Quantifying the effect of swab pool size on the detection of influenza A viruses in broiler chickens and its implications for surveillance

Abstract

BackgroundTimely diagnosis of influenza A virus infections is critical for outbreak control. Due to their rapidity and other logistical advantages, lateral flow immunoassays can support influenza A virus surveillance programs and here, their field performance was proactively assessed.The performance of real-time polymerase chain reaction and two lateral flow immunoassay kits (FluDETECT and VetScan) in detecting low pathogenicity influenza A virus in oropharyngeal swab samples from experimentally inoculated broiler chickens was evaluated and at a flock-level, different testing scenarios were analyzed.ResultsFor real-time polymerase chain reaction positive individual-swabs, FluDETECT respectively detected 37% and 58% for the H5 and H7 LPAIV compared to 28% and 42% for VetScan. The mean virus titer in H7 samples was higher than for H5 samples. For real-time polymerase chain reaction positive pooled swabs (containing one positive), detections by FluDETECT were significantly higher in the combined 5- and 6-swab samples compared to 11-swab samples. FluDETECT detected 58%, 55.1% and 44.9% for the H7 subtype and 28.3%, 34.0% and 24.6% for the H5 in pools of 5, 6 and 11 respectively.In our testing scenario analysis, at low flock-level LPAIV infection prevalence, testing pools of 11 detected slightly more infections while at higher prevalence, testing pools of 5 or 6 performed better. For highly pathogenic avian influenza virus, testing pools of 11 (versus 5 or 6) detected up to 5% more infections under the assumption of similar sensitivity across pools and detected less by 3% when its sensitivity was assumed to be lower.ConclusionsMuch as pooling a bigger number of swab samples increases the chances of having a positive swab included in the sample to be tested, this study’s outcomes indicate that this practice may actually reduce the chances of detecting the virus since it may result into lowering the virus titer of the pooled sample. Further analysis on whether having more than one positive swab in a pooled sample would result in increased sensitivity for low pathogenicity avian influenza virus is needed.

Estimating within-flock transmission rate parameter for H5N2 highly pathogenic avian influenza virus in Minnesota turkey flocks during the 2015 epizootic

“…Within-flock models of HPAI spread have been used to inform several risk management decisions such as the choice of active surveillance protocol options for early detection (see, e.g. [4]). The implications of improved estimation of parameters for such within-flock models are beneficial to the improved prevention of between-flock transmission [5, 6].…”

Implementation of Antibody Rapid Diagnostic Testing versus Real-Time Reverse Transcription-PCR Sample Pooling in the Screening of COVID-19: a Case of Different Testing Strategies in Africa

“…(i) Sample pooling for rRT-PCR. Sample pooling was first suggested by Robert Dorfman in 1943 as a way of optimizing syphilis testing, and since then, it has been applied in surveillance and screening for infections such as human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV), malaria, and influenza virus (19)(20)(21)(22)(23)(24)(25). Sample pooling has popularly been employed in serological work but also in molecular diagnostics and research.…”

Effects of swab pool size and transport medium on the detection and isolation of avian influenza viruses in ostriches

“…To maintain the country’s international status as the largest export producer of ostrich products, South African farmers must adhere to strict bio-security requirements and undertake rigorous and costly testing to prove freedom of IAV infection. Pooling 5 ostrich tracheal swabs is the current standard practice as pooling increases not only testing throughput, but it also reduces the number of tests needed to meet sample size requirements and consequently the test costs [ 9 , 13 ]. Pools of up to 11 swabs for chicken or turkey swabs are validated and used internationally [ 7 , 9 , 11 , 13 , 14 ], therefore in the current study we investigated the effects of also increasing ostrich tracheal swab pools to 10.…”

“…Pooling 5 ostrich tracheal swabs is the current standard practice as pooling increases not only testing throughput, but it also reduces the number of tests needed to meet sample size requirements and consequently the test costs [ 9 , 13 ]. Pools of up to 11 swabs for chicken or turkey swabs are validated and used internationally [ 7 , 9 , 11 , 13 , 14 ], therefore in the current study we investigated the effects of also increasing ostrich tracheal swab pools to 10. Our results showed that increasing the ostrich swabs to 10 per pool had no detrimental effect on the sensitivity of the RT-rtPCR assay in detecting H5N8 HPAIV or H7N1 LPAIV; and doubling the swab pool size even seemed to improve the sensitivity of IAV detection.…”

“…LPAIV infections are more difficult to detect than HPAIV because levels of genome in swabs are generally lower than are typically found in HP infections [ 9 ] but this hasn’t yet been experimentally determined for ostriches. In other studies, at low-level LPAIV infection prevalence, testing pools of 11 detected slightly more infections while at higher prevalence, testing pools of 5 or 6 performed better [ 13 ]. If LPAIV does circulate at lower levels in ostriches, it is likely that swab pools of 10 will be sufficient to detect HPAI virus as well.…”