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


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.



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)


  1. 1.
    Abed Y, Boivin G (2006) Human parechovirus types 1, 2 and 3 infections in Canada. Emerg Infect Dis 12:969–975CrossRefGoogle Scholar
  2. 2.
    Alam MM, Khurshid A, Shaukat S, Rana MS, Sharif S, Angez M, Nisar N, Naeem M, Zahoor Zaidi SS (2013) Human parechovirus genotypes-10, -13 and -15 in Pakistani children with acute dehydrating gastroenteritis. PLoS One 8:e78377CrossRefGoogle Scholar
  3. 3.
    Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2008) Molecular biology of the cell, 5th edn. Garland Science, New YorkGoogle Scholar
  4. 4.
    Baranowski E, Ruiz-Jarabo CM, Sevilla N, Andreu D, Beck E, Domingo E (2000) Cell recognition by foot-and-mouth disease virus that lacks the RGD integrin-binding motif: flexibility in aphthovirus receptor usage. J Virol 74:1641–1647CrossRefGoogle Scholar
  5. 5.
    Benschop K, Thomas X, Serpenti C, Molenkamp R, Wolthers K (2008) High prevalence of human Parechovirus (HPeV) genotypes in the Amsterdam region and identification of specific HPeV variants by direct genotyping of stool samples. J Clin Microbiol 46:3965–3970CrossRefGoogle Scholar
  6. 6.
    Benschop KS, Schinkel J, Luken ME, van den Broek PJ, Beersma MF, Menelik N, van Eijk HW, Zaaijer HL, VandenBroucke-Grauls CM, Beld MG, Wolthers KC (2006) Fourth human parechovirus serotype. Emerg Infect Dis 12:1572–1575CrossRefGoogle Scholar
  7. 7.
    Benschop KS, Schinkel J, Minnaar RP, Pajkrt D, Spanjerberg L, Kraakman HC, Berkhout B, Zaaijer HL, Beld MG, Wolthers KC (2006) Human parechovirus infections in Dutch children and the association between serotype and disease severity. Clin Infect Dis 42:204–210CrossRefGoogle Scholar
  8. 8.
    Boonyakiat Y, Hughes PJ, Ghazi F, Stanway G (2001) Arginine-glycine-aspartic acid motif is critical for human parechovirus 1 entry. J Virol 75:10000–10004CrossRefGoogle Scholar
  9. 9.
    Boros A, Uj M, Pankovics P, Reuter G (2010) Detection and characterization of human parechoviruses in archived cell cultures, in Hungary. J Clin Virol 47:379–381CrossRefGoogle Scholar
  10. 10.
    Böttcher S, Obermeier PE, Diedrich S, Kaboré Y, D’Alfonso R, Pfister H, Kaiser R, Di Cristanziano V (2017) Genome sequence of novel human parechovirus type 17. Genome Announc 5:e01649–16CrossRefGoogle Scholar
  11. 11.
    Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ (2014) BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol 10:e1003537CrossRefGoogle Scholar
  12. 12.
    Bubba L, Martinelli M, Pellegrinelli L, Primache V, Tanzi E, Pariani E, Binda S (2017) A 4-year study on epidemiologic and molecular characteristics of human parechoviruses and enteroviruses circulating in children younger than 5 years in Northern Italy. Pediatr Infect Dis J 36:13–19CrossRefGoogle Scholar
  13. 13.
    Cabrerizo M, Díaz-Cerio M, Muñoz-Almagro C, Rabella N, Tarragó D, Romero MP, Pena MJ, Calvo C, Rey-Cao S, Moreno-Docón A, Martínez-Rienda I, Otero A, Trallero G (2017) Molecular epidemiology of enterovirus and parechovirus infections according to patient age over a 4-year period in Spain. J Med Virol 89:435–442CrossRefGoogle Scholar
  14. 14.
