title: Respiratory tract versus cloacal sampling of migratory ducks for influenza A viruses: are both ends relevant?
abstract: BACKGROUND
  Early studies in dabbling ducks showed that cloacal swabs yielded a larger number of avian influenza virus (AIV) isolates than did respiratory tract swabs. Historically, AIV surveillance has been performed by collecting cloacal or environmental fecal samples only. Highly pathogenic avian influenza H5N1 virus emerged in 1996 and replicated to higher titers in the respiratory rather than the gastrointestinal tract of ducks, prompting the collection of respiratory samples in addition to cloacal swabs from wild birds. Studies confirmed that some virus subtypes, especially H9 and highly pathogenic H5, are shed primarily through the respiratory tract and may not be detected in cloacal swabs.
  
  
  OBJECTIVE
  To examine prevalence and subtype differences for AIV isolates from cloacal or respiratory swabs of wild ducks and to determine whether individual respiratory tract samples should be included in AIV surveillance studies in wild birds.
  
  
  METHODS
  Individual respiratory tract and cloacal swabs were collected from each of 1036 wild ducks in Alberta, Canada, during the month of August from 2007 to 2010 in an ongoing surveillance study. Virus isolation in eggs and subtype identification by antigenic and molecular methods were performed.
  
  
  CONCLUSIONS
  Respiratory tract and cloacal swabs yielded ten influenza virus HA subtypes representing 28 HA-NA combinations. Three HA-NA subtype combinations were found exclusively in respiratory tract samples. Only four HA subtypes (H1, H3, H4, and H7) were recovered from respiratory samples, but respiratory shedding was associated with the dominance of 1 year's subtype. Might respiratory shedding provide a risk assessment indicator?
authors.affiliation: Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA.
authors.forename: Scott
authors.initials: S
authors.lastname: Krauss
authors.forename: Sydney Paul
authors.initials: SP
authors.lastname: Pryor
authors.forename: Garnet
authors.initials: G
authors.lastname: Raven
authors.forename: Angela
authors.initials: A
authors.lastname: Danner
authors.forename: Ghazi
authors.initials: G
authors.lastname: Kayali
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Webby
authors.forename: Robert G
authors.initials: RG
authors.lastname: Webster
mesh_terms: D000416:Alberta; D025041:Animal Migration; D000818:Animals; D000835:Animals, Wild / Q000821:virology; D002170:Canada; D002988:Cloaca / Q000821:virology*; D004372:Ducks / Q000821:virology*; D009980:Influenza A virus / Q000145:classification / Q000302:isolation & purification*; D005585:Influenza in Birds / Q000453:epidemiology* / Q000821:virology; D009960:Oropharynx / Q000821:virology; D015995:Prevalence; D012137:Respiratory System / Q000821:virology*; D018571:Sentinel Surveillance / Q000662:veterinary*; D013048:Specimen Handling / Q000379:methods