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Genotypes, recombinant forms, and variants of norovirus GII.4 in Gipuzkoa (Basque Country, Spain), 2009-2012.

Arana A, Cilla G, Montes M, Gomariz M, Pérez-Trallero E - PLoS ONE (2014)

Bottom Line: Recombinant strains were confirmed by PCR of the ORF1/ORF2 junction region.Nine different genotypes of NoV genogroup II were detected; among these, intergenotype recombinant strains represented an important part, highlighting the role of recombination in the evolution of NoVs.Detection of new NoV strains, not only GII.4 strains, shortly after their first detection in other parts of the world shows that many NoV strains can spread rapidly.

View Article: PubMed Central - PubMed

Affiliation: Servicio de Microbiología, Hospital Universitario Donostia-Instituto de Investigación Biodonostia, San Sebastián, Spain.

ABSTRACT

Background: Noroviruses (NoVs) are genetically diverse, with genogroup II-and within it-genotype 4 (GII.4) being the most prevalent cause of acute gastroenteritis worldwide. The aim of this study was to characterize genogroup II NoV causing acute gastroenteritis in the Basque Country (northern Spain) from 2009-2012.

Methods: The presence of NoV RNA was investigated by reverse transcriptase-polymerase chain reaction (RT-PCR) in stool specimens from children younger than 15 years old with community-acquired acute gastroenteritis, and from hospitalized adults or elderly residents of nursing homes with acute gastroenteritis. For genotyping, the open reading frames ORF1 (encoding the polymerase) and ORF2 (encoding the major capsid protein) were partially amplified and sequenced. Recombinant strains were confirmed by PCR of the ORF1/ORF2 junction region.

Results: NoV was detected in 16.0% (453/2826) of acute gastroenteritis episodes in children younger than 2 years, 9.9% (139/1407) in children from 2 to 14 years, and 35.8% (122/341) in adults. Of 317 NoVs characterized, 313 were genogroup II and four were genogroup I. The GII.4 variants Den Haag-2006b and New Orleans-2009 predominated in 2009 and 2010-2011, respectively. In 2012, the New Orleans-2009 variant was partially replaced by the Sydney-2012 variant (GII.Pe/GII.4) and New Orleans-2009/Sydney-2012 recombinant strains. The predominant capsid genotype in all age groups was GII.4, which was the only genotype detected in outbreaks. The second most frequent genotype was GII.3 (including the recently described recombination GII.P16/GII.3), which was detected almost exclusively in children.

Conclusion: Nine different genotypes of NoV genogroup II were detected; among these, intergenotype recombinant strains represented an important part, highlighting the role of recombination in the evolution of NoVs. Detection of new NoV strains, not only GII.4 strains, shortly after their first detection in other parts of the world shows that many NoV strains can spread rapidly.

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Phylogenetic analyses of GII.3 and GII.P16 norovirus recombinant strains.a) partial capsid (ORF2) GII.3 gene (259 nt) and b) partial polymerase (ORF1) GII.P16 gene (719 nt), from distinct patients with acute gastroenteritis, detected in Gipuzkoa (Basque Country, Spain) in 2009–2012, compared with some representative strains. The trees were constructed in Mega 6 through the Maximun Likelihood method using the best model, Kimura 2-parameter+G, as determined also in Mega 6 using the Bayesian information criterion, with 1000 bootstrap replications for branch support. Bootstrap values >75% are shown. Scale bars indicate the number of substitutions per nucleotide position. Norovirus strains detected in this study are marked with the following symbols: ▴, GII.P16-GII.3; ▪, GII.P16-GII.13; ♦, GII.P21-GII.3 detected in 2009; •, GII.P21-GII.3 detected in 2012. a.- Capsid (ORF2). b.- Polymerase (ORF1). Footnote (figure 1b). *When this sequence was analyzed in the Noronet typing tool, was classified as GII.P16/GII.13.
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pone-0098875-g001: Phylogenetic analyses of GII.3 and GII.P16 norovirus recombinant strains.a) partial capsid (ORF2) GII.3 gene (259 nt) and b) partial polymerase (ORF1) GII.P16 gene (719 nt), from distinct patients with acute gastroenteritis, detected in Gipuzkoa (Basque Country, Spain) in 2009–2012, compared with some representative strains. The trees were constructed in Mega 6 through the Maximun Likelihood method using the best model, Kimura 2-parameter+G, as determined also in Mega 6 using the Bayesian information criterion, with 1000 bootstrap replications for branch support. Bootstrap values >75% are shown. Scale bars indicate the number of substitutions per nucleotide position. Norovirus strains detected in this study are marked with the following symbols: ▴, GII.P16-GII.3; ▪, GII.P16-GII.13; ♦, GII.P21-GII.3 detected in 2009; •, GII.P21-GII.3 detected in 2012. a.- Capsid (ORF2). b.- Polymerase (ORF1). Footnote (figure 1b). *When this sequence was analyzed in the Noronet typing tool, was classified as GII.P16/GII.13.

Mentions: The partial capsid sequence analysis of the GII.3 NoVs showed that strains associated with GII.P16 polymerase segregated in a cluster, the identity of the intracluster nucleotides being >98%, and nucleotide identity with GII.3 strains associated to GII.P21 circulating the same year being 91.7–93.4% (Figure 1a). On the other hand, analysis of the partial polymerase gene of GII.P16 NoV strains segregated them in two well defined clusters, according to the associated capsid: one grouping the GII.2 and GII.16 strains and the other grouping the recently described recombinations with GII.3 and GII.13 strains, as well as two GII.2 strains detected in Japan in 2010 and 2011 (Figure 1b).


