Evolution and conservation in human parechovirus genomes

Williams, Çiğdem H.; Panayiotou, Maria; Girling, Gareth; Peard, Curtis I.; Oikarinen, Sami; Hyöty, Heikki; Stanway, Glyn

doi:10.1099/vir.0.008813-0

Cited by 49 publications

(58 citation statements)

References 50 publications

(48 reference statements)

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“…In summary, our findings of frequent intertypic recombination between capsid and non-structural proteins and of rare intratypic, intra-capsid recombination confirm and extend the notion that parechoviruses are not different from most other human picornaviruses in their recombination behaviour (Benschop et al, 2008bCalvert et al, 2010;Williams et al, 2009;Zoll et al, 2009). The major finding in this study is that the cohesion of non-structural protein genes of Brazilian viruses with total geographical restriction and exclusiveness of the 3C protein gene.…”

Section: Validation Of Coalescent Dating Assumptionssupporting

confidence: 71%

“…Tree order was disrupted upon transition to the 2A region for all HPeV types with the exception of HPeV3. Only one Dutch HPeV3 isolate (termed 651689) showed signs of recombination in the P2 and P3 genome region with other parechoviruses, while all other HPeV3 grouped consistently over the whole genome, confirming previous reports (Benschop et al, 2008bCalvert et al, 2010;de Souza Luna et al, 2008;Williams et al, 2009;Zoll et al, 2009). …”

supporting

confidence: 75%

“…Recombination in HPeV has been described previously (Benschop et al, 2008bCalvert et al, 2010;de Souza Luna et al, 2008;Williams et al, 2009;Zoll et al, 2009). In agreement with these reports, a preliminary analysis of the novel dataset using phylogenetic compatibility matrices implemented in the SIMMONICS package (Simmonds & Smith, 1999) and bootscanning (Salminen et al, 1995) implemented in SIMPLOT v.3.5.1 (Lole et al, 1999) detected multiple recombination events, with most crossover points mapping to the regions immediately bordering the P1 genome region (data not shown).…”

Section: Whole Genome Analysis Of Hpevsupporting

confidence: 60%

“…1(b). Except for HPeV3 for which absence of recombination has already been described (Benschop et al, 2008bCalvert et al, 2010;de Souza Luna et al, 2008;Williams et al, 2009;Zoll et al, 2009), different strains only grouped across rather short regions, often situated in or between the 2B and 3D portions of genomes. However, it was noted that all Brazilian strains grouped together in more than half of the genome, extending from the 3D gene into the 2C gene (Fig.…”

mentioning

confidence: 99%

“…HPeV genetic and evolutionary properties also resemble those of enteroviruses. They feature both high mutation rate (Faria et al, 2009) and frequent natural recombination (Benschop et al, 2008bCalvert et al, 2010;Williams et al, 2009;Zoll et al, 2009). Unfortunately, analyses of recombination patterns have been limited by the low number of available full-length genome sequences and, most critically, limited geographical coverage of HPeV isolates.…”

mentioning

confidence: 99%

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Full genome sequence analysis of parechoviruses from Brazil reveals geographical patterns in the evolution of non-structural genes and intratypic recombination in the capsid region

