Intertypic recombination of human parechovirus 4 isolated from infants with sepsis-like disease

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Highlights

  • 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 2B 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.

Abstract

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.

Section snippets

Background

Human parechoviruses (HPeVs) are non-enveloped, single-stranded, positive-sense RNA-viruses and members of the family Picornaviridae. The HPeV genome, approximately 7350 nucleotides (nt) in size, encodes for a single polyprotein, which consists of three regions: P1, P2 and P3. The polyprotein is cleaved post-translationally into three structural (VP0, VP3 and VP1 from P1) and seven non-structural proteins (2A, 2B, 2C from P2 and 3A-3D from P3) [1]. Both ends of the coding sequence (CDS) are

Objectives

Three HPeV-4 isolates from different infants were isolated during autumn 2012, sequenced and their complete coding sequences were analyzed for sequence similarity and recombination events. These HPeV–4 s were the first type 4 HPeVs found in Finland, and caused a small outbreak of sepsis-like disease in infants. Sepsis-like disease is a more common clinical outcome for HPeV-3, so these viruses caused more severe symptoms than previously reported for HPeV-4 [13], [14]. Prior to this study, there

Samples

Three HPeV-4 viruses FI121236, FI121290 and FI121301 were isolated from stool and serum samples of three patients (described earlier [13], [14]). All patients were hospitalized with suspected sepsis in Helsinki, October 2012. Children were aged 1–2 months, two were boys and one girl. The viruses were isolated and passaged 1–2 times in human colon adenocarcinoma cells (HT-29, ATCC) prior to viral RNA extraction with QIAamp Viral RNA kit (Qiagen) according to the manufacturer’s instructions.

Complete coding region sequences of the Finnish HPeV-4 isolates

An almost complete genome sequence, approximately 7200 nucleotides long (excluding only about 70 nucleotides from the 5′ end) was determined for HPeV-4 isolates FI121236, FI121290 and FI121301. The nucleotide sequences of these isolates were 99.8% similar to each other and therefore clustered closely together in the sequence analysis independent of the region under observation. These isolates can be considered to be of one strain, which circulated in the Helsinki region in fall 2012 causing

Discussion

This study presents complete coding sequences for three HPeV-4 isolates, that caused sepsis-like disease in Finnish infants in autumn 2012 [13], [14]. The sequencing of complete coding regions allowed analysis for their phylogenetic relations and recombination. Four main observations were made: 1) In the P1 and P2 regions, the Finnish HPeV-4 isolates were highly similar to the HPeV-4 strain isolated in the Netherlands in 2002; 2) the Finnish isolates had a 3 nucleotide deletion compared with

Funding

This work was financially supported by the Jane and Aatos Erkko Foundation, and HUSLAB (grant no. TYH2011305; Helsinki University Hospital, Finland).

Competing interests

None declared

Ethical approval

Not required, all clinical samples were analyzed anonymously encoded.

Acknowledgments

Anni Kauppinen is thanked for technical assistance. CSC − IT Center for Science Ltd. (Espoo, Finland) is acknowledged for the allocation of computational resources. The Finnish institute of Molecular Medicine (FIMM, Helsinki, Finland) is thanked for technical assistance.

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