title: Molecular Epidemiology of Human Rhinoviruses and Enteroviruses Highlights Their Diversity in Sub-Saharan Africa.
abstract: Human rhinoviruses (HRVs) and enteroviruses (HEVs) belong to the Enterovirus genus and are the most frequent cause of infection worldwide, but data on their molecular epidemiology in Africa are scarce. To understand HRV and HEV molecular epidemiology in this setting, we enrolled febrile pediatric patients participating in a large prospective cohort assessing the causes of fever in Tanzanian children. Naso/oropharyngeal swabs were systematically collected and tested by real-time RT-PCR for HRV and HEV. Viruses from positive samples were sequenced and phylogenetic analyses were then applied to highlight the HRV and HEV types as well as recombinant or divergent strains. Thirty-eight percent (378/1005) of the enrolled children harboured an HRV or HEV infection. Although some types were predominant, many distinct types were co-circulating, including a vaccinal poliovirus, HEV-A71 and HEV-D68. Three HRV-A recombinants were identified: HRV-A36/HRV-A67, HRV-A12/HRV-A67 and HRV-A96/HRV-A61. Four divergent HRV strains were also identified: one HRV-B strain and three HRV-C strains. This is the first prospective study focused on HRV and HEV molecular epidemiology in sub-Saharan Africa. This systematic and thorough large screening with careful clinical data management confirms the wide genomic diversity of these viruses, brings new insights about their evolution and provides data about associated symptoms.
authors.affiliation: Geneva University Hospitals and Medical School, 4 rue Gabrielle-Perret-Gentil, 1211 Geneva 14, Switzerland. arnaud.lhuillier@hcuge.ch.
authors.forename: Arnaud G
authors.initials: AG
authors.lastname: L'Huillier
authors.affiliation: Geneva University Hospitals and Medical School, 4 rue Gabrielle-Perret-Gentil, 1211 Geneva 14, Switzerland. laurent.kaiser@hcuge.ch.
authors.forename: Laurent
authors.initials: L
authors.lastname: Kaiser
authors.affiliation: Swiss Institute of Bioinformatics, Centre Medical Universitraire, 1 rue Michel-Servet, 1211 Geneva 4, Switzerland. tompetty2@gmail.com.
authors.forename: Tom J
authors.initials: TJ
authors.lastname: Petty
authors.affiliation: Amana Regional Referral Hospital, PO box 25411, Dar es Salaam TZ-02, United Republic of Tanzania. mckilowoko@yahoo.com.
authors.forename: Mary
authors.initials: M
authors.lastname: Kilowoko
authors.affiliation: St-Francis Hospital, PO box 73, Ifakara TZ-16, United Republic of Tanzania. noemie.boillat@chuv.ch.
authors.forename: Esther
authors.initials: E
authors.lastname: Kyungu
authors.affiliation: St-Francis Hospital, PO box 73, Ifakara TZ-16, United Republic of Tanzania. noemie.boillat@chuv.ch.
authors.forename: Philipina
authors.initials: P
authors.lastname: Hongoa
authors.affiliation: Geneva University Hospitals and Medical School, 4 rue Gabrielle-Perret-Gentil, 1211 Geneva 14, Switzerland. gael.vieille@hcuge.ch.
authors.forename: Gaël
authors.initials: G
authors.lastname: Vieille
authors.affiliation: Geneva University Hospitals and Medical School, 4 rue Gabrielle-Perret-Gentil, 1211 Geneva 14, Switzerland. lara.turin@hcuge.ch.
authors.forename: Lara
authors.initials: L
authors.lastname: Turin
authors.affiliation: Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel 4051, Switzerland. Blaise.Genton@chuv.ch.|Centre Hospitalier Universitaire Vaudois, 21 rue du Bugnon, Lausanne 1011, Switzerland. Blaise.Genton@chuv.ch.
authors.forename: Blaise
authors.initials: B
authors.lastname: Genton
authors.affiliation: Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel 4051, Switzerland. Valerie.Dacremont@chuv.ch.|Centre Hospitalier Universitaire Vaudois, 21 rue du Bugnon, Lausanne 1011, Switzerland. Valerie.Dacremont@chuv.ch.
authors.forename: Valérie
authors.initials: V
authors.lastname: D'Acremont
authors.affiliation: Geneva University Hospitals and Medical School, 4 rue Gabrielle-Perret-Gentil, 1211 Geneva 14, Switzerland. caroline.tapparel@hcuge.ch.
authors.forename: Caroline
authors.initials: C
authors.lastname: Tapparel
mesh_terms: D004770:Enterovirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D004769:Enterovirus Infections / Q000453:epidemiology / Q000821:virology*; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D017720:Molecular Epidemiology; D009305:Nasopharynx / Q000821:virology; D009960:Oropharynx / Q000821:virology; D010802:Phylogeny; D010850:Picornaviridae Infections / Q000453:epidemiology / Q000821:virology*; D015995:Prevalence; D011446:Prospective Studies; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012229:Rhinovirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D017422:Sequence Analysis, DNA; D013636:Tanzania / Q000453:epidemiology
keywords: Tanzania; children; emergent; enterovirus; fever; molecular epidemiology; new type; picornavirus; recombinant; rhinovirus