Complete genome sequences of the first parechoviruses A associated with sporadic pediatric acute gastroenteritis in Russia

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Complete genome sequences of the first parechoviruses A associated with sporadic pediatric acute gastroenteritis in Russia. / Zhirakovskaia, E.; Tikunov, A.; Babkin, I. et al.

In: Infection, Genetics and Evolution, Vol. 80, 104214, 06.2020.

Research output: Contribution to journal › Article › peer-review

BibTeX

@article{9b88a0dcce3c49c2820591c783192d57,

title = "Complete genome sequences of the first parechoviruses A associated with sporadic pediatric acute gastroenteritis in Russia",

abstract = "Parechovirus (the Picornaviridae family), recently classified as Parechovirus A and formerly known as Human parechovirus (HPeV), can cause a wide range of human diseases. Over the past decade, several studies have reported HPeV epidemiology in different regions; however, information from Russia is limited. A total of 632 stool samples collected in Novosibirsk, Russia during January–March 2012 were screened for HPeV by RT-PCR. The study cohort comprised 572 patients with acute gastroenteritis and 60 healthy children. Seven of 572 (1.2%) gastroenteritis cases were HPeV-positive, including one co-infection with rotavirus and astrovirus. All positive patients were ≤1 year old, and five of them were younger than 3 months. None of the healthy controls provided an HPeV-positive sample. Six HPeV isolates were classified as HPeV-1 and one as HPeV-5 using phylogenetic analysis. Two complete genome sequences of HPeV-1 and one of HPeV-5 were determined and analyzed. Phylogenetic analysis showed that the studied Russian strains are probably recombinants. P1 region sequences of two Russian HPeV-1 strains clustered with rare contemporary HPeV-1A strains, whereas their P3 regions were phylogenetically closer to the archival Harris strain. The Russian HPeV-5 strain formed a common cluster with other HPeV-5 strains only for the P1 region, while the P3 region grouped with the German HPeV-2 strain. In the Russian HPeV-5 strain, the lack of the arginine-glycine-aspartic acid (RGD) motif at the C-terminus of VP1 was observed. This is the first complete genome characterization of the Russian HPeV strains detected in sporadic cases of pediatric acute gastroenteritis.",

keywords = "Gastroenteritis, Genome sequence, Genotype, Human parechovirus, Phylogenetic analysis, INFECTIONS, PREVALENCE, IDENTIFICATION, HOSPITALIZED CHILDREN, GENETIC DIVERSITY, GENOTYPES, ENTEROVIRUS, MOLECULAR-DETECTION, EPIDEMIOLOGY, STOOL SAMPLES",

author = "E. Zhirakovskaia and A. Tikunov and I. Babkin and N. Tikunova",

year = "2020",

month = jun,

doi = "10.1016/j.meegid.2020.104214",

language = "English",

volume = "80",

journal = "Infection, Genetics and Evolution",

issn = "1567-1348",

publisher = "Elsevier",

}

RIS

TY - JOUR

T1 - Complete genome sequences of the first parechoviruses A associated with sporadic pediatric acute gastroenteritis in Russia

AU - Zhirakovskaia, E.

AU - Tikunov, A.

AU - Babkin, I.

AU - Tikunova, N.

PY - 2020/6

Y1 - 2020/6

N2 - Parechovirus (the Picornaviridae family), recently classified as Parechovirus A and formerly known as Human parechovirus (HPeV), can cause a wide range of human diseases. Over the past decade, several studies have reported HPeV epidemiology in different regions; however, information from Russia is limited. A total of 632 stool samples collected in Novosibirsk, Russia during January–March 2012 were screened for HPeV by RT-PCR. The study cohort comprised 572 patients with acute gastroenteritis and 60 healthy children. Seven of 572 (1.2%) gastroenteritis cases were HPeV-positive, including one co-infection with rotavirus and astrovirus. All positive patients were ≤1 year old, and five of them were younger than 3 months. None of the healthy controls provided an HPeV-positive sample. Six HPeV isolates were classified as HPeV-1 and one as HPeV-5 using phylogenetic analysis. Two complete genome sequences of HPeV-1 and one of HPeV-5 were determined and analyzed. Phylogenetic analysis showed that the studied Russian strains are probably recombinants. P1 region sequences of two Russian HPeV-1 strains clustered with rare contemporary HPeV-1A strains, whereas their P3 regions were phylogenetically closer to the archival Harris strain. The Russian HPeV-5 strain formed a common cluster with other HPeV-5 strains only for the P1 region, while the P3 region grouped with the German HPeV-2 strain. In the Russian HPeV-5 strain, the lack of the arginine-glycine-aspartic acid (RGD) motif at the C-terminus of VP1 was observed. This is the first complete genome characterization of the Russian HPeV strains detected in sporadic cases of pediatric acute gastroenteritis.

AB - Parechovirus (the Picornaviridae family), recently classified as Parechovirus A and formerly known as Human parechovirus (HPeV), can cause a wide range of human diseases. Over the past decade, several studies have reported HPeV epidemiology in different regions; however, information from Russia is limited. A total of 632 stool samples collected in Novosibirsk, Russia during January–March 2012 were screened for HPeV by RT-PCR. The study cohort comprised 572 patients with acute gastroenteritis and 60 healthy children. Seven of 572 (1.2%) gastroenteritis cases were HPeV-positive, including one co-infection with rotavirus and astrovirus. All positive patients were ≤1 year old, and five of them were younger than 3 months. None of the healthy controls provided an HPeV-positive sample. Six HPeV isolates were classified as HPeV-1 and one as HPeV-5 using phylogenetic analysis. Two complete genome sequences of HPeV-1 and one of HPeV-5 were determined and analyzed. Phylogenetic analysis showed that the studied Russian strains are probably recombinants. P1 region sequences of two Russian HPeV-1 strains clustered with rare contemporary HPeV-1A strains, whereas their P3 regions were phylogenetically closer to the archival Harris strain. The Russian HPeV-5 strain formed a common cluster with other HPeV-5 strains only for the P1 region, while the P3 region grouped with the German HPeV-2 strain. In the Russian HPeV-5 strain, the lack of the arginine-glycine-aspartic acid (RGD) motif at the C-terminus of VP1 was observed. This is the first complete genome characterization of the Russian HPeV strains detected in sporadic cases of pediatric acute gastroenteritis.

KW - Gastroenteritis

KW - Genome sequence

KW - Genotype

KW - Human parechovirus

KW - Phylogenetic analysis

KW - INFECTIONS

KW - PREVALENCE

KW - IDENTIFICATION

KW - HOSPITALIZED CHILDREN

KW - GENETIC DIVERSITY

KW - GENOTYPES

KW - ENTEROVIRUS

KW - MOLECULAR-DETECTION

KW - EPIDEMIOLOGY

KW - STOOL SAMPLES

UR - http://www.scopus.com/inward/record.url?scp=85078767813&partnerID=8YFLogxK

U2 - 10.1016/j.meegid.2020.104214

DO - 10.1016/j.meegid.2020.104214

M3 - Article

C2 - 32006708

AN - SCOPUS:85078767813

VL - 80

JO - Infection, Genetics and Evolution

JF - Infection, Genetics and Evolution

SN - 1567-1348

M1 - 104214

ER -

ID: 23328113