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This study revealed a high genetic diversity of PeV-A circulating in Japanese infants and children with AGE and the PeV-A2, a rare genotype, was detected for the first time in Japan in patients with AGE. Five different PeV-A genotypes including PeV-A1B, −A2, −A3, −A4, and -A6 were detected with predominant of PeV-A1 clade B genotype. Of 1070 stool samples collected from Japanese infants and children with AGE during the 2-year period from July 2016 to June 2018, 76 were positive for PeV-A by multiplex reverse transcriptase-polymerase chain reaction (RT-PCR) and were subjected to genotyping based on viral protein 1 (VP1) sequences. Take advantage of our previous findings on the genetic diversity of PeV-A circulating in Japanese children with acute gastroenteritis (AGE), this study was conducted to investigate the genetic diversity of PeV-A isolated from children with AGE in Japan as well as their clinical symptoms. Parechovirus A (PeV-A), previously known as human parechovirus, is a common pathogen in children that can cause respiratory and gastrointestinal diseases as well as severe neurological disease. Genotyping results confirm previously reported association of more severe illness with HPeV-3 and HPeV-1B strains. The investigation adds data on the whole coding sequences of the rare HPeV-2 strain. In conclusion, this paper a high genetic diversity of HPeV in stool samples, including rare strains.
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Regarding clinical manifestations, severe disease occurred HPeV-1B, −3 and − 6 infections. In phylogenetic analysis VP1 of strain LPZ04–2008 clustered with a recent HPeV-2 strain from the UK. In complete VP1 analysis strain LPZ04-2008 showed 81.2% nucleic acid identity with HPeV-2 reference strain Williamson. To ascertain the assigned HPeV-2 genotype of uncommon strain LPZ04-2008, analysis of complete coding sequences was performed. Those prevailed minor HPeV-6 (n = 3) as well as HPeV-2, −4 and −5 (n = 1, each) strains. Genotyping was based on VP3/VP1 junction nucleic acid sequences and revealed predominant HPeV-1B (n = 16) and HPeV-3 (n = 12) strains. The HPeV detection rate was highest (8.8%) in samples derived from infants and young children under the age of two years.
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Real-time RT-PCR showed HPeV RNA in 34 (6.3%) of the samples. To gain insight into the diversity of circulating HPeV genotypes, stool samples from patients (n = 539) with clinical signs of infectious gastroenteritis which showed negative results for other common viral and bacterial enteric pathogens were obtained during three years, 2008 to 2010. They are known to cause various clinical manifestations including acute gastroenteritis. Human parechoviruses (HPeV) are ubiquitous and mainly occur in early infancy.