    Calvert J, Chieochansin T, Benschop KS, McWilliam Leitch EC, Drexler JF, Grywna K, da Costa Ribeiro H, Drosten C, Harvala H, Poovorawan Y, Wolthers KC, Simmonds P (2010) Recombination dynamics of human parechoviruses: investigation of type-specific differences in frequency and epidemiological correlates. J Gen Virol 91:1229–1238CrossRefGoogle Scholar
  15. 15.
    Chaimongkol N, Khamrin P, Suantai B, Saikhreang W, Thongprachum A, Malasao R, Ukarapol N, Kongsricharoern T, Ushijima H, Maneekarn N (2012) A wide variety of diarrhea viruses circulating in pediatric patients in Thailand. Clin Lab 58:117–123Google Scholar
  16. 16.
    Chen H, Yao Y, Liu X, Xiao N, Xiao Y, Huang Y, Chen Q, Yu S (2014) Molecular detection of human parechovirus in children with acute gastroenteritis in Guangzhou, China. Arch Virol 159:971–977CrossRefGoogle Scholar
  17. 17.
    Chieochansin T, Vichiwattana P, Korkong S, Theamboonlers A, Poovorawan Y (2011) Molecular epidemiology, genome characterization, and recombination event of human parechovirus. Virology 421:159–166CrossRefGoogle Scholar
  18. 18.
    Chuchaona W, Khamrin P, Yodmeeklin A, Saikruang W, Kongsricharoern T, Ukarapol N, Okitsu S, Hayakawa S, Ushijima H, Maneekarn N (2015) Detection and characterization of a novel human parechovirus genotype in Thailand. Infect Genet Evol 31:300–304CrossRefGoogle Scholar
  19. 19.
    Chuchaona W, Khamrin P, Yodmeeklin A, Kumthip K, Saikruang W, Thongprachum A, Okitsu S, Ushijima H, Maneekarn N (2017) Detection and characterization of Aichi virus 1 in pediatric patients with diarrhea in Thailand. J Med Virol 89:234–238CrossRefGoogle Scholar
  20. 20.
    de Crom SC, Rossen JW, van Furth AM, Obihara CC (2016) Enterovirus and parechovirus infection in children: a brief overview. Eur J Pediatr 175:1023–1029CrossRefGoogle Scholar
  21. 21.
    Drexler JF, Grywna K, Stöcker A, Almeida PS, Medrado-Ribeiro TC, Eschbach-Bludau M, Petersen N, da Costa-Ribeiro-Jr H, Drosten C (2009) Novel human parechovirus from Brazil. Emerg Infect Dis 15:310–313CrossRefGoogle Scholar
  22. 22.
    Esposito S, Rahamat-Langendoen J, Ascolese B, Senatore L, Castellazzi L, Niesters HG (2014) Pediatric parechovirus infections. J Clin Virol 60:84–89CrossRefGoogle Scholar
  23. 23.
    Faria NR, de Vries M, van Hemert FJ, Benschop K, van der Hoek L (2009) Rooting human parechovirus evolution in time. BMC Evol Biol 9:164CrossRefGoogle Scholar
  24. 24.
    Ghazi F, Hughes PJ, Hyypiä T, Stanway G (1998) Molecular analysis of human parechovirus type 2 (formerly echovirus 23). J Gen Virol 79(Pt 11):2641–2650CrossRefGoogle Scholar
  25. 25.
    Graul S, Böttcher S, Eibach D, Krumkamp R, Käsmaier J, Adu-Sarkodie Y, May J, Tannich E, Panning M (2017) High diversity of human parechovirus including novel types in stool samples from Ghanaian children. J Clin Virol 96:116–119CrossRefGoogle Scholar
  26. 26.
    Green KY (2013) Caliciviridae: the noroviruses. In: Knip DM, Howley PM (eds) Fields virology. Lippincott Williams & Wilkins, Philadelphia, pp 584–587Google Scholar
  27. 27.
    Han TH, Kim CH, Park SH, Chung JY, Hwang ES (2011) Detection of human parechoviruses in children with gastroenteritis in South Korea. Arch Virol 156:1471–1475CrossRefGoogle Scholar
  28. 28.