Genotypes, recombinant forms, and variants of norovirus GII.4 in Gipuzkoa (Basque Country, Spain), 2009-2012.

Arana A, Cilla G, Montes M, Gomariz M, Pérez-Trallero E - PLoS ONE (2014)

Phylogenetic analyses of GII.3 and GII.P16 norovirus recombinant strains.a) partial capsid (ORF2) GII.3 gene (259 nt) and b) partial polymerase (ORF1) GII.P16 gene (719 nt), from distinct patients with acute gastroenteritis, detected in Gipuzkoa (Basque Country, Spain) in 2009–2012, compared with some representative strains. The trees were constructed in Mega 6 through the Maximun Likelihood method using the best model, Kimura 2-parameter+G, as determined also in Mega 6 using the Bayesian information criterion, with 1000 bootstrap replications for branch support. Bootstrap values >75% are shown. Scale bars indicate the number of substitutions per nucleotide position. Norovirus strains detected in this study are marked with the following symbols: ▴, GII.P16-GII.3; ▪, GII.P16-GII.13; ♦, GII.P21-GII.3 detected in 2009; •, GII.P21-GII.3 detected in 2012. a.- Capsid (ORF2). b.- Polymerase (ORF1). Footnote (figure 1b). *When this sequence was analyzed in the Noronet typing tool, was classified as GII.P16/GII.13.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4043750&req=5

pone-0098875-g001: Phylogenetic analyses of GII.3 and GII.P16 norovirus recombinant strains.a) partial capsid (ORF2) GII.3 gene (259 nt) and b) partial polymerase (ORF1) GII.P16 gene (719 nt), from distinct patients with acute gastroenteritis, detected in Gipuzkoa (Basque Country, Spain) in 2009–2012, compared with some representative strains. The trees were constructed in Mega 6 through the Maximun Likelihood method using the best model, Kimura 2-parameter+G, as determined also in Mega 6 using the Bayesian information criterion, with 1000 bootstrap replications for branch support. Bootstrap values >75% are shown. Scale bars indicate the number of substitutions per nucleotide position. Norovirus strains detected in this study are marked with the following symbols: ▴, GII.P16-GII.3; ▪, GII.P16-GII.13; ♦, GII.P21-GII.3 detected in 2009; •, GII.P21-GII.3 detected in 2012. a.- Capsid (ORF2). b.- Polymerase (ORF1). Footnote (figure 1b). *When this sequence was analyzed in the Noronet typing tool, was classified as GII.P16/GII.13.
Mentions: The partial capsid sequence analysis of the GII.3 NoVs showed that strains associated with GII.P16 polymerase segregated in a cluster, the identity of the intracluster nucleotides being >98%, and nucleotide identity with GII.3 strains associated to GII.P21 circulating the same year being 91.7–93.4% (Figure 1a). On the other hand, analysis of the partial polymerase gene of GII.P16 NoV strains segregated them in two well defined clusters, according to the associated capsid: one grouping the GII.2 and GII.16 strains and the other grouping the recently described recombinations with GII.3 and GII.13 strains, as well as two GII.2 strains detected in Japan in 2010 and 2011 (Figure 1b).

Bottom Line: Recombinant strains were confirmed by PCR of the ORF1/ORF2 junction region.Nine different genotypes of NoV genogroup II were detected; among these, intergenotype recombinant strains represented an important part, highlighting the role of recombination in the evolution of NoVs.Detection of new NoV strains, not only GII.4 strains, shortly after their first detection in other parts of the world shows that many NoV strains can spread rapidly.

View Article: PubMed Central - PubMed

Affiliation: Servicio de Microbiología, Hospital Universitario Donostia-Instituto de Investigación Biodonostia, San Sebastián, Spain.

ABSTRACT

Background: Noroviruses (NoVs) are genetically diverse, with genogroup II-and within it-genotype 4 (GII.4) being the most prevalent cause of acute gastroenteritis worldwide. The aim of this study was to characterize genogroup II NoV causing acute gastroenteritis in the Basque Country (northern Spain) from 2009-2012.

Methods: The presence of NoV RNA was investigated by reverse transcriptase-polymerase chain reaction (RT-PCR) in stool specimens from children younger than 15 years old with community-acquired acute gastroenteritis, and from hospitalized adults or elderly residents of nursing homes with acute gastroenteritis. For genotyping, the open reading frames ORF1 (encoding the polymerase) and ORF2 (encoding the major capsid protein) were partially amplified and sequenced. Recombinant strains were confirmed by PCR of the ORF1/ORF2 junction region.

Results: NoV was detected in 16.0% (453/2826) of acute gastroenteritis episodes in children younger than 2 years, 9.9% (139/1407) in children from 2 to 14 years, and 35.8% (122/341) in adults. Of 317 NoVs characterized, 313 were genogroup II and four were genogroup I. The GII.4 variants Den Haag-2006b and New Orleans-2009 predominated in 2009 and 2010-2011, respectively. In 2012, the New Orleans-2009 variant was partially replaced by the Sydney-2012 variant (GII.Pe/GII.4) and New Orleans-2009/Sydney-2012 recombinant strains. The predominant capsid genotype in all age groups was GII.4, which was the only genotype detected in outbreaks. The second most frequent genotype was GII.3 (including the recently described recombination GII.P16/GII.3), which was detected almost exclusively in children.

Conclusion: Nine different genotypes of NoV genogroup II were detected; among these, intergenotype recombinant strains represented an important part, highlighting the role of recombination in the evolution of NoVs. Detection of new NoV strains, not only GII.4 strains, shortly after their first detection in other parts of the world shows that many NoV strains can spread rapidly.

Show MeSH
Related in: MedlinePlus