The effect of swab sample choice on the detection of avian influenza in apparently healthy wild ducks

Avian Diseases
By: , and 



Historically, avian influenza viruses have been isolated from cloacal swab specimens, but recent data suggest that the highly pathogenic avian influenza (HPAI) H5N1 virus can be better detected from respiratory tract specimens. To better understand how swab sample type affects the detection ability of low pathogenic avian influenza (LPAI) viruses we collected and tested four swab types: oropharyngeal swabs (OS), cloacal swabs (CS), the two swab types combined in the laboratory (LCS), and the two swab types combined in the field (FCS). A total of 1968 wild waterfowl were sampled by each of these four methods and tested for avian influenza virus using matrix gene reverse-transcription (RT)-PCR. The highest detection rate occurred with the FCS (4.3%) followed by the CS (4.0%). Although this difference did not achieve traditional statistical significance, Bayesian analysis indicated that FCS was superior to CS with an 82% probability. The detection rates for both the LCS (2.4%) and the OS (0.4%) were significantly different from the FCS. In addition, every swab type that was matrix RT-PCR positive was also tested for recovery of viable influenza virus. This protocol reduced the detection rate, but the ordering of swab types remained the same: 1.73% FCS, 1.42% CS, 0.81% LCS, and 0% OS. Our data suggest that the FCS performed at least as well as any other swab type for detecting LPAI viruses in the wild ducks tested. When considering recent studies showing that HPAI H5N1 can be better detected in the respiratory tract, the FCS is the most appropriate sample to collect for HPAI H5N1 surveillance while not compromising LPAI studies.

Study Area

Publication type Article
Publication Subtype Journal Article
Title The effect of swab sample choice on the detection of avian influenza in apparently healthy wild ducks
Series title Avian Diseases
DOI 10.1637/9832-061311-Reg.1
Volume 56
Issue 1
Year Published 2012
Language English
Publisher American Association of Avian Pathologists
Publisher location Jacksonville, FL
Contributing office(s) National Wildlife Health Center
Description 6 p.
First page 114
Last page 119
Country United States
State California, Colorado, North Dakota
Other Geospatial Delevan National WIldlife Refuge
Online Only (Y/N) N
Additional Online Files (Y/N) N
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