Ecology and Evolution of the Paramyxoviridae
Classical epidemiological theory uses compartmental susceptible-infected-removed (SIR) models to quantitatively explore epidemics caused by acute, immunizing viruses that sweep through local populations. While the basic theory explains viral-host dynamics in some systems, added model complexity crea...
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ftpennstate:OAI:PSUETD:ETD-2871 2023-05-15T16:33:11+02:00 Ecology and Evolution of the Paramyxoviridae Pomeroy, Laura Warlow Ottar N. Bjørnstad Réka Albert Bryan Grenfell Edward C. Holmes Peter Hudson 2010-09-01 application/pdf http://etda.libraries.psu.edu/theses/approved/WorldWideIndex/ETD-2871/index.html en eng Penn State WorldWide Copyright information available at source archive http://etda.libraries.psu.edu/theses/approved/WorldWideIndex/ETD-2871/index.html Biology text 2010 ftpennstate 2011-09-13T08:16:19Z Classical epidemiological theory uses compartmental susceptible-infected-removed (SIR) models to quantitatively explore epidemics caused by acute, immunizing viruses that sweep through local populations. While the basic theory explains viral-host dynamics in some systems, added model complexity creates a more accurate context for other systems. As a case study, I investigate the system of phocine distemper virus (PDV), a morbillivirus, in harbor seals (Phoca vitulina) in the North Sea. Using this dataset, I extend the classical theory by incorporating host age or stage heterogeneities, geographical heterogeneities, and host movement heterogeneities. First, I investigated age or stage heterogeneities in transmission among the harbor seals in the Dutch 2002 PDV epidemic by creating three models to see which best fit the data. The model with the highest degree of heterogeneity best fit the host stage-structure (p=0.0004). I also estimated the who acquires infection from whom (WAIFW) matrix from detailed incidence data and confirmed with an R0 calculation using next-generation formalism. Next, I addressed geographic heterogeneity in the host population by addressing error inherent in the PDV incidence data in the entire North Sea with a Bayesian framework to estimate the initial population of susceptible individuals (S0), the rate of pathogen transmission (â), and the time series of infected individuals with imperfect binomial reporting to the biweekly incidence time series and used this information to create distance and gravity based models to discriminate how different geographic locations are coupled by infected host movement. Results show that the distance model has a better fit to the seal stranding data, indicating that the distance between harbor seal haulouts drives the spatial spread of PDV. Lastly, I looked at the epidemiological and evolutionary dynamics of the viral family Paramyxoviridae by investigating serially-sampled genomes of measles virus, mumps virus, and canine distemper virus. Using a Bayesian coalescent approach, we estimate viral substitution rates, the time to common ancestry and elements of their demographic history. Strikingly, the mean Time to the Most Recent Common Ancestor (TMRCA) was both similar and very recent among the viruses studied, ranging from only 58 to 91 years (1908 to 1943). Text harbor seal Phoca vitulina PennState: Electronic Theses and Dissertations (eTD) |
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Biology Pomeroy, Laura Warlow Ecology and Evolution of the Paramyxoviridae |
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description |
Classical epidemiological theory uses compartmental susceptible-infected-removed (SIR) models to quantitatively explore epidemics caused by acute, immunizing viruses that sweep through local populations. While the basic theory explains viral-host dynamics in some systems, added model complexity creates a more accurate context for other systems. As a case study, I investigate the system of phocine distemper virus (PDV), a morbillivirus, in harbor seals (Phoca vitulina) in the North Sea. Using this dataset, I extend the classical theory by incorporating host age or stage heterogeneities, geographical heterogeneities, and host movement heterogeneities. First, I investigated age or stage heterogeneities in transmission among the harbor seals in the Dutch 2002 PDV epidemic by creating three models to see which best fit the data. The model with the highest degree of heterogeneity best fit the host stage-structure (p=0.0004). I also estimated the who acquires infection from whom (WAIFW) matrix from detailed incidence data and confirmed with an R0 calculation using next-generation formalism. Next, I addressed geographic heterogeneity in the host population by addressing error inherent in the PDV incidence data in the entire North Sea with a Bayesian framework to estimate the initial population of susceptible individuals (S0), the rate of pathogen transmission (â), and the time series of infected individuals with imperfect binomial reporting to the biweekly incidence time series and used this information to create distance and gravity based models to discriminate how different geographic locations are coupled by infected host movement. Results show that the distance model has a better fit to the seal stranding data, indicating that the distance between harbor seal haulouts drives the spatial spread of PDV. Lastly, I looked at the epidemiological and evolutionary dynamics of the viral family Paramyxoviridae by investigating serially-sampled genomes of measles virus, mumps virus, and canine distemper virus. Using a Bayesian coalescent approach, we estimate viral substitution rates, the time to common ancestry and elements of their demographic history. Strikingly, the mean Time to the Most Recent Common Ancestor (TMRCA) was both similar and very recent among the viruses studied, ranging from only 58 to 91 years (1908 to 1943). |
author2 |
Ottar N. Bjørnstad Réka Albert Bryan Grenfell Edward C. Holmes Peter Hudson |
format |
Text |
author |
Pomeroy, Laura Warlow |
author_facet |
Pomeroy, Laura Warlow |
author_sort |
Pomeroy, Laura Warlow |
title |
Ecology and Evolution of the Paramyxoviridae |
title_short |
Ecology and Evolution of the Paramyxoviridae |
title_full |
Ecology and Evolution of the Paramyxoviridae |
title_fullStr |
Ecology and Evolution of the Paramyxoviridae |
title_full_unstemmed |
Ecology and Evolution of the Paramyxoviridae |
title_sort |
ecology and evolution of the paramyxoviridae |
publisher |
Penn State |
publishDate |
2010 |
url |
http://etda.libraries.psu.edu/theses/approved/WorldWideIndex/ETD-2871/index.html |
genre |
harbor seal Phoca vitulina |
genre_facet |
harbor seal Phoca vitulina |
op_source |
http://etda.libraries.psu.edu/theses/approved/WorldWideIndex/ETD-2871/index.html |
op_rights |
WorldWide Copyright information available at source archive |
_version_ |
1766022896899063808 |