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Human astrovirus types 1, 4 and 5 circulating among children with acute gastroenteritis in a rural Brazilian state, 2010-2016

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Abstract

This study combined conventional epidemiology of human astroviruses. From 2010 to 2016, 232 stool samples from children under 5 years of age were screened using NGS and conventional RT-PCR followed by genetic analysis in order to investigate the genotypic diversity of classical human astrovirus (HAstV) circulating in Tocantins State, Brazil. HAstV was detected in 16 cases (6.9%). Seven specimens (43.7%; 7/16) were positive according RT-PCR and next-generation sequencing (NGS) to investigate the molecular to both NGS and RT-PCR. NGS and RT-PCR individually revealed six (37.5%; 6/16) and three (18.8%; 3/16) additional positive samples, respectively. Sequencing of the HAstV-positive samples revealed HAstV-1a (9/16), HAstV-4c (3/16), and HAstV-5c (4/16) lineages.

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Acknowledgements

We would like to thank Luciano Monteiro da Silva for administrative support, as well as 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 São Paulo Research Foundation (FAPESP) grant number 2016/01735-2 and the Brazilian National Council for Scientific and Technological Development (CNPq) grant number 400354/2016-0. Antonio Charlys da Costa is supported by FAPESP grant number 2017/00021-9, Adriana Luchs is supported by FAPESP grant number 2015/12944-9, Vanessa S. Morais is supported by FAPESP grant number 2019/21706-5, Elcio Leal is supported by CNPq grant number 302677/2019-4, Yasmin França Viana Pires de Souza is supported by FAPESP grant number 2020/02469-0, and Roberta Salzone Medeiros is supported by FAPESP grant number 2020/11182-6.

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Author notes

  1. Adriana Luchs and Kaelan Tardy have contributed equally to this work.

  2. Eric Delwart, Ester Cerdeira Sabino, Elcio Leal, Antonio Charlys da Costa have jointly supervised this work.

Authors and Affiliations

  1. Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, Av. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brazil

    Adriana Luchs, Simone Guadagnucci Morillo, Lais Sampaio de Azevedo, Ellen Viana de Souza, Roberta Salzone Medeiros & Yasmin França Viana Pires de Souza

  2. Instituto de Medicina Tropical, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil

    Kaelan Tardy, Roozbeh Tahmasebi, Vanessa dos Santos Morais, Steven S. Witkin, Ester Cerdeira Sabino & Antonio Charlys da Costa

  3. Universidade Federal do Tocantins, Tocantins, Brazil

    Flavio Augusto de Pádua Milagres & Rafael Brustulin

  4. Laboratório Central de Saúde Pública do Tocantins (Lacen-TO), Tocantins, Brazil

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

  5. Coordenação Geral de Laboratórios de Saúde Pública, Departamento de Articulação Estratégica de Vigilância em Saúde da Secretaria de Vigilância em Saúde do Ministério da Saúde do Brasil (CGLAB/DAEVS/SVS-MS), Brasília, Brazil

    Emerson Luiz Lima Araújo

  6. Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, USA

    Steven S. Witkin

  7. Vitalant Research Institute, San Francisco, USA

    Xutao Deng & Eric Delwart

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

    Xutao Deng & Eric Delwart

  9. Instituto de Ciências Biológicas, Universidade Federal do Pará, Pará, Brazil

    Elcio Leal

Authors
  1. Adriana Luchs
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  2. Kaelan Tardy
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  3. Roozbeh Tahmasebi
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Contributions

AL and ACC conceived the study; AL, ED, ECS, EL, and ACC designed the study protocol; KT, RT, FAPM, VSM, RB, MART, ELL, and SSW participated in the study itself, including in the collection and screening of the specimens; SGM, EVS, LSA, RSM, and YFVPS performed the conventional RT-PCR and Sanger sequencing assays; RT, VSM, SSW, and ACC performed the deep-sequencing assays; XD, ED, EL, and ACC analyzed the big data; AL and KT performed the phylogenetic analyses; AL, KT, ED, ECS, EL, and ACC analyzed and interpreted the data; ED, ECS, EL, and ACC supervised the study; AL and KT drafted the manuscript; all of the authors critically revised the manuscript for intellectual content and approved the final version. AL and ACC are guarantors of the paper.

Corresponding authors

Correspondence to Adriana Luchs or Antonio Charlys da Costa.

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The authors have no conflicts of interest to disclose.

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Ethical approval was granted by the School of Medicine of the Universidade de São Paulo (CAAE Registry No. 53153916.7.0000.0065) and the Centro Universitário Luterano de Palmas (ULBRA) (CAAE Registry No. 53153916.7.3007.5516).

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Luchs, A., Tardy, K., Tahmasebi, R. et al. Human astrovirus types 1, 4 and 5 circulating among children with acute gastroenteritis in a rural Brazilian state, 2010-2016. Arch Virol 166, 3165–3172 (2021). https://doi.org/10.1007/s00705-021-05206-8

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