[Source: Journal of Clinical Virology, full page: (LINK). Abstract, edited.]
Intertypic recombination of human parechovirus 4 isolated from infants with sepsis-like disease
Pekka Kolehmainen, Anu Siponen, Teemu Smura, Hannimari Kallio-Kokkoemail, Olli Vapalahti, Anne Jääskeläinen1, Sisko Tauriainen1
1These authors contributed equally.
Publication History: Published online: January 03, 2017 – Accepted: January 2, 2017 – Received in revised form: December 30, 2016 – Received: October 13, 2016
- Three HPeV-4 complete coding sequences were determined.
- The P1 and P2 regions were highly similar to an HPeV-4 from the Netherlands, 2002.
- Sequence similarity with HPeV-4 was lost in the 3D region indicating recombination.
- The 2 B to 3A region clustered together with several HPeV-3 strains.
- A three nucleotide deletion, compared to other HPeV-4s, was found in the 1C region.
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.
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.
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.
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.
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.
Abbreviations: CDS (coding sequences), HPeV (human parechovirus), NGS (next generation sequencing), nt (nucleotide(s)), UTR (untranslated region)
Keywords: Human parechovirus, HPeV-4, Complete coding sequence, Sepsis-like disease, Recombination, Phylogenetic analysis
Keywords: Parechovirus; Picornavirus; Sepsis.