Archives of Virology

, Volume 164, Issue 3, pp 747–755 | Cite as

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

  • Sondes Haddad-Boubaker
  • Marie-Line Joffret
  • Philippe Pérot
  • Mael Bessaud
  • Zina Meddeb
  • Hinda Touzi
  • Françis Delpeyroux
  • Henda Triki
  • Marc EloitEmail author
Original Article


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.



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.


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] ( and the Tunisian Ministry for Scientific Research and Technology.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no competing interests.

Supplementary material

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Supplementary material 1 (DOCX 54 kb)
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Supplementary material 2 (PDF 165 kb)
705_2018_4141_MOESM3_ESM.pdf (173 kb)
Supplementary material 3 (PDF 172 kb)
705_2018_4141_MOESM4_ESM.pptx (62 kb)
Supplementary material 4 (PPTX 61 kb)


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Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2019

Authors and Affiliations

  • Sondes Haddad-Boubaker
    • 1
    • 2
  • Marie-Line Joffret
    • 3
    • 4
  • Philippe Pérot
    • 5
  • Mael Bessaud
    • 3
    • 4
  • Zina Meddeb
    • 1
    • 2
  • Hinda Touzi
    • 1
    • 2
  • Françis Delpeyroux
    • 3
    • 4
  • Henda Triki
    • 1
    • 2
  • Marc Eloit
    • 5
    • 6
    Email author
  1. 1.Laboratory of Clinical Virology, Institut Pasteur de TunisUniversity of Tunis El ManarTunisTunisia
  2. 2.WHO Regional Reference Laboratory for Poliomyelitis and Measles in Eastern Mediterranean RegionInstitut Pasteur de TunisTunisTunisia
  3. 3.Enteric Virus UnitInstitut PasteurParisFrance
  4. 4.Institut National de la Santé et de la Recherche Médicale (INSERM), U994ParisFrance
  5. 5.Pathogen Discovery Laboratory and Biology of Infection UnitInserm U1117, Institut PasteurParisFrance
  6. 6.Ecole Nationale Vétérinaire d’Alfort, VirologyMaisons AlfortFrance

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