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. 2016 Sep;54(9):2306-14.
doi: 10.1128/JCM.00207-16. Epub 2016 Jun 29.

Newly Identified Enterovirus C Genotypes, Identified in the Netherlands through Routine Sequencing of All Enteroviruses Detected in Clinical Materials from 2008 to 2015

Coretta C Van Leer-Buter  1 , Randy Poelman  2 , Renze Borger  2 , Hubert G M Niesters  2
Affiliations

Newly Identified Enterovirus C Genotypes, Identified in the Netherlands through Routine Sequencing of All Enteroviruses Detected in Clinical Materials from 2008 to 2015

Coretta C Van Leer-Buter et al. J Clin Microbiol. 2016 Sep.

Abstract

Enteroviruses (EVs) are a group of human and animal viruses that are capable of causing a variety of clinical syndromes. Different genotypes classified into species can be distinguished on the basis of sequence divergence in the VP1 capsid-coding region. Apparently new genotypes are discovered regularly, often as incidental findings in studies investigating respiratory syndromes or as part of poliovirus surveillance. Recently, some EVs have become recognized as significant respiratory pathogens, and a number of new genotypes belonging to species C have been identified. The circulation of these newly identified species C EVs, such as EV-C104, EV-C105, EV-C109, and EV-C117, nevertheless appears to be limited. In this report, we show the results of routine genotyping of all enteroviruses detected in our tertiary care hospital between January 2008 and April 2015. We detected 365 EVs belonging to 40 genotypes. Interestingly, several newly identified species C EVs were detected during the study period. Sequencing of the 5' untranslated region (5' UTR) of these viruses shows divergence in this region, which is a target region in many detection assays.

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Figures

FIG 1
FIG 1
Enterovirus genotypes detected in this study per clinical material from which they were isolated. E, echovirus; EV, enterovirus; CV, coxsackievirus; CSF, cerebrospinal fluid.
FIG 2
FIG 2
Age distribution of the enterovirus genotypes detected in cerebrospinal fluid. E, echovirus; EV, enterovirus; CV, coxsackievirus.
FIG 3
FIG 3
Age distribution of the enterovirus genotypes detected in respiratory materials. E, echovirus; EV, enterovirus; CV, coxsackievirus.
FIG 4
FIG 4
Neighbor-joining phylogeny showing the relationships among the 6 EV-C109 strains from this study (A) as well as the 6 strains that are available in GenBank, based on the alignment of and partial VP1 (322 to 325 nucleotides [nt]) sequences. (B) The neighbor-joining phylogenetic relationships among the 4 CV-A21 strains from this study and reference strains from GenBank. Trees were constructed using BioNumerics software. Bootstrap values (percentage of 1,000 pseudoreplicate data sets) are shown at the nodes. Bars represent the genetic distance. A strain name indicates a GenBank accession number/country or area/year of isolation. GRO, these sequences have been identified as part of this present study. Bar, nucleotide distance as substitutions per site.
FIG 5
FIG 5
Phylogenetic relationships based on partial VP1 sequences (A) and 5′-UTR sequences (B) of the EV-C isolates from this study, identified by GRO (yellow dots), compared with prototype strains of EV-A, EV-B, EV-C, EV-D, and rhinovirus (RV)-A, RV-B, and RV-C (green dots). Relationships were constructed using the neighbor-joining algorithm. Genotype and country of isolation of each reference strain are indicated. Bootstrap values (percentage of 1,000 pseudoreplicate data sets) are shown at the nodes. Bar, nucleotide distance as substitutions per site.
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References

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