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postgraduate thesis: Molecular epidemiology and evolution of type 2 porcine reproductive and respiratory syndrome virus in Ontario, Canada

TitleMolecular epidemiology and evolution of type 2 porcine reproductive and respiratory syndrome virus in Ontario, Canada
Authors
Issue Date2011
PublisherThe University of Hong Kong (Pokfulam, Hong Kong)
Citation
Brar, M. S.. (2011). Molecular epidemiology and evolution of type 2 porcine reproductive and respiratory syndrome virus in Ontario, Canada. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b4716692
Abstract´╗┐Recently, progress was made in collecting, classifying, and characterizing the genetic diversity of type 2 porcine reproductive and respiratory syndrome virus (PRRSV) using all known and publically available sequencing information. Despite this voluminous attempt, these analyses were largely na?ve of the Canadian contribution to circulating viruses. This represented a vital omission in the study of molecular epidemiology due to the fact that Canada had recorded the earliest evidence of the existence of type 2 PRRSV. To this end, the genetic diversity and evolutionary aspects of PRRSVs distributed in the Province of Ontario in Canada were characterized to abridge this existing knowledge gap on type 2 PRRSV. Genotyping of type 2 strains is primarily based on either a phylogenetic or restriction fragment length polymorphism (RFLP) approach. Classification of Ontario PRRSV field isolates (n = 505) from 1999 to 2010, based on a global type 2 PRRSV ORF5 phylogenetic framework, revealed genetic diversity comparable to PRRSV in the USA, with sequences assigned to five of nine lineages (1, 2, 5, 8 and 9). A majority (~85%) of these isolates were typed to the first two lineages (1 and 2). Despite a relatively smaller sample size to the USA, the topology of the phylogenetic tree indicated Canadian origins of these two lineages. Mapping RFLP patterns of Ontario isolates onto the phylogenetic tree revealed numerous examples of different patterns located within the same phylogenetic cluster. Examples of the non-specificity of RFLP patterns to any particular lineage or sub-lineage were abound. Statistical analysis showed occurrences where similar RFLP patterns masked diverse genetic distances and instances of close genetic proximity with divergent RFLP patterns. An examination of the most abundant 15 RFLP patterns revealed that the discrepancy between RFLP typing and genetic distances was not attributable to a single or few patterns but was rather a permeating feature. Importantly, the tree topology also indicated a Canadian ancestry for the highly virulent MN184-related strains that first emerged in 2001 in the USA. Selective pressure analyses highlighted a handful of positively selected sites most of which were located in the ORF5 ectodomains of outbreak strains, implicating the host immune system as the possible selective agent. This was in contrast to the closely-related Ontario strains which were subject to strong purifying selection. A broader survey of transmission dynamics in North America unveiled a higher virus flow from Canada to the USA with the primary targets being the Lake States and Corn Belt. In turn, these regions served to disseminate viruses to other swine production regions in the USA. Virus flow from the USA to Canada occurred on a much smaller scale. Collectively, extensive genetic diversity prevails in type 2 PRRSV in one region of the North American swine industry and it is not described adequately by RFLP typing which might have some value in differentiating strains at the local farm level, instead. For diagnostic and research purposes, phylogenetic typing should be the preferred method. Finally, stronger surveillance needs to be adopted to minimize cross-border virus transmission.
DegreeMaster of Philosophy
SubjectPorcine reproductive and respiratory syndrome - Molecular aspects.
Molecular epidemiology.
Dept/ProgramBiological Sciences
Persistent Identifierhttp://hdl.handle.net/10722/180058

 

DC FieldValueLanguage
dc.contributor.authorBrar, Manreetpal Singh.-
dc.date.accessioned2013-01-17T02:03:46Z-
dc.date.available2013-01-17T02:03:46Z-
dc.date.issued2011-
dc.identifier.citationBrar, M. S.. (2011). Molecular epidemiology and evolution of type 2 porcine reproductive and respiratory syndrome virus in Ontario, Canada. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b4716692-
dc.identifier.urihttp://hdl.handle.net/10722/180058-
dc.description.abstract´╗┐Recently, progress was made in collecting, classifying, and characterizing the genetic diversity of type 2 porcine reproductive and respiratory syndrome virus (PRRSV) using all known and publically available sequencing information. Despite this voluminous attempt, these analyses were largely na?ve of the Canadian contribution to circulating viruses. This represented a vital omission in the study of molecular epidemiology due to the fact that Canada had recorded the earliest evidence of the existence of type 2 PRRSV. To this end, the genetic diversity and evolutionary aspects of PRRSVs distributed in the Province of Ontario in Canada were characterized to abridge this existing knowledge gap on type 2 PRRSV. Genotyping of type 2 strains is primarily based on either a phylogenetic or restriction fragment length polymorphism (RFLP) approach. Classification of Ontario PRRSV field isolates (n = 505) from 1999 to 2010, based on a global type 2 PRRSV ORF5 phylogenetic framework, revealed genetic diversity comparable to PRRSV in the USA, with sequences assigned to five of nine lineages (1, 2, 5, 8 and 9). A majority (~85%) of these isolates were typed to the first two lineages (1 and 2). Despite a relatively smaller sample size to the USA, the topology of the phylogenetic tree indicated Canadian origins of these two lineages. Mapping RFLP patterns of Ontario isolates onto the phylogenetic tree revealed numerous examples of different patterns located within the same phylogenetic cluster. Examples of the non-specificity of RFLP patterns to any particular lineage or sub-lineage were abound. Statistical analysis showed occurrences where similar RFLP patterns masked diverse genetic distances and instances of close genetic proximity with divergent RFLP patterns. An examination of the most abundant 15 RFLP patterns revealed that the discrepancy between RFLP typing and genetic distances was not attributable to a single or few patterns but was rather a permeating feature. Importantly, the tree topology also indicated a Canadian ancestry for the highly virulent MN184-related strains that first emerged in 2001 in the USA. Selective pressure analyses highlighted a handful of positively selected sites most of which were located in the ORF5 ectodomains of outbreak strains, implicating the host immune system as the possible selective agent. This was in contrast to the closely-related Ontario strains which were subject to strong purifying selection. A broader survey of transmission dynamics in North America unveiled a higher virus flow from Canada to the USA with the primary targets being the Lake States and Corn Belt. In turn, these regions served to disseminate viruses to other swine production regions in the USA. Virus flow from the USA to Canada occurred on a much smaller scale. Collectively, extensive genetic diversity prevails in type 2 PRRSV in one region of the North American swine industry and it is not described adequately by RFLP typing which might have some value in differentiating strains at the local farm level, instead. For diagnostic and research purposes, phylogenetic typing should be the preferred method. Finally, stronger surveillance needs to be adopted to minimize cross-border virus transmission.-
dc.languageeng-
dc.publisherThe University of Hong Kong (Pokfulam, Hong Kong)-
dc.relation.ispartofHKU Theses Online (HKUTO)-
dc.rightsThe author retains all proprietary rights, (such as patent rights) and the right to use in future works.-
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.source.urihttp://hub.hku.hk/bib/B47166927-
dc.subject.lcshPorcine reproductive and respiratory syndrome - Molecular aspects.-
dc.subject.lcshMolecular epidemiology.-
dc.titleMolecular epidemiology and evolution of type 2 porcine reproductive and respiratory syndrome virus in Ontario, Canada-
dc.typePG_Thesis-
dc.identifier.hkulb4716692-
dc.description.thesisnameMaster of Philosophy-
dc.description.thesislevelMaster-
dc.description.thesisdisciplineBiological Sciences-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.5353/th_b4716692-
dc.date.hkucongregation2012-

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