Drexler

Grywna

Lukashev

et al. 2010

Journal of General Virology

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Due to high genome plasticity, the evolutionary fate and geographical history of picornaviruses is hard to follow. Here, we determined the complete coding sequences of eight human parechoviruses (HPeV) of types 1, 5 and 6 directly from clinical samples from Brazil. The capsid genes of these strains were not remarkably different from European, North American and Japanese HPeV. Full genome analysis revealed frequent intertypic recombination in the nonstructural genome region. In addition, evidence of recombination between viruses of the same type in the capsid-encoding genome region among HPeV1 and HPeV4 was obtained. Bayesian phylogenetic analysis indicated that strains without evidence of recombination with each other in any genome region were separated by no more than 35 years of circulation. Interestingly, in the 3C gene, all Brazilian parechoviruses grouped together regardless of serotype. The most recent common ancestor of these strains dated back 108 years, suggesting long-term endemicity of this particular P3 genome lineage in South America. Our results support the idea that picornavirus replicative genes acquire capsid proteins introduced by new strains. Under certain epidemiological conditions, replicative genes may be maintained in circumscript geographical regions. INTRODUCTIONHuman parechoviruses (HPeV) are small non-enveloped viruses that define a genus of the family Picornaviridae. Their positive-sense RNA genome encodes a single polyprotein that is cleaved into three structural proteins, VP0, VP3 and VP1 (defining the P1 genome region), and seven non-structural proteins, 2A-2C (P2) and 3A-3D (P3). The first two HPeV serotypes were isolated in the 1950s and designated echovirus 22 and 23. In the 1990s, parechoviruses were reclassified into a new genus based on their distinct genome organization (Hyypiä et al., 1992). High prevalence of HPeV was not truly appreciated until the last few years. Recently, HPeVs were shown to be highly diverse, with up to 14 provisionally assigned types (AlSunaidi et al., 2007;Benschop et al., 2008a; Drexler et al., 2009;Ito et al., 2004; Kim Pham et al., 2010;Li et al., 2009;Watanabe et al., 2007). HPeV also proved highly prevalent in the human population, with seropositivity rates reaching 88 % at the age of 2 years (Joki-Korpela & Hyypiä, 1998;Takao et al., 2001), and an important cause of meningitis and sepsis-like disease of newborns (Baumgarte et al., 2008; 3These authors contributed equally to this work.The GenBank/EMBL/DDBJ accession numbers for the sequences reported in this paper are HQ696570-HQ696577. Wolthers et al., 2008). In general, recent reports showed that epidemiological and clinical features of HPeV are similar to the most common picornavirus genus, Enterovirus. HPeV genetic and evolutionary properties also resemble those of enteroviruses. They feature both high mutation rate (Faria et al., 2009) and frequent natural recombination (Benschop et al., 2008bCalvert et al., 2010;Williams et al., 2009;Zoll et al., 2009). Unfortunately, analyses of re...

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Section: Validation Of Coalescent Dating Assumptionssupporting

confidence: 71%

supporting

confidence: 75%

Section: Whole Genome Analysis Of Hpevsupporting

confidence: 60%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Full genome sequence analysis of parechoviruses from Brazil reveals geographical patterns in the evolution of non-structural genes and intratypic recombination in the capsid region

Drexler

Grywna

Lukashev

et al. 2010

Journal of General Virology

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Enteroviruses and Parechoviruses

Stellrecht,

Lamson,

Romero

2023

ClinMicroNow

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Enteroviruses (EVs) are members of the Picornaviridae family, with “pico” meaning very small, “rna” indicating an RNA genome, and “viridae” signifying viruses. Traditional criteria for taxonomy and identification of EVs to subgroups were based on patterns of replication in cell cultures, clinical syndromes, or disease and on disease manifestations in suckling mice. EVs and Parechoviruses (PeVs) cause a wide array of both localized and systemic infections that affect many organ systems in patients of all ages. Specimen selection is important for making a diagnosis of EV infection, as asymptomatic shedding, especially in stool, is common. Nucleic acid amplification tests, such as reverse transcriptase PCR, are the recommended method for the detection of EV and PeV because of their enhanced sensitivity and rapid turnaround times. In the clinical setting, situations may arise where EV serology is requested; such is the case for myocarditis and determination of congenital infection in pregnant women.

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Whole genomic characterization of a Korean human parechovirus type 1 (HPeV1) identifies recombination events

2014

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A human parechovirus (HPeV) strain CAU10-NN was detected from a stool sample of a 2-year-old healthy female infant in South Korea using a metagenomic approach. The CAU10-NN virus was isolated using a cell culture system and its whole genome was analyzed. The RNA genome of the CAU10-NN strain consists of 7,348 nucleotides (nt), excluding a poly(A) tail. A large open reading frame of 6,540 nt that encodes a putative polyprotein precursor of 2,180 amino acids is flanked by a 5'-untranslated region (UTR) of 708 nt and 3'-UTR of 88 nt followed by a poly(A) tail. Phylogenetic analysis shows that the CAU10-NN strain belongs to HPeV1. SimPlot and Bootscan analyses reveal that the virus genome is composed of regions related to corresponding genomic regions of other HPeVs. Recombination analysis indicates that the CAU10-NN strain might be a product of more than one genomic recombination event that occurred among HPeV1, HPeV3, and HPeV4 strains.

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Evolution and conservation in human parechovirus genomes

Cited by 49 publications

References 50 publications

Full genome sequence analysis of parechoviruses from Brazil reveals geographical patterns in the evolution of non-structural genes and intratypic recombination in the capsid region

Full genome sequence analysis of parechoviruses from Brazil reveals geographical patterns in the evolution of non-structural genes and intratypic recombination in the capsid region

Enteroviruses and Parechoviruses

Whole genomic characterization of a Korean human parechovirus type 1 (HPeV1) identifies recombination events

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