Abstract. This study charted 237 fatal cases of bovine respiratory disease (BRD) observed from

The extent of human genomic structural variation suggests that there must be portions of the genome yet to be discovered, annotated and characterized at the sequence level. We present a resource and analysis of 2,363 novel insertion sequences corresponding to 720 genomic loci. We show that a substantial fraction of these sequences are either missing, fragmented or mis-assigned when compared to recent de novo sequence assemblies from short-read next-generation sequence data. We determine that 18–37% of these novel insertions are copy-number polymorphic, including loci that show extensive population stratification among Europeans, Asians and Africans. Complete sequencing of 156 of these insertions identifies novel exons and conserved non-coding sequences not yet represented in the reference genome. We develop a method to accurately genotype these novel insertions by mapping next-generation sequencing datasets to the breakpoint thereby providing a means to characterize copy-number status for regions previously inaccessible to SNP microarrays.

Bovine respiratory disease (BRD) research has provided significant understanding of the disease over the past 26 years. Modern research tools that have been used include monoclonal antibodies, genomics, polymerase chain reaction, immunohistochemistry (IHC), DNA vaccines and viral vectors coding for immunogens. Emerging/reemerging viruses and new antigenic strains of viruses and bacteria have been identified. Methods of detection and the role for cattle persistently infected bovine viral diarrhea virus (BVDV) were identified; viral subunits, cellular components and bacterial products have been characterized. Product advances have included vaccines for bovine respiratory syncytial virus, Mannheimia haemolytica and Pasteurella multocida; the addition of BVDV2 to the existing vaccines and new antibiotics. The role of Mycoplasma spp., particularly Mycoplasma bovis in BRD, has been more extensively studied. Bovine immunology research has provided more specific information on immune responses, T cell subsets and cytokines. The molecular and genetic basis for viral-bacterial synergy in BRD has been described. Attempts have been made to document how prevention of BRD by proper vaccination and management prior to exposure to infectious agents can minimize disease and serve as economic incentives for certified health programs.

The study objective was to determine health and performance of ranch calves from different preconditioning strategies during a 42-d receiving period when commingled with calves of unknown health histories from multiple sources. Steer calves from a single source ranch (RANCH) were weaned and immediately shipped to a feedlot (WEAN, initial BW = 247 +/- 29 kg); weaned on the ranch for 45 d before shipping, but did not receive any vaccinations (WEAN45, initial BW = 231 +/- 26 kg); or weaned, vaccinated with modified live viral vaccine, and held on the ranch for 45 d before shipping (WEANVAC45, initial BW = 274 +/- 21 kg). Multiple-source steers were purchased through auction markets (MARKET, initial BW = 238 +/- 13 kg), and upon receiving, a portion of ranch-origin steers from each weaning group was commingled with a portion of MARKET cattle (COMM). The experimental design was completely randomized with a 2 x 3 +1 factorial arrangement of treatments. Factors were RANCH vs. COMM and weaning management (WEAN vs. WEAN45 vs. WEANVAC45) as the factors; MARKET cattle served as the control. Calves of WEAN, WEAN45, and MARKET were vaccinated on arrival at the feedlot. Ranch-origin calves tended (P = 0.06) to have greater ADG than COMM or MARKET calves, although ADG was not affected (P = 0.46) by weaning management. Across the 42-d receiving period, DMI was not affected (P = 0.85) by cattle origin. However, MARKET, WEAN45, and WEANVAC45 calves consumed more (P < 0.001) DM than WEAN calves. Gain efficiency was not affected (P > or = 0.11) by treatment. Ranch-origin calves were less (P < 0.001) likely to be treated for bovine respiratory disease than MARKET calves; COMM calves were intermediate. Calves that were retained on the ranch after weaning (WEAN45 and WEANVAC45) were also less likely to be treated (P = 0.001) than MARKET or WEAN calves. As expected, differences in morbidity related to differences in health costs. Calves of WEAN45 and WEANVAC45 had less (P < 0.001) health costs than MARKET and WEAN calves. On arrival, serum haptoglobin concentrations were greater (P < 0.001) in MARKET and WEAN compared with WEAN45 and WEANVAC45 calves. Calves from a single source that are retained on the ranch for 45 d after weaning exhibit less morbidity and less health costs during the receiving period at the feedyard than when cattle are commingled or trucked to the feedyard immediately after weaning.

Bovine viral diarrhea virus (BVDV) is divided into 2 different species within the Pestivirus genus, BVDV type 1 (BVDV-1) and BVDV type 2 (BVDV-2). Further phylogenetic analysis has revealed subgenotype groupings within the 2 types. Thus far, 12 BVDV-1 subgenotypes (a-l) and 2 BVDV-2 subgenotypes (a and b) have been identified. The purpose of the current study was to determine the prevalence of BVDV subgenotypes in the United States and Australia and to determine if there are detectable antigenic differences between the prevalent subgenotypes. To determine prevalence, phylogenetic analysis was performed on 2 blinded panels of isolates consisting of 351 viral isolates provided by the Elizabeth Macarthur Laboratory, New South Wales, and 514 viral isolates provided by Oklahoma State University. Differences were observed in the prevalence of BVDV subgenotypes between the United States (BVDV-1b most prevalent subgenotype) and Australia (BVDV-1c most prevalent subgenotype). To examine antigenic differences between the subgenotypes identified in samples from the United States and Australia, polyclonal antisera was produced in goats by exposing them at 3-week intervals to 2 noncytopathic and 1 cytopathic strain of either BVDV-1a, BVDV-1b, BVDV-1c, BVDV-2a, or Border disease virus (BDV). Virus neutralization (VN) assays were then performed against 3 viruses from each of the 5 subgenotypes. Comparison of VN results suggests that there are antigenic differences between BVDV strains belonging to different subgenotypes. The present study establishes a foundation for further studies examining whether vaccine protection can be improved by basing vaccines on the BVDV subgenotypes prevalent in the region in which the vaccine is to be used.