An Investigation of the Classification, Seasonality, and Genotype Diversity of Rotavirus in Swine Populations in Canada

Abstract

Rotavirus is an important cause of acute gastroenteritis affecting swine globally and this thesis examined important characteristics of rotavirus in swine populations in Canada to enhance current disease control practices. A classification tool was developed using machine learning alongside alignment-based methodology for dual classification of group A rotavirus genotypes and demonstrated strong performance. Seasonality of group A, B, and C rotaviruses was explored through descriptive analysis, time-series decomposition, and statistical analysis of surveillance data obtained from a diagnostic laboratory and was identified to not be present in Canada between 2016-2020. Genotype diversity of group A, B and C rotaviruses was investigated between 2011-2021 and no major shifts in the patterns of circulating genotypes were identified in group A and B rotaviruses, although proportion of laboratory positivity for genotype G6 of group C rotaviruses showed an increasing trend when evaluated descriptively on an annual basis.