Epidemiology and Infection

Original Papers


Evaluation of the pooling of swabs for real-time PCR detection of low titre shedding of low pathogenicity avian influenza in turkeys

M. E. ARNOLDa1 c1, M. J. SLOMKAa1, V. J. COWARDa1, S. MAHMOODa1, P. J. RALEIGHa2 and I. H. BROWNa1

a1 Animal Health Veterinary Laboratories Agency (AHVLA) Weybridge, Addlestone, Surrey, UK

a2 Central Veterinary Research Laboratory, Department of Agriculture, Fisheries and Food Laboratories, Celbridge, Co. Kildare, Ireland


The purpose of this study was to determine whether pooling avian influenza (AI)-positive swabs with negative swabs has a detrimental effect on the sensitivity of AI real-time reverse transcription–polymerase chain reactions (rRT–PCRs). Cloacal and buccal swabs were sampled daily from 12 turkeys infected with A/goose/England/07(H2N2). For half the turkeys, each swab was mixed with four swabs from known AI-negative turkeys, and for the other half the swabs were tested individually. Bayesian modelling was used to (i) determine whether pooling the positive swabs compromised the cycle threshold (Ct) value obtained from the rRT–PCRs, and (ii) estimate the likelihood of detection of an H2N2 infected turkey flock via rRT–PCR for pooled and individually tested swabs (cloacal and buccal) vs. the number of days post-infection of the flock. Results indicated that there was no significant effect of compromising AI rRT–PCR sensitivity by pooling a weak positive swab with negative swabs on the Ct values which were obtained. Pooled sampling was able to widen the detection window compared to individual sampling, for the same number of rRT–PCR tests. This indicates that pooled sampling would be an effective method of reducing the number of tests to be performed to determine flock status during an AI outbreak and for surveillance.

(Received March 27 2012)

(Revised June 15 2012)

(Accepted July 25 2012)

(Online publication September 03 2012)

Key words

  • Avian flu;
  • Bayesian analysis;
  • outbreaks;
  • surveillance


c1 Author for correspondence: Dr M. E Arnold, AHVLA Sutton Bonington, The Elms, College Road, Sutton Bonington, Loughborough, LE12 5RB, UK. (Email: mark.arnold@ahvla.gsi.gov.uk)