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Metagenomic analysis identifies human adenovirus 31 in children with acute flaccid paralysis in Tunisia

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Abstract

A variety of viruses can cause acute flaccid paralysis (AFP). However, the causative agent, sometimes, remains undetermined. Metagenomics helps in identifying viruses not diagnosed by conventional methods. Stool samples from AFP (n = 104) and non-AFP (n = 114) cases that tested enterovirus-negative by WHO standard methods were investigated. A metagenomics approach, first used on five pools of four samples each, revealed the presence of adenovirus sequences. Amplification in A549 cells and full-genome sequencing were used for complete virus identification and for designing a PCR assay to screen individual related samples. Metagenomic analysis showed that adenovirus sequences that were closely to the A31 and A61 genotypes were the most abundant. Two out of the corresponding 20 individual samples were found positive by PCR, and isolates were obtained in cell culture. Phylogenetic analysis based on complete genome sequences showed that the viruses belong to HAdV-A31 genotype (98-100% nucleotide sequence identity). PCR analysis of stool samples from all AFP and non-AFP cases revealed that a larger proportion of the positive samples were from AFP cases (17.3%) than from non-AFP cases (2.4%). These results open the way to studies aiming to test a possible role of HAdV-A31 in the pathogenesis of AFP.

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Acknowledgements

The authors thank the directory of Primary Health Care in Tunisia, and the national staff of the Ministry of Health at all levels, for their efforts in the field work as part of the case investigations and for providing epidemiological and clinical data, and the company PathoQuest (Paris) for the bioinformatics analysis of NGS data from the five pools of stools.

Funding

This study was funded by Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ [grant number ANR-10-LABX-62-IBEID], “programme Transversal de Recherche PTR484”, Action Concertée des Instituts Pasteur ACIP A22-16, by the Fondation Total [grant number S-CM15010-05B] (http://fondation.total/fr) and the Tunisian Ministry for Scientific Research and Technology.

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Author notes

  1. Françis Delpeyroux, Henda Triki, Marc Eloit are senior authors contributed equally to this work.

Authors and Affiliations

  1. Laboratory of Clinical Virology, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia

    Sondes Haddad-Boubaker, Zina Meddeb, Hinda Touzi & Henda Triki

  2. WHO Regional Reference Laboratory for Poliomyelitis and Measles in Eastern Mediterranean Region, Institut Pasteur de Tunis, 13 Place Pasteur, BP74, 1002, Tunis, Tunisia

    Sondes Haddad-Boubaker, Zina Meddeb, Hinda Touzi & Henda Triki

  3. Enteric Virus Unit, Institut Pasteur, 23 rue du Dr Roux, 75015, Paris, France

    Marie-Line Joffret, Mael Bessaud & Françis Delpeyroux

  4. Institut National de la Santé et de la Recherche Médicale (INSERM), U994, Paris, France

    Marie-Line Joffret, Mael Bessaud & Françis Delpeyroux

  5. Pathogen Discovery Laboratory and Biology of Infection Unit, Inserm U1117, Institut Pasteur, 28 rue du Dr Roux, 75015, Paris, France

    Philippe Pérot & Marc Eloit

  6. Ecole Nationale Vétérinaire d’Alfort, Virology, 7 av du Gal de Gaulle, 94704, Maisons Alfort, France

    Marc Eloit

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  1. Sondes Haddad-Boubaker
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Haddad-Boubaker, S., Joffret, ML., Pérot, P. et al. Metagenomic analysis identifies human adenovirus 31 in children with acute flaccid paralysis in Tunisia. Arch Virol 164, 747–755 (2019). https://doi.org/10.1007/s00705-018-04141-5

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