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Norovirus strains in patients with acute gastroenteritis in rural and low-income urban areas in northern Brazil

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Abstract

From 2010-2016, a total of 251 stool samples were screened for norovirus using next-generation sequencing (NGS) followed by phylogenetic analysis to investigate the genotypic diversity of noroviruses in rural and low-income urban areas in northern Brazil. Norovirus infection was detected in 19.9% (50/251) of the samples. Eight different genotypes were identified: GII.4_Sydney[P31] (64%, 32/50), GII.6[P7] (14%, 7/50), GII.17[P17] (6%, 3/50), GII.1[P33] (6%, 3/50), GII.3[P16] (4%, 2/50), GII.2[P16] (2%, 1/50), GII.2[P2] (2%, 1/50), and GII.4_New Orleans[P4] (2%, 1/50). Distinct GII.6[P7] variants were recognized, indicating the presence of different co-circulating strains. Elucidating norovirus genetic diversity will improve our understanding of their potential health burden, in particular for the GII.4_Sydney[P31] variant.

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Acknowledgements

We thank Luciano Monteiro da Silva for administrative support. Our thanks also to the Coordenação Geral de Laboratórios de Saúde Pública do Departamento de Articulação Estratégica da Secretaria de Vigilância em Saúde do Ministério da Saúde (CGLAB/DAEVS/SVS-MS), MP Biomedicals Inc., and Zymo Research Corporation, for the donation of reagents.

Funding

This study was partially supported by FAPESP #2016/01735-2 and CNPq #400354/2016-0. Antônio Charlys da Costa is funded by FAPESP #2017/00021-9, Adriana Luchs is funded by FAPESP #2015/12944-9, Vanessa S. Morais is funded by FAPESP #2019/21706-5, and Elcio Leal is funded by CNPq #302677/2019-4.

Author information

Author notes

  1. Rory J. Tinker, Antonio Charlys da Costa, and Roozbeh Tahmasebi contributed equally to this work.

  2. Eric Delwart, Ester Cerdeira Sabino, Elcio Leal, and Adriana Luchs jointly supervised this work.

Authors and Affiliations

  1. Instituto de Medicina Tropical, Universidade de São Paulo, Sao Paulo, Brasil

    Rory J. Tinker, Antonio Charlys da Costa, Roozbeh Tahmasebi, Vanessa dos Santos Morais & Ester Cerdeira Sabino

  2. Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom

    Rory J. Tinker

  3. Federal University of Tocantins, Tocantins, Brazil

    Flavio Augusto de Pádua Milagres & Rafael Brustulin

  4. Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins, Brazil

    Flavio Augusto de Pádua Milagres, Rafael Brustulin & Maria da Aparecida Rodrigues Teles

  5. Centre for Drug Design Discovery and Development, SRM University Delhi NCR, Sonepat, India

    Ramendra Pati Pandey

  6. Department of Molecular Biology in Medicine, Civil Hospital of Guadalajara, “Fray Antonio Alcalde”, Guadalajara, Mexico

    Alexis José-Abrego

  7. Vectorborne Disease Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil

    Mariana Sequetin Cunha

  8. General Coordination of Public Health Laboratories of the Strategic Articulation Department of the Health Surveillance Secretariat of the Ministry of Health (CGLAB/DAEVS/SVS-MS), Brasília, Brazil

    Emerson Luiz Lima Araújo

  9. Molecular and Genetic Biology Division, Department of Molecular Biology, Clemente Estable Biological Research Institute, Montevideo, Uruguay

    Mariela Martínez Gómez

  10. Vitalant Research Institute, San Francisco, USA

    Xutao Deng & Eric Delwart

  11. Department Laboratory Medicine, University of California San Francisco, San Francisco, USA

    Xutao Deng & Eric Delwart

  12. Institute of Biological Sciences, Federal University of Pará, Pará, Brazil

    Elcio Leal

  13. Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, Av. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brazil

    Adriana Luchs

Authors
  1. Rory J. Tinker
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  2. Antonio Charlys da Costa
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  3. Roozbeh Tahmasebi
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  4. Flavio Augusto de Pádua Milagres
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  5. Vanessa dos Santos Morais
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  6. Ramendra Pati Pandey
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  7. Alexis José-Abrego
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  8. Rafael Brustulin
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  9. Maria da Aparecida Rodrigues Teles
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  10. Mariana Sequetin Cunha
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  11. Emerson Luiz Lima Araújo
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  12. Mariela Martínez Gómez
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  13. Xutao Deng
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  14. Eric Delwart
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  15. Ester Cerdeira Sabino
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  16. Elcio Leal
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  17. Adriana Luchs
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Contributions

RJT, ACC, RT, ED, ECS, EL and AL conceived the study; RJT, ACC, EL and AL designed the study protocol; FAPM, RB and MART participated in the conduct of the study, collection and screening of the specimens; ACC, RT and VSM performed the deep-sequencing assays; ACC, XD, ED and EL analyzed the big data; RJT, ACC, RT, RPP, AJA, MSC, ELLA, MMG, ECS, EL and AL analyzed and interpreted the data; ED, ECS, EL and AL supervised the study; RJT, ACC, MSC, MMG, EL and AL drafted the manuscript; all authors critically revised the manuscript for intellectual content and approved the final version. ACC and AL are guarantors of the paper.

Corresponding authors

Correspondence to Antonio Charlys da Costa or Adriana Luchs.

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Conflict of interest

None.

Ethical approval

Previous Ethics Committee approval was granted by the Faculdade de Medicina da Universidade de São Paulo (CAAE: 53153916.7.0000.0065) and the Centro Universitário Luterano de Palmas - ULBRA (CAAE 53153916.7.3007.5516).

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Handling Editor: Reimar Johne.

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Tinker, R.J., da Costa, A.C., Tahmasebi, R. et al. Norovirus strains in patients with acute gastroenteritis in rural and low-income urban areas in northern Brazil. Arch Virol 166, 905–913 (2021). https://doi.org/10.1007/s00705-020-04944-5

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  • DOI: https://doi.org/10.1007/s00705-020-04944-5

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