    Han TH, Chung JY, You SJ, Youn JL, Shim GH (2013) Human parechovirus-3 infection in children, South Korea. J Clin Virol 58:194–199CrossRefGoogle Scholar
  29. 29.
    Harvala H, Robertson I, McWilliam Leitch EC, Benschop K, Wolthers KC, Templeton K, Simmonds P (2008) Epidemiology and clinical associations of human parechovirus respiratory infections. J Clin Microbiol 46:3446–3453CrossRefGoogle Scholar
  30. 30.
    Harvala H, Simmonds P (2009) Human parechoviruses: biology, epidemiology and clinical significance. J Clin Virol 45:1–9CrossRefGoogle Scholar
  31. 31.
    Hyypiä T, Horsnell C, Maaronen M, Khan M, Kalkkinen N, Auvinen P, Kinnunen L, Stanway G (1992) A distinct picornavirus group identified by sequence analysis. Proc Natl Acad Sci USA 89:8847–8851CrossRefGoogle Scholar
  32. 32.
    Ito M, Yamashita T, Tsuzuki H, Takeda N, Sakae K (2004) Isolation and identification of a novel human parechovirus. J Gen Virol 85:391–398CrossRefGoogle Scholar
  33. 33.
    Joki-Korpela P, Marjomaki V, Krogerus C, Heino J, Hyypia T (2001) Entry of human parechovirus 1. J Virol 75:1958–1967CrossRefGoogle Scholar
  34. 34.
    Khamrin P, Kumthip K, Supadej K, Thongprachum A, Okitsu S, Hayakawa S, Ushijima H, Maneekarn N (2017) Noroviruses and sapoviruses associated with acute gastroenteritis in pediatric patients in Thailand: increased detection of recombinant norovirus GII.P16/GII.13 strains. Arch Virol 162:3371–3380CrossRefGoogle Scholar
  35. 35.
    Kolehmainen P, Siponen A, Smura T, Kallio-Kokko H, Vapalahti O, Jääskeläinen A, Tauriainen S (2017) Intertypic recombination of human parechovirus 4 isolated from infants with sepsis-like disease. J Clin Virol 88:1–7CrossRefGoogle Scholar
  36. 36.
    Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular Evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874CrossRefGoogle Scholar
  37. 37.
    Kumthip K, Khamrin P, Ushijima H, Maneekarn N (2017) Multiple enterovirus genotypes circulating in children hospitalized with acute gastroenteritis in Thailand. Infect Genet Evol 55:324–331CrossRefGoogle Scholar
  38. 38.
    Kumthip K, Khamrin P, Ushijima H, Maneekarn N (2018) Molecular epidemiology of classic, MLB and VA astroviruses isolated from < 5 year-old children with gastroenteritis in Thailand, 2011–2016. Infect Genet Evol 65:373–379CrossRefGoogle Scholar
  39. 39.
    Li L, Victoria J, Kapoor A, Naeem A, Shaukat S, Sharif S, Alam MM, Angez M, Zaidi SZ, Delwart E (2009) Genomic characterization of novel human parechovirus type. Emerg Infect Dis 15:288–291CrossRefGoogle Scholar
  40. 40.
    Ljubin-Sternak S, Juretić E, Šantak M, Pleša M, Forčić D, Vilibić-Čavlek T, Aleraj B, Mlinarić-Galinović G (2011) Clinical and molecular characterization of a parechovirus type 1 outbreak in neonates in Croatia. J Med Virol 83:137–141CrossRefGoogle Scholar
  41. 41.
    McNeale D, Wang CYT, Arden KE, Mackay IM (2018) HPeV-3 predominated among Parechovirus A positive infants during an outbreak in 2013-2014 in Queensland, Australia. J Clin Virol 98:28–32CrossRefGoogle Scholar
  42. 42.
