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Intertypic recombination of human parechovirus 4 isolated from infants with sepsis-like disease
Pekka Kolehmainen1, Anu Siponen2, Teemu Smura3
1Department of Virology, University of Turku, Kiinamyllynkatu 13, 20520, Turku, Finland; Department of Virology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 3, 00290, Helsinki, Finland.
Insights
Human parechoviruses (HPeVs) are common in children. Genetic analysis reveals intertypic recombination in HPeV-4 strains, suggesting frequent recombination events in parechovirus evolution.
Area of Science:
- Virology
- Molecular Biology
- Evolutionary Genetics
Background:
- Human parechoviruses (HPeVs) are prevalent pediatric pathogens.
- Research on HPeV genetic diversity and evolution is limited.
- HPeVs belong to the Picornaviridae family.
Purpose of the Study:
- To investigate the phylogenetic relationships of HPeV-4 isolates from Finnish children.
- To identify potential recombination events in HPeV evolution.
- To analyze the genetic diversity of HPeV.
Main Methods:
- Sequencing of complete coding regions of three HPeV-4 isolates.
- Phylogenetic analysis using complete genome sequences from GenBank.
- Recombination analysis using similarity plot and bootscanning methods.
Main Results:
- HPeV-4 isolates showed high nucleotide similarity (99.8%).
- Capsid genes clustered with HPeV-4, but non-structural genes (2A-3C) showed mixed clustering with HPeV-1, HPeV-3, and some HPeV-4 strains.
- Phylogenetic analysis and recombination scans confirmed intertypic recombination events in HPeV-4 evolution.
Conclusions:
- Intertypic recombination has occurred in the evolution of HPeV-4.
- Frequent intratypic recombination is suggested among parechoviruses.
- Limited availability of parechovirus genomes hinders precise identification of recombination partners.
Background:
Human parechoviruses (HPeVs) (family Picornaviridae), are common pathogens in young children. Despite their high prevalence, research on their genetic identity, diversity and evolution have remained scarce.
Objectives:
Complete coding regions of three previously reported HPeV-4 isolates from Finnish children with sepsis-like disease were sequenced in order to elucidate the phylogenetic relationships and potential recombination events during the evolution of these isolates.
Study Design:
The isolated viruses were sequenced and aligned with all HPeV complete genome sequences available in GenBank. Phylogenetic trees were constructed and similarity plot and bootscanning methods were used for recombination analysis.
Results:
The three HPeV-4 isolates had 99.8% nucleotide sequence similarity. The phylogenetic analysis indicated that capsid-encoding sequences of these HPeV-4 isolates were closely related to other HPeV-4 strains (80.7-94.7% nucleotide similarity), whereas their non-structural region genes 2A to 3C clustered together with several HPeV-1 and HPeV-3 strains, in addition to the HPeV-4 strain K251176-02 (isolated 2002 in the Netherlands), but not with other HPeV-4 strains. However, in 3D-encoding sequence the Finnish HPeV-4 isolates did not cluster with the strain HPeV-4/K251176-02, but instead, formed a distinct group together with several HPeV-1 and HPeV-3 strains. Similarity plot and Bootscan analyses further confirmed intertypic recombination events in the evolution of the Finnish HPeV-4 isolates.
Conclusion:
Intertypic recombination event(s) have occurred during the evolution of HPeV-4 isolates from children with sepsis-like disease. However, due to the low number of parechovirus complete genomes available, the precise recombination partners could not be detected. The results suggest frequent intratypic recombination among parechoviruses.
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