Statistical analyses were performed using JMP software version 14 (SAS Institute, Cary, NC, USA). Viral GC values were transformed to log10 (log10 GC +1) to better meet the assumptions of the parametric analysis. Log10 GC of IBV and NDV per mg of dust were analysed using a restricted maximum likelihood model fitting location of dust collection (plate number) nested within flock as a random effect and dpv, location, flock and their interactions as fixed effects. Log10 GC of IBV and NDV per tracheal and choanal cleft swabs were analysed using a general linear model fitting dpv, flock and their interactions as fixed effects. Dust deposition rate was analysed by fitting chicken age, flock, plate location and their interaction as fixed effects in a general linear model. Discrete data such as IBV and NDV positive or negative RT-PCR results for choanal cleft and tracheal swabs at different dpv were subjected to contingency table analysis. Level of agreement in log10 IBV and NDV GC between paired tracheal and choanal cleft swabs was determined by intraclass correlation coefficient (ICC). ICC values < 0.5, 0.5–0.75, 0.75–0.9 and > 0.9 were considered as indicative of poor, moderate, good and excellent agreement respectively [35]. The agreement between paired tracheal and choanal cleft swabs in detecting IBV and NDV positive birds was tested by McNemar’s test. Kappa value was used to determine the strength of agreement. Values ≤ 0 were considered to have no agreement, 0.01–0.20 as slight, 0.21–0.40 as fair, 0.41–0.60 as moderate, 0.61–0.80 as substantial, and 0.81–1.00 as almost perfect agreement [36]. The association between prevalence of IBV and NDV in tracheal and choanal cleft swabs from individual birds with IBV and NDV GC in dust was determined by linear regression analysis.

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