title: Epidemiological dynamics of an urban Dengue 4 outbreak in São Paulo, Brazil.
abstract: BACKGROUND
  Dengue studies at the urban scale are scarce and required for guiding control efforts. In Brazil, the burden of dengue is high and challenges city public health administrations with limited resources. Here we studied the dynamics of a dengue epidemic in a single city.
  
  
  METHODS
  Serum samples from dengue suspected cases were collected and tested, from December 2012 and July 2013 in Guarujá, Brazil. We use incidence series analysis to provide a detailed view of the reproduction number dynamics and a Bayesian analysis to infer the spread of the serotype using geographic and temporal data.
  
  
  RESULTS
  We obtained nucleotide sequences from 354 envelope genes and georeferenced 286 samples during the course of the outbreak. Serotype 4 was responsible for the epidemic. We identified at least two major lineages that overlapped in distribution. We observed high reproduction numbers and high cladogenesis prior to the escalation of clinical case notifications. Three densely populated non-adjacent neighborhoods played a pivotal role during the onset and/or course of the epidemic.
  
  
  CONCLUSIONS
  Our findings point to high dengue virus transmission with a substantial proportion of unapparent cases that led to a late recognition of an outbreak. Usually source reductions initiatives tend to be insufficient once an epidemic has been established. Nevertheless, health authorities in Guarujá prioritized vector control on specific places with clusters of georeferenced viremic patients, which appear to have diminished the epidemic impact.
authors.affiliation: Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo , São Paulo , Brazil.
authors.forename: Christian Julián
authors.initials: CJ
authors.lastname: Villabona-Arenas
authors.affiliation: Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil; Department of Biomedicine, University of Mogi das Cruzes, Mogi das Cruzes, São Paulo, Brazil.
authors.forename: Jessica Luana
authors.initials: JL
authors.lastname: de Oliveira
authors.affiliation: Office of Epidemiological Surveillance, Department of Health of Guarujá , Guarujá, São Paulo , Brazil.
authors.forename: Carla
authors.initials: C
authors.lastname: de Sousa-Capra
authors.affiliation: Clinical Laboratory Analysis Center, ITAPEMA , Guarujá , Brazil.
authors.forename: Karime
authors.initials: K
authors.lastname: Balarini
authors.affiliation: Clinical Laboratory Analysis Center, ITAPEMA , Guarujá , Brazil.
authors.forename: Celso Ricardo Theoto
authors.initials: CR
authors.lastname: Pereira da Fonseca
authors.affiliation: Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo , São Paulo , Brazil.
authors.forename: Paolo Marinho de Andrade
authors.initials: PM
authors.lastname: Zanotto
keywords: Basic reproduction number; Brazil; Dengue; Dengue virus; Epidemic; Mosquito control; Outbreak; Phylogeny