title: Enteroviruses and Rhinoviruses: Molecular Epidemiology of the Most Influenza-Like Illness Associated Viruses in Senegal.
abstract: 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.
authors.affiliation: Unité de Virologie Médicale, Institut Pasteur de Dakar, Dakar, Sénégal.
authors.forename: Amary
authors.initials: A
authors.lastname: Fall
authors.affiliation: Unité de Virologie Médicale, Institut Pasteur de Dakar, Dakar, Sénégal.
authors.forename: Ndongo
authors.initials: N
authors.lastname: Dia
authors.affiliation: Unité de Virologie Médicale, Institut Pasteur de Dakar, Dakar, Sénégal.
authors.forename: Ousmane
authors.initials: O
authors.lastname: Kébé
authors.affiliation: Unité d'Epidémiologie des Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Sénégal.
authors.forename: Fatoumata Diene
authors.initials: FD
authors.lastname: Sarr
authors.affiliation: Unité de Virologie Médicale, Institut Pasteur de Dakar, Dakar, Sénégal.
authors.forename: Davy E
authors.initials: DE
authors.lastname: Kiori
authors.affiliation: Unité de Virologie Médicale, Institut Pasteur de Dakar, Dakar, Sénégal.
authors.forename: El Hadj Abdoul Khadir
authors.initials: el HA
authors.lastname: Cissé
authors.affiliation: Unité de Virologie Médicale, Institut Pasteur de Dakar, Dakar, Sénégal.
authors.forename: Sara
authors.initials: S
authors.lastname: Sy
authors.affiliation: Unité de Virologie Médicale, Institut Pasteur de Dakar, Dakar, Sénégal.
authors.forename: Deborah
authors.initials: D
authors.lastname: Goudiaby
authors.affiliation: Unité d'Epidémiologie des Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Sénégal.
authors.forename: Vincent
authors.initials: V
authors.lastname: Richard
authors.affiliation: Unité de Virologie Médicale, Institut Pasteur de Dakar, Dakar, Sénégal.
authors.forename: Ousmane Madiagne
authors.initials: OM
authors.lastname: Diop
authors.affiliation: Unité de Virologie Médicale, Institut Pasteur de Dakar, Dakar, Sénégal. niang@pasteur.sn.
authors.forename: Mbayame Ndiaye
authors.initials: MN
authors.lastname: Niang
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics; D000293:Adolescent; D000328:Adult; D036022:Capsid Proteins / Q000235:genetics; D002648:Child; D002675:Child, Preschool; D029822:Enterovirus B, Human / Q000737:chemistry / Q000235:genetics* / Q000302:isolation & purification; D004769:Enterovirus Infections / Q000175:diagnosis / Q000453:epidemiology* / Q000821:virology; D005260:Female; D006801:Humans; D015994:Incidence; D007223:Infant; D007231:Infant, Newborn; D008297:Male; D008875:Middle Aged; D017720:Molecular Epidemiology; D009305:Nasopharynx / Q000821:virology; D010802:Phylogeny; D010850:Picornaviridae Infections / Q000175:diagnosis / Q000453:epidemiology* / Q000821:virology; D062486:Public Health Surveillance; D060888:Real-Time Polymerase Chain Reaction; D012141:Respiratory Tract Infections / Q000175:diagnosis / Q000453:epidemiology* / Q000821:virology; D012229:Rhinovirus / Q000737:chemistry / Q000235:genetics* / Q000302:isolation & purification; D012675:Senegal / Q000453:epidemiology; D014764:Viral Proteins / Q000235:genetics
chemical_list: D020121:5' Untranslated Regions; D036022:Capsid Proteins; C442544:VP2 protein, Rhinovirus; D014764:Viral Proteins; C074995:viral protein 1, rhinovirus