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Molecular epidemiology and genetic diversity of human parechoviruses in children hospitalized with acute diarrhea in Thailand during 2011-2016

  • Rungnapa Malasao
  • Pattara Khamrin
  • Kattareeya Kumthip
  • Hiroshi Ushijima
  • Niwat ManeekarnEmail author
Original Article
  • 38 Downloads

Abstract

Little is known about human parechovirus (HPeV) infection in Thailand. The genotype distribution of HPeV strains in children admitted to hospitals with acute gastroenteritis was investigated using polymerase chain reaction (PCR) and nucleotide sequencing of the VP1 region as the detection and genotype identification methods, respectively. Of a total of 2,002 stool samples, 49 (2.4%) were positive for HPeV. Of these, HPeV-1 was the most predominant genotype (40.8%), followed by HPeV-3 (16.3%) and HPeV-14 (16.3%), while HPeV-5, -6, -2, -4, and -8 strains were less frequently detected, at 10.2%, 8.2%, 2%, 2%, and 2%, respectively. HPeV infections were detected throughout the year with the biannual peaks of infection in the rainy (Jun-Jul-Aug) and winter (Nov-Dec-Jan) months in Thailand. Based on VP1 amino acid sequence alignment, the arginyl-glycyl-aspartic acid (RGD) motif was found in HPeV-1, -2, -4, and -6 strains. Additionally, an amino acid insertion at the N-terminus of VP1 was observed in HPeV-4 and HPeV-5 strains. Phylogenetic analysis revealed that small clades of HPeV-1 and HPeV-3 strains emerged in 2016 and 2015, respectively, and dominated in the year of their emergence. The HPeV strains detected in Thailand in this study were most closely related to reference strains from Asia and Europe. The evolutionary rate of HPeV strains was 2.87 × 10−4 (95% highest posterior density (HPD) 0.10-6.14 × 10−4) substitutions/site/year. These findings provide information about the genetic diversity and evolutionary dynamics of HPeV genotypes circulating in pediatric patients with acute gastroenteritis in Thailand.

Notes

Acknowledgements

This research was supported by the Center of Excellence in Emerging and Re-emerging Diarrheal Viruses (Grant number CoE2560) and a post-doctoral fellowship in 2017 from Chiang Mai University, Chiang Mai, Thailand.

Compliance of ethical standards

Conflict of interest

The authors have declared no conflict of interest.

Ethical approval

The study was conducted with the approval of the Ethical Committee for Human Rights Related to Human Experimentation, Faculty of Medicine, Chiang Mai University (MIC-11-04-20-14-328).

Supplementary material

705_2019_4249_MOESM1_ESM.xlsx (54 kb)
Supplementary Material 1 Complete predicted amino acid sequences of VP1 of 45 strains of HPeV in Thailand arranged by genotypes. The dots and dashes represent the identical amino acids and aligned gaps, respectively. The amino acid positions based on HPeV-1 strain Harris (L02971) are shown in the first line. (XLSX 53 kb)

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Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2019

Authors and Affiliations

  • Rungnapa Malasao
    • 1
    • 2
  • Pattara Khamrin
    • 2
    • 3
  • Kattareeya Kumthip
    • 2
    • 3
  • Hiroshi Ushijima
    • 4
  • Niwat Maneekarn
    • 2
    • 3
    Email author
  1. 1.Department of Community Medicine, Faculty of MedicineChiang Mai UniversityChiang MaiThailand
  2. 2.Center of Excellence in Emerging and Re-emerging Diarrheal VirusesChiang Mai UniversityChiang MaiThailand
  3. 3.Department of Microbiology, Faculty of MedicineChiang Mai UniversityChiang MaiThailand
  4. 4.Division of Microbiology, Department of Pathology and MicrobiologyNihon University School of MedicineTokyoJapan

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