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. 2008 Dec;46(12):3965-70.
doi: 10.1128/JCM.01379-08. Epub 2008 Oct 22.

High prevalence of human Parechovirus (HPeV) genotypes in the Amsterdam region and identification of specific HPeV variants by direct genotyping of stool samples

K Benschop  1 , X Thomas, C Serpenti, R Molenkamp, K Wolthers
Affiliations

High prevalence of human Parechovirus (HPeV) genotypes in the Amsterdam region and identification of specific HPeV variants by direct genotyping of stool samples

K Benschop et al. J Clin Microbiol. 2008 Dec.

Abstract

Human parechoviruses (HPeV) are widespread pathogens belonging to the Picornavirus family. Six genotypes, which have predominantly been isolated from children, are known. Data on prevalence of HPeV genotypes are generally based on cell culture, which may underestimate the prevalence of certain HPeV strains that are difficult to grow. We studied 1,824 stool samples from 1,379 children (<5 years old) sent to the Academic Medical Center, Amsterdam, The Netherlands, between 2004 and 2006. Samples were screened using specific human enterovirus (HEV) and HPeV real-time PCRs based on the 5' untranslated region. A high percentage of HPeV infections (16.3%), comparable to the percentage of HEV infections (18.4%), were found by PCR in stool samples. HPeV-positive stool samples were directly genotyped based on the VP1 region for the first time to avoid a culture bias. HPeV1 was found to be the most prevalent type. The majority of the HPeV1 strains clustered separately from the prototype strain, Harris, which has not been reported to circulate lately. However, we could identify three strains as HPeV1 Harris. HPeV3 was identified as the second most predominant type during 2004 and 2006 but was not found in 2005. HPeV4 to -6 were found in smaller numbers. One strain could not be associated with a known HPeV type (VP1 gene nucleotide similarity: 71%), possibly indicating a new genotype. Also, we report the first identification of three HPeV5 strains and one HPeV1 strain with a different motif at the C-terminal end of VP1, where the arginine-glycine-aspartic acid (RGD) motif is normally located.

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Figures

FIG. 1.
FIG. 1.
Rooted phylogenetic tree based on amino acid differences in the capsid protein VP1 (236 amino acids). The tree was constructed by using the neighbor-joining method. Numbers represent the frequencies of occurrence of nodes in 1,000 bootstrap replicates. The Dutch strains sequenced within this study are identified by a six-digit numbering system and have been color-coded by year of isolation (2004, red; 2005, green; 2006, blue). The different HPeV genotype clusters have been color-coded within the tree: HPeV1, purple; HPeV2, orange; HPeV3, light brown; HPeV4, light blue; HPeV5, pink; HPeV6, light green. As an outgroup, Ljungan virus 145 SL (AF327922) was used. HPeV1 reference strains and isolates, obtained from GenBank (accession numbers are in parentheses), are Harris (S45208); BNI788st (EF051629); 450343 (DQ172430); 550163 (DQ172425); 450976 (DQ172417); 451294 (DQ172440); 452176 (DQ172431); 4522252 (DQ172435); A317/99, A354/99, A628/99, A942/99, A1086/99, and A10987/00 (AB112482 to AB112487); A301/01 (AB300943); A177/01, A584/00, A573/00, A486/00, and A477/00 (AB300937 to AB300941); A708/99 (AB300935); A669/99 (AB300932); A657/99 (AB300931); A527/99 (AB300928); A233/04, A244/04, A248/04, A249/04, A258/04, A322/04, A329/04, A351/04, A62/05, A65/05, A150/05, and A151/05 (AB300954 to AB300965); A295/02, A336/02, and A177/03 (AB300949 to AB300951); A136/02 (AB300946); A347/06 (AB300985); A191/05, A222/05, A229/05, A234/05, A241/05, A242/05, and A258/05 (AB300966 to AB300972); and BNI-R90/03, BNI-R04/03, BNI-R09/03, BNI-R15/03, BNI-R21/03, BNI-R30/03, and BNI-R32/03 (EU024630 to EU024636); the HPeV2 strain is Williamson (AF055846); HPeV3 strains and isolates are A308/99 (AB084913); CAN82853-01 (AJ889918); 451371 (DQ172449); 451517 (DQ172447); 450936 (DQ172446); A390/01 (AB300944); A415/01 (AB300945); A1027/99 (AB300936); A683/99 (AB300934); A680/99 (AB300933); A606/99 (AB300930); A531/99 (AB300929); A492/99 (AB300927); A319/99 (AB300926); A153/04 (AB300952); A141/02 (AB300947); A265/02 (AB300948); A471/06 (AB300986); and A188/05, A225/06, A246/06, A255/06, A257/06, A259/06, A264/06, A265/06, A281/06, A285/06, A287/06, and A320/06 (AB300973 to AB300984); HPeV4 strains and isolates are K251176-02 (DQ315670), T75-4077 (AM235750), T82-203 (AM234727), and T73-838 (AM234725); HPeV5 strains and isolates are CT86-6760 (AJ005695), T92-15 (AM235749), T820169 (AM234728), T82-659 (AM234726), and T83-2051 (AM234724); HPeV6 strains and isolates are NII561-2000 (AB252582), BNI67-03 (EU024629), 2005/823 (EU077518), and A231/01 (AB300942).
FIG. 2.
FIG. 2.
The prevalences of the known HPeV types in 2004 (HPeV1, n = 30; HPeV3, n = 19; HPeV4, n = 4; HPeV5, n = 1; HPeV6, n = 1), 2005 (HPeV1, n = 19; HPeV5, n = 1; HPeV6, n = 1) and 2006 (HPeV1, n = 35; HPeV3, n = 10; HPeV4, n = 5; HPeV5, n = 2; HPeV6, n = 1) identified in the Amsterdam region.
FIG. 3.
FIG. 3.
Alignment of the VP1 region flanking the RGD motif. The strains containing the RGD motif are shown in black. The strains lacking the RGD motif are shown in blue. The three HPeV5 strains and one HPeV1 strain containing a different motif at the C-terminal end of VP1 are shown in red. The arrowhead marks the cleavage site of the VP1-2A junction.
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