Fig. 2

Prevalence and relative abundance of respiratory pathogens at the time of treatment for BRD. The prevalence and relative abundance of respiratory pathogens in the upper respiratory tract of calves from Herd 2 was determined by RT-qPCR (BCV) or qPCR (bacterial pathogens) in 48 pools of nasal swabs from 234 calves treated for BRD. Numbers of positive and negative pools for each respiratory pathogen detected in nasal swab specimens collected August 5 (MT-1) are shown in the first column (panels a, d, g, and j; 15 pools < 39.4 °C and 5 pools ≥39.4 °C) and those collected on August 12 (MT-2) are shown in the second column (panels b, e, h, and k; 15 pools < 39.4 °C and 13 pools ≥39.4 °C). The third column (panels c, f, i, and l) shows the cycle threshold (Ct) values for PCR positive pools. The Ct value is inversely associated with the amount of pathogen RNA or DNA detected; therefore, the lower the Ct value, the greater the amount of pathogen specific nucleic acid was present in the nasal swab specimen. A Ct < 40 was considered positive for all pathogens