Document Type

Dissertation - Open Access

Award Date


Degree Name

Doctor of Philosophy (PhD)

Department / School

Veterinary and Biomedical Sciences

First Advisor

Christopher Chase


Bovine Astrovirus, In Situ Hybridization, Metagenomic Sequencing, Porcine Parvovirus 2, Porcine Rotavirus A, Respiratory Disease


Respiratory disease is arguably the most important health concern for the production animal industry [1-3]. Respiratory problems accounted for the highest mortality both in the swine and beef industries [1, 4]. Respiratory pathogens remain the most vital for swine and bovine research and disease monitoring [2, 5-7]. As pathogens, in particular viral pathogens, mutate, novel disease-causing viruses emerge, and there becomes an increasing concern and need for identification with control perimeters. One frequently identified disease syndrome is Porcine Respiratory Disease Complex (PRDC). PRDC is characterized by pneumonia of mixed respiratory infections with contributions from the environment and management practices. The main pathogens associated with PRDC include viruses, such as swine influenza virus (SIV), porcine respiratory and reproductive virus (PRRSV), and porcine circovirus 2 (PCV2), and bacteria, such as Mycoplasma hyopneumoniae, Pasteurella multocida, Streptococcus suis, Bordetella bronchiseptica, and Actinobacillus suis. Viral and bacterial pathogens can be classified as primary pathogens, capable of subverting host defense mechanisms and establishing infection on their own, or opportunistic pathogens [8]. Often, coinfections and superinfections with primary and/ or opportunistic pathogens occur with PRDC. The bovine counterpart to PRDC is Bovine Respiratory Disease (BRD). Like PRDC, BRD is a general term for a complex multi-factorial disease that encompasses upper and lower respiratory tract diseases. BRD is caused by stress, viral infection, and/ or bacterial infection with contributions from environmental factors (in particular transportation) and host characteristics (such as age, immune status, and genetics) [2, 9]. Bacterial and viral agents that are implicated in BRD include bovine viral diarrhea virus (BVDV), bovine respiratory syncytial virus (BRSV), bovine herpesvirus 1 (BoHV-1), parainfluenza 3 virus (PI3V), bovine coronavirus (BCoV), Mannheimia haemolytica, Mycoplasma bovis, Pasteurella multocida, and Histophilus somni [10]. BRD is a costly disease of beef cattle with NAHMS Beef Feedlot 2011 Study reporting the direct cost of treatment for respiratory disease in feedlot cattle at $23.60 USD per case, resulting in a total cost of $54.12 million, not including production loses due to morbidity and mortality [2, 4]. With rising costs of food, the morbidity and mortality associated with respiratory diseases is economically disastrous. Many diagnostic panels are available for common respiratory pathogens for both swine and cattle. Although these panels are helpful, emerging, novel, variant, and underdiagnosed pathogens are often missed. Monitoring for these pathogens, often using metagenomic sequencing, can aid in their control and prevention. Once identified, research can begin on prevalence, pathogenesis, and control and prevention of these pathogens. This review is focused on the discovery of respiratory viral pathogens.

Library of Congress Subject Headings

Respiratory organs -- Diseases.
Swine -- Virus diseases.
Cattle -- Virus diseases.

Number of Pages



South Dakota State University



Rights Statement

In Copyright