Document Type

Thesis - Open Access

Award Date


Degree Name

Master of Science (MS)


Biology and Microbiology

First Advisor

Dan Wang

Second Advisor

Feng Li


Equine influenza, Influenza B virus, Phylogenetic analysis, Replication kinetics


Influenza viruses are respiratory pathogens that cause significant mortality worldwide. The subtype of influenza A virus currently affecting worldwide equine populations is H3N8, leading to epidemics and transboundary pandemics. The individual gene segments of an isolate named A/equine/Montana/9564-1/2015 were phylogenetically characterized. BLASTn search revealed that the polymerase basic protein 1 (PB1), polymerase acidic (PA), hemagglutinin (HA), nucleoprotein (NP), and matrix (M) segments of this H3N8 isolate shared the highest percentage identity to A/equine/Tennessee/29A/2014 (H3N8) and the polymerase basic protein 2 (PB2), neuraminidase (NA), and non-structural protein (NS) segments to A/equine/Malaysia/M201/2015 (H3N8). Maximum likelihood phylogenetic trees constructed using H3N8 viral genomes of both equine and canine origin, established that A/equine/Montana/9564-1/2015 belonged to the Florida Clade 1 viruses. A review of the current progress in influenza B virus (IBV) research includes the peerreviewed articles that have been published on five IBV proteins. Understanding the biology of the proteins encoded in the IBV genome, and their differences from IAV, is crucial in for vaccine research. The current understanding of the evolutionary dynamics and epidemiology of IBV is discussed which helps inform vaccine strategies and prevent IBV infections. Although IBV is thought to primarily infect humans, there is evidence of sporadic infections occurring in other species. These studies of natural and experimental infections of IBV are discussed, followed by a summary of the current literature on the studies done in ferrets. Swine are susceptible to infection by IBV, indicating that IBV could be a swine pathogen and natural reservoir for IBV. The second study looked at the replication kinetics of Victoria and Yamagata lineages of IBV in swine primary nasal turbinate, trachea and lung epithelial cells. Productive replication of B/Brisbane/60/2008 (BR08); B/Florida/04/06 (FL06); B/Hong Kong/286/2017 (HK17) and B/Utah/09/2014 (UT14) was seen at 0.01 and 0.1 multiplicities of infection. Peak titers at 33˚C were greater than or equal to titers at 37˚C for most of the experiments. HK17 (Victoria lineage) grew to the highest titers in nasal turbinate and lung cells. Lineage-specific differences in replication could not be observed in this study. Molecular analysis of will shed more light on the role of swine in the pathogenesis of IBV.

Library of Congress Subject Headings

Influenza A virus.
Equine influenza.
Swine influenza.
Influenza viruses.
Viruses -- Reproduction.
Epithelial cells.



Number of Pages



South Dakota State University


In Copyright - Educational Use Permitted


Year Manuscript Completed: 2019

Included in

Virology Commons