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Detection of Common, Emerging and Uncommon VP4, and VP7 Human Group A Rotavirus Genotypes from Urban Sewage Samples in Uruguay

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Abstract

Environmental approach has proven to be a useful tool for epidemiological studies demonstrating through environmental studies the diversity of viruses circulating in a given population. The aim of this study was to perform a phylogenetic characterization of the group A rotavirus (RVA) glycoprotein (G)- and protease-sensitive (P)-genotypes obtained from sewage samples (n = 116) collected in six cities of Uruguay during March 2011 to April 2013. A worldwide standardized semi-nested multiplex RT-PCR (SNM RT-PCR) protocol directed against VP4 and VP7 genes were conducted for RVA detection and consensual DNA fragments were submitted to nucleotide sequencing. P and/or G genotype was successfully determined by phylogenetic analysis in 61 % (n = 37) of the positive samples obtained by SNM RT-PCR (n = 61). The RVA genotypes were as follow: G1 (n = 2), G2 (n = 14), G3 (n = 5), G12 (n = 2), P[4] (n = 4), P[8] (n = 16), and P[3] (n = 2). Interestingly, through phylogenetic analysis, emerging, and uncommon human genotypes could be detected. Results obtained from the comparison of RVA genotypes detected in the current study and Uruguayan RVA strains previously described for contemporary clinical pediatric cases showed that monitoring sewage may be a good screening option for a rapid and economical overview of the circulating genotypes in the surrounding human population and a useful approximation to study RVA epidemiology in a future vaccine monitoring program. The present study represents the first report in Uruguay that describes the phylogenetic diversity of RVA from urban sewage samples.

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Acknowledgments

We want to thank the financial support by the program ‘‘Polo de Desarrollo Universitario’’ (PDU), Universidad de la República (UdelaR), Uruguay; Project PCPP 023/2011 of ‘‘Coordenação de Aperfeiçoamento de Pessoal de Nível Superior’’ (CAPES, Brazil); ‘‘Agencia Nacional de Investigación e Innovación’’ project ANII-ALI-2009-1-1603; and project CSIC I+D 2010, Universidad de la República (UdelaR). We also thank “Sección Bioquímica, Instituto de Biología, Facultad de Ciencias” and “Instituto Pasteur, Montevideo, Uruguay”, for technical assistance.

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Authors and Affiliations

  1. Laboratorio de Virología Molecular, Departamento de Ciencias Biológicas, Regional Norte – CENUR Litoral Norte, Universidad de la República, Gral. Rivera 1350, 50000, Salto, Uruguay

    Luis Fernando Lopez Tort, Matías Victoria, Andrés Lizasoain, Mariana García & Rodney Colina

  2. Sección Virología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay

    Mabel Berois

  3. Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay

    Juan Cristina

  4. Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil 4365, Rio de Janeiro, 21040-360, Brazil

    José Paulo Gagliardi Leite, Mariela Martínez Gómez & Marize Pereira Miagostovich

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  1. Luis Fernando Lopez Tort
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Electronic supplementary material

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12560_2015_9213_MOESM1_ESM.pdf

Supplementary material 1 (PDF 197 kb). Online Resource 1 Table of primers used for G/P detection and ty** of group A rotavirus (RVA) by semi-nested multiplex RT-PCR and phylogenetic analysis

12560_2015_9213_MOESM2_ESM.pdf

Supplementary material 2 (PDF 265 kb). Online Resource 2 Table of sewage samples analyzed in this study with their respective G- and/or P-types types determined by phylogenetic studies

12560_2015_9213_MOESM3_ESM.tif

Supplementary material 3 (TIFF 3239 kb). Online Resource 3 G- and P-types distribution of group A rotavirus (RVA) detected according to the collection sites in Northwestern -a) to d)- and Eastern -e) and f)- regions of Uruguay

12560_2015_9213_MOESM4_ESM.tif

Supplementary material 4 (TIFF 3013 kb). Online Resource 4 Maximum likelihood phylogenetic tree analysis of the G3 group A rotavirus (RVA) strains detected in sewage from Uruguay. Strains in the trees are shown by name following the RV strain nomenclature proposed by the Rotavirus Classification Working Group (RCWG). Prototype strains previously described are also shown by accession numbers. Strains isolated in this study at the Northwestern region of Uruguay are marked with a filled square. Strains isolated in this study at the Eastern region of Uruguay are marked with a filled triangle. Uruguayan strains previously described that were detected from clinical samples collected from hospitalized children with acute diarrhea in Salto city, Uruguay, in 2011 and 2012, are marked with a filled circle. The trees were constructed with Tamura 3-parameter+G+I model as determined by using the jModelTest program. Numbers at the internal nodes in the tree indicate Bootstrap values (only values above 70 % are shown). The scale bar at the bottom represents substitutions per nucleotide position (nt.subst./site)

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Tort, L.F.L., Victoria, M., Lizasoain, A. et al. Detection of Common, Emerging and Uncommon VP4, and VP7 Human Group A Rotavirus Genotypes from Urban Sewage Samples in Uruguay. Food Environ Virol 7, 342–353 (2015). https://doi.org/10.1007/s12560-015-9213-5

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