title: Clinical characterisation and phylogeny of respiratory syncytial virus infection in hospitalised children at Red Cross War Memorial Children's Hospital, Cape Town.
abstract: Respiratory syncytial virus (RSV) is a major cause of lower respiratory tract infection in young children in both the community and hospital setting.
  
  
  
  The clinical presentation, patient and phylogenetic characteristicsof laboratory-confirmed cases of RSV, as well as risk factors for nosocomial infectionat Red Cross War Memorial Children's Hospital in Cape Town were analysed. A multiplex PCR assay that detects 7 respiratory viruses was used to identify RSV nucleic acid on respiratory specimens.
  
  
  
  A total of 226 children were studied, ages ranging between 1 week and 92.5 months (median: 2.8 months, IQR: 1.3-6.3 months) and 51.8 % were males. The median duration of symptoms prior to diagnosis was 2 days (IQR: 1-4 days). Nosocomial infections wereidentified in 22 (9.7 %) children. There were pre-existing medical conditions in 113 (50.0 %) excluding HIV, most commonly prematurity (n = 58, 50.0 %) and congenital heart disease (n = 34, 29.3 %). The commonest presenting symptoms were cough (196, 86.7 %), difficulty in breathing (115, 50.9 %) and fever (91, 41.6 %).A case fatality rate of 0.9 % was recorded. RSV group A predominated (n = 181, 80.1 %) while group B accounted for only 45 (19.9 %) of the infections. The prevalent genotypes were NA1 (n = 127,70.1 %), ON1 (n = 45,24.9 %) and NA2 (n = 9,5.0 %) for group A while the only circulating RSV B genotype was BA4. There was no significant difference in the genotype distribution between the nosocomial and community-acquired RSV infections. Age ≥ 6 months was independently associated with nosocomial infection.
  
  
  
  A large percentage of children with RSV infection had pre-existing conditions. Approximately one tenth of the infections were nosocomial with age 6 months or older being a risk factor. Though both RSV groups co-circulated during the season, group A was predominant and included the novel ON1 genotype. Continued surveillance is necessary to identify prevalent and newly emerging genotypes ahead of vaccine development and efficacy studies.
authors.affiliation: Paediatric Infectious Diseases Unit, Red Cross War Memorial Children's Hospital, Cape Town, South Africa. ginaolad@gmail.com.|Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa. ginaolad@gmail.com.
authors.forename: Regina
authors.initials: R
authors.lastname: Oladokun
authors.affiliation: Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa.
authors.forename: Rudzani
authors.initials: R
authors.lastname: Muloiwa
authors.affiliation: Division of Medical Virology, University of Cape Town, Cape Town, South Africa.|National Health Laboratory Service, Grootes Schuur Hospital, Cape Town, South Africa.
authors.forename: Nei-Yuan
authors.initials: NY
authors.lastname: Hsiao
authors.affiliation: Centre for Respiratory Diseases and Meningitis, Virology, National Institute for Communicable Diseases, Sandringham, Johannesburg, South Africa.|Faculty of Health Sciences, Department of Clinical Laboratory Sciences Medical Virology, University of Cape Town, Cape Town, South Africa.
authors.forename: Ziyaad
authors.initials: Z
authors.lastname: Valley-Omar
authors.affiliation: Paediatric Infectious Diseases Unit, Red Cross War Memorial Children's Hospital, Cape Town, South Africa.|Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa.
authors.forename: James
authors.initials: J
authors.lastname: Nuttall
authors.affiliation: Paediatric Infectious Diseases Unit, Red Cross War Memorial Children's Hospital, Cape Town, South Africa.|Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa.
authors.forename: Brian
authors.initials: B
authors.lastname: Eley
mesh_terms: D002648:Child; D002673:Child, Hospitalized / Q000706:statistics & numerical data; D002675:Child, Preschool; D003428:Cross Infection / Q000453:epidemiology / Q000821:virology; D005260:Female; D005838:Genotype; D006776:Hospitals, Pediatric; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D008297:Male; D010802:Phylogeny; D018357:Respiratory Syncytial Virus Infections / Q000453:epidemiology* / Q000821:virology; D018113:Respiratory Syncytial Virus, Human / Q000145:classification / Q000302:isolation & purification*; D013019:South Africa / Q000453:epidemiology
keywords: Clinical characteristics; Genetic diversity; Nosocomial infection; Respiratory syncytial virus