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Enteroviruses and Rhinoviruses: Molecular Epidemiology of the Most Influenza-Like Illness Associated Viruses in Senegal

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  • 1 Unité de Virologie Médicale, Institut Pasteur de Dakar, Dakar, Sénégal.
  • | 2 Unité d'Epidémiologie des Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Sénégal.

Different viruses have been identified as etiologic agents of respiratory tract infections, including severe cases. Among these, human rhinoviruses (HRVs) and human enteroviruses (HEVs) are recognized as leading causes. The present study describes the molecular epidemiology of HRVs and HEVs in Senegal over a 3-year surveillance period. From January 2012 to December 2014, nasopharyngeal and oropharyngeal swabs specimen were collected from patients with influenza-like illness (ILI). A real-time reverse transcription polymerase chain reaction was performed for HRV and HEV detection using the RV16 kit. Two regions were targeted for the molecular characterization of RVs: 5′ untranslated region (5′UTR) and viral protein 4/viral protein 2 (VP4/VP2) transition region. For enteroviruses (EVs) phylogeny, VP1 gene was targeted. A total of 4,194 samples were collected. Children up to 5 years accounted for 52.9%. Among them, 1,415 (33.7%) were positive for HRV, 857 (20.4%) for HEV, and 437 cases of dual infections HRV/HEV. HRVs and HEVs were identified significantly in children aged 5 years or less. Only cough and vomiting signs were observed with significant association with viral infection. Both viruses co-circulated all year long with a marked increase of activity during rainy and cold period. All HRV types circulate in Senegal. HRV-A and C groups were the most common. HEV serotyping identified coxsackie B viruses (CBV) only. VP1 region revealed different CBV (CBV1, CBV2, CBV3, CBV4, and CBV5), echoviruses, coxsackieviruses A4–like strains and a poliovirus 2. The results suggest strong year-round respiratory picornavirus activity in children up to 5 years of age. Molecular studies identified a wide variety of RVs along with diverse EVs in samples from patients with ILI.

Author Notes

* Address correspondence to Mbayame Ndiaye Niang, Unité de Virologie Médicale, Institut Pasteur de Dakar, 36 Avenue Pasteur, BP 220, Dakar, Sénégal. E-mail: niang@pasteur.sn† These authors contributed equally to this work.

Financial support: This work was supported by the Department of Health and Human Service (DHSS) via the International Network of Pasteur Institutes and Pasteur Institute of Dakar.

Authors' addresses: Amary Fall, Ndongo Dia, Ousmane Kébé, Davy E. Kiori, El Hadj Abdoul Khadir Cissé, Sara Sy, Deborah Goudiaby, Ousmane Madiagne Diop, and Mbayame Ndiaye Niang, Medical Virology Unit, Institut Pasteur de Dakar, Senegal, E-mails: amary022@hotmail.com, ndia@pasteur.sn, bigouze87@live.fr, dekiori@pasteur.sn, akacisse@pasteur.sn, sarasy16@outlook.fr, dgoudiaby@pasteur.sn, diopo@who.int, and niang@pasteur.sn. Fatoumata Diene Sarr and Vincent Richard, Epidemiology Unit, Institut Pasteur de Dakar, Senegal, E-mails: fdsarr@yahoo.fr and virc@hotmail.fr.

Reprint requests: Mbayame N. Niang, Institut Pasteur de Dakar, 36 Avenue Pasteur, BP 220, Dakar, Senegal, E-mail: niang@pasteur.sn, Tel: 00 221 839 92 22.

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