    Menage L, Yodmeeklin A, Khamrin P, Kumthip K, Maneekarn N (2017) Prevalence of human cosavirus and saffold virus with an emergence of saffold virus genotype 6 in patients hospitalized with acute gastroenteritis in Chiang Mai, Thailand, 2014–2016. Infect Genet Evol 53:1–6CrossRefGoogle Scholar
  43. 43.
    Merilahti P, Tauriainen S, Susi P (2016) Human parechovirus 1 infection occurs via αVβ1 integrin. PLoS One 11:e0154769CrossRefGoogle Scholar
  44. 44.
    Mladenova Z, Dikova A, Thongprachum A, Petrov P, Pekova L, Komitova R, Iturriza-Gomara M, Ushijima H (2015) Diversity of human parechoviruses in Bulgaria, 2011: detection of rare genotypes 8 and 10. Infect Genet Evol 36:315–322CrossRefGoogle Scholar
  45. 45.
    Nix WA, Khetsuriani N, Peñaranda S, Maher K, Venczel L, Cselkó Z, Freire MC, Cisterna D, Lema CL, Rosales P, Rodriguez JR, Rodriguez W, Halkyer P, Ronveaux O, Pallansch MA, Oberste MS (2013) Diversity of picornaviruses in rural Bolivia. J Gen Virol 94:2017–2028CrossRefGoogle Scholar
  46. 46.
    Oberste MS, Maher K, Pallansch MA (1998) Complete sequence of echovirus 23 and its relationship to echovirus 22 and other human enteroviruses. Virus Res 56:217–223CrossRefGoogle Scholar
  47. 47.
    Olijve L, Jennings L, Walls T (2018) Human parechovirus: an increasingly recognized cause of sepsis-like illness in young infants. Clin Microbiol Rev 31:e00047–17Google Scholar
  48. 48.
    Pajkrt D, Benschop KS, Westerhuis B, Molenkamp R, Spanjerberg L, Wolthers KC (2009) Clinical characteristics of human parechoviruses 4–6 infections in young children. Pediatr Infect Dis J 28:1008–1010CrossRefGoogle Scholar
  49. 49.
    Patil PR, Ganorkar NNGV (2018) Epidemiology and genetic diversity of human parechoviruses circulating among children hospitalised with acute gastroenteritis in Pune, Western India: a 5-years study. Epidemiol Infect 146:11–18CrossRefGoogle Scholar
  50. 50.
    Pham NT, Trinh QD, Khamrin P, Maneekarn N, Shimizu H, Okitsu S, Mizuguchi M, Ushijima H (2010) Diversity of human parechoviruses isolated from stool samples collected from Thai children with acute gastroenteritis. J Clin Microbiol 48:115–119CrossRefGoogle Scholar
  51. 51.
    Pham NT, Chan-It W, Khamrin P, Nishimura S, Kikuta H, Sugita K, Baba T, Yamamoto A, Shimizu H, Okitsu S, Mizuguchi M, Ushijima H (2011) Detection of human parechovirus in stool samples collected from children with acute gastroenteritis in Japan during 2007–2008. J Med Virol 83:331–336CrossRefGoogle Scholar
  52. 52.
    Pham NT, Takanashi S, Tran DN, Trinh QD, Abeysekera C, Abeygunawardene A, Khamrin P, Okitsu S, Shimizu H, Mizuguchi M, Ushijima H (2011) Human parechovirus infection in children hospitalized with acute gastroenteritis in Sri Lanka. J Clin Microbiol 49:364–366CrossRefGoogle Scholar
  53. 53.
    Pringle CR (1996) Virus taxonomy 1996—a bulletin from the Xth international congress of virology in Jerusalem. Arch Virol 141:2251–2256CrossRefGoogle Scholar
  54. 54.
    Romero JR, Selvarangan R (2011) The human parechoviruses: an overview. Adv Pediatr 58:65–85CrossRefGoogle Scholar
  55. 55.
