains of enteroviruses require partial determination of different genomic regions. The development is described of a simple method allowing amplification and partial sequencing of the P1, P2 and P3 genomic regions of field human enterovirus strains isolated in cell cultures, by performing PCR on cDNAs generated through a single RT reaction. A set of generic primers were designed and tested on a panel of 90 field and prototype viruses belonging to the five species of human enteroviruses. This assay was shown to amplify efficiently the targeted regions of all the 90 genomes tested. The generated amplicons were sequenced successfully without the need for gel purification. This assay could be a valuable tool for laboratories interested in molecular epidemiology and evolution studies implicating a great number of human enterovirus strains isolated from human or environmental samples.