Between 1958 and 2005, there were 37 human cases of zoonotic swine-origin influenza A virus (IAV) infection reported (Myers et al 2007; Van Reeth 2007). A majority of these infections were with classical swine H1N1 viruses and these 37 cases did not include the Fort Dix cases in 1976 that resulted in 1 death and up to 230 soldiers infected (Myers et al. 2007; Van Reeth 2007). However, a recent report of pig to human transmission was at an Ohio County Fair in 2007 (Vincent et al. 2009b). The sequence analysis of the HA gene segment of the IAVs isolated from the humans and pigs in this case revealed that it was a strain that was currently circulating in the U.S. pig population. The internal genes of this isolate were determined to be of the triple-reassortant swine influenza lineage, including a conserved avian PB2 gene sequence (Vincent et al. 2009b).
On June 11, 2009 the first influenza pandemic in 41 years was declared by the World Health Organization. This virus was like no virus previously seen in the human population with gene segments from both Eurasian and North American swine viruses. The 2009 pandemic H1N1 virus was called a "quadruple-reassortant" virus because it is composed of neuraminidase (NA) and matrix (M) gene segments from Eurasian swine influenza viruses combined with triple-reassortant proteins of North American swine influenza viruses (human-origin polymerase B1 (PB1), avian-origin polymerase B2 (PB2) and polymerase A (PA), and classical swine-origin hemagglutinin (HA), nucleoprotein (NP) and non-structural (NS) (Garten et al. 2009; Smith et al. 2009). The evolutionary analysis of the 2009 pandemic H1N1 shows that the generation of this strain was not likely a recent event. In fact, in order to facilitate human-to-human spread, it probably adapted to the human host through secondary reassortments in humans (Ding et al. 2009). However, the original source of this virus has not yet been determined.
The emergence of the 2009 pandemic H1N1 virus and scattered reports of human infections with swine-origin isolates underscores the importance of fully understanding the genetic, antigenic, and pathogenic characteristics of influenza A viruses so that we may limit the introduction of novel IAVs to the swine population and monitor for newly emerging and evolving viruses. In order to improve our understanding of IAVs in swine, the goal of this dissertation is to address the ability of genetic characterization to predict variations in virus phenotype, such as viral binding and antigenicity.
Understanding the genetic, antigenic and pathogenic features of viruses is important to prevent introduction of human and avian viruses into swine herds and the potential spillback of those viruses to the human population, as wells as preventing the sustained transmission of IAVs within an endemically infected herd. The control of influenza viruses in pig populations continues to be dynamic and complex, and is reliant on a number of factors. Two of these factors include appropriate selection and application of (1) diagnostic tests and (2) vaccines.
Routine surveillance for influenza viruses at the farm level, either syndromic or active surveillance, is often accomplished using real time RT-PCR tests on nasal swabs from live pigs and lung tissue samples from post-mortem examinations. Easily collected sample methods, such as oral fluids, could provide additional viruses for characterization of IAVs in swine. Oral fluids have been used extensively for diagnostic tests in human medicine and are now being applied in swine herds for detecting pathogens and antibodies against the pathogens (Prickett et al. 2010). As part of this dissertation, porcine oral fluids were validated as a viable sample collection method for routine RT-PCR and virus isolation tests (chapter 2). Another important control measure for influenza viruses in pigs continues to be vaccines. In order to assure continued efficacy of vaccines against currently circulating strains of virus, vaccine challenge trials are performed. In this dissertation, the efficacy of a commercial vaccine was examined against challenge with a contemporary field isolate (chapter 3).
To address the genetic and phenotypic characterization of influenza A viruses from swine, two sets of viruses were selected from the influenza database at the University of Minnesota, Veterinary Diagnostic Laboratory and sequenced. The first set was isolated from a group of endemically infected farms treated by the same veterinarian from 2005 to 2009. The selected viruses were either used to produce autogenous vaccines or they were the epizootic viruses found during outbreaks in the vaccinated herds (chapter 4). The second set of viruses were isolated from nursery pigs in one endemically infected multi-site swine production system (farm M) from 2007 to 2009 and either contained a distinct two amino acid insertion or were presumptive ancestral viruses without the insertion (chapter 5). The viruses from farm M were further characterized along with representative viruses that have been previously studied in vivo using a new technique called virus histochemistry to examine the patterns of virus attachment in the respiratory tract (chapter 6).
For the purposes of this dissertation IAVs were classified as virulent increased virulence have some of the following clinical/case presentations: (a) morbidity approaching 90% and mortality approaching 10 percent, (b) sudden, unexpected deaths occurring early in the disease outbreak, (c) gross lesions that are not typical of swine influenza including profuse hemorrhage and/or edema, and (d) sufficient health and production records along with laboratory results that indicate that a highly virulent influenza virus is involved. The characteristics of highly virulent influenza viruses, such as A/swine/KS/77778/2007 H1N1 and A/swine/OH/511445/2007 H1N1, have been previously described in the literature (Ma et al. 2010; Vincent et al. 2009b). This classification was not related to the criteria for classification of avian viruses as having high or low pathogenicity.