title: Onset of a pandemic: characterizing the initial phase of the swine flu (H1N1) epidemic in Israel.
abstract: BACKGROUND
  The swine influenza H1N1 first identified in Mexico, spread rapidly across the globe and is considered the fastest moving pandemic in history. The early phase of an outbreak, in which data is relatively scarce, presents scientific challenges on key issues such as: scale, severity and immunity which are fundamental for establishing sound and rapid policy schemes. Our analysis of an Israeli dataset aims at understanding the spatio-temporal dynamics of H1N1 in its initial phase.
  
  
  METHODS
  We constructed and analyzed a unique dataset from Israel on all confirmed cases (between April 26 to July 7, 2009), representing most swine flu cases in this period. We estimated and characterized fundamental epidemiological features of the pandemic in Israel (e.g. effective reproductive number, age-class distribution, at-risk social groups, infections between sexes, and spatial dynamics). Contact data collected during this stage was used to estimate the generation time distribution of the pandemic.
  
  
  RESULTS
  We found a low effective reproductive number (Re=1.06), an age-class distribution of infected individuals (skewed towards ages 18-25), at-risk social groups (soldiers and ultra Orthodox Jews), and significant differences in infections between sexes (skewed towards males). In terms of spatial dynamics, the pandemic spread from the central coastal plain of Israel to other regions, with higher infection rates in more densely populated sub-districts with higher income households.
  
  
  CONCLUSIONS
  Analysis of high quality data holds much promise in reducing uncertainty regarding fundamental aspects of the initial phase of an outbreak (e.g. the effective reproductive number Re, age-class distribution, at-risk social groups). The formulation for determining the effective reproductive number Re used here has many advantages for studying the initial phase of the outbreak since it neither assumes exponential growth of infectives and is independent of the reporting rate. The finding of a low Re (close to unity threshold), combined with identification of social groups with high transmission rates would have enabled the containment of swine flu during the summer in Israel. Our unique use of contact data provided new insights into the differential dynamics of influenza in different ages and sexes, and should be promoted in future epidemiological studies. Thus our work highlights the importance of conducting a comprehensive study of the initial stage of a pandemic in real time.
authors.affiliation: Biomathematics Unit, Department of Zoology, Faculty of Life Sciences, Tel-Aviv University, 69978 Tel-Aviv, Israel.
authors.forename: Uri
authors.initials: U
authors.lastname: Roll
authors.forename: Rami
authors.initials: R
authors.lastname: Yaari
authors.forename: Guy
authors.initials: G
authors.lastname: Katriel
authors.forename: Oren
authors.initials: O
authors.lastname: Barnea
authors.forename: Lewi
authors.initials: L
authors.lastname: Stone
authors.forename: Ella
authors.initials: E
authors.lastname: Mendelson
authors.forename: Michal
authors.initials: M
authors.lastname: Mandelboim
authors.forename: Amit
authors.initials: A
authors.lastname: Huppert
mesh_terms: D000293:Adolescent; D000328:Adult; D000367:Age Factors; D050936:Basic Reproduction Number; D002648:Child; D002675:Child, Preschool; D016358:Contact Tracing; D005260:Female; D005843:Geography; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D053118:Influenza A Virus, H1N1 Subtype / Q000302:isolation & purification*; D007251:Influenza, Human / Q000453:epidemiology* / Q000821:virology*; D007557:Israel / Q000453:epidemiology; D008297:Male; D058873:Pandemics; D012737:Sex Factors; D012959:Socioeconomic Factors; D013997:Time Factors; D055815:Young Adult