    Saikruang W, Khamrin P, Suantai B, Okitsu S, Hayakawa S, Ushijima H, Maneekarn N (2014) Detection of diarrheal viruses circulating in adult patients in Thailand. Arch Virol 159:3371–3375CrossRefGoogle Scholar
  56. 56.
    Shah G, Robinson JL (2014) The particulars on parechovirus. Can J Infect Dis Med Microbiol 25:186–188CrossRefGoogle Scholar
  57. 57.
    Shakeel S, Westerhuis BM, Ora A, Koen G, Bakker AQ, Claassen Y, Wagner K, Beaumont T, Wolthers KC, Butcher SJ (2015) Structural basis of human parechovirus neutralization by human monoclonal antibodies. J Virol 89:9571–9580CrossRefGoogle Scholar
  58. 58.
    Stanway G, Kalkkinen N, Roivainen M, Ghazi F, Khan M, Smyth M, Meurman O, Hyypiä T (1994) Molecular and biological characteristics of echovirus 22, a representative of a new picornavirus group. J Virol 68:8232–8238Google Scholar
  59. 59.
    Stanway G, Hyypiä T (1999) Parechoviruses. J Virol 73:5249–5254Google Scholar
  60. 60.
    Stanway G, Joki-Korpela P, Hyypiä T (2000) Human parechoviruses—biology and clinical significance. Rev Med Virol 10:57–69CrossRefGoogle Scholar
  61. 61.
    Supadej K, Khamrin P, Kumthip K, Malasao R, Chaimongkol N, Saito M, Oshitani H, Ushijima H, Maneekarn N (2019) Distribution of norovirus and sapovirus genotypes with emergence of NoV GII.P16/GII.2 recombinant strains in Chiang Mai, Thailand. J Med Virol 91:215–224CrossRefGoogle Scholar
  62. 62.
    Triantafilou K, Triantafilou M (2001) A biochemical approach reveals cell-surface molecules utilised by Picornaviridae: Human Parechovirus 1 and Echovirus 1. J Cell Biochem 80:373–381CrossRefGoogle Scholar
  63. 63.
    Watanabe K, Oie M, Higuchi M, Nishikawa M, Fujii M (2007) Isolation and characterization of novel human parechovirus from clinical samples. Emerg Infect Dis 13:889–895CrossRefGoogle Scholar
  64. 64.
    Watanabe K, Hirokawa C, Tazawa T (2016) Seropositivity and epidemiology of human parechovirus types 1, 3, and 6 in Japan. Epidemiol Infect 144:3451–3460CrossRefGoogle Scholar
  65. 65.
    Wigand R, Sabin AB (1961) Properties of ECHO types 22, 23 and 24 viruses. Arch Gesamte Virusforsch 11:224–247CrossRefGoogle Scholar
  66. 66.
    Yip CC, Lo KL, Que TL, Lee RA, Chan KH, Yuen KY, Woo PC, Lau SK (2014) Epidemiology of human parechovirus, Aichi virus and salivirus in fecal samples from hospitalized children with gastroenteritis in Hong Kong. Virol J 11:182CrossRefGoogle Scholar
  67. 67.
    Yodmeeklin A, Khamrin P, Kumthip K, Malasao R, Ukarapol N, Ushijima H, Maneekarn N (2018) Increasing predominance of G8P[8] species A rotaviruses in children admitted to hospital with acute gastroenteritis in Thailand, 2010-2013. Arch Virol 163:2165–2178CrossRefGoogle Scholar
  68. 68.
    Zhao X, Shi Y, Xia Y (2016) Genome analysis revealed novel genotypes and recombination of the human parechoviruses prevalent in children in Eastern China. Gut Pathog 8:52CrossRefGoogle Scholar
  69. 69.
    Zhong H, Lin Y, Sun J, Su L, Cao L, Yang Y, Xu J (2011) Prevalence and genotypes of human parechovirus in stool samples from hospitalized children in Shanghai, China, 2008 and 2009. J Med Virol 83:1428–1434CrossRefGoogle Scholar

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

Personalised recommendations