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Phylodynamic analyses reveal rapid evolution of rubella virus

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TitleInfo
Title
Phylodynamic analyses reveal rapid evolution of rubella virus
Name (type = personal)
NamePart (type = family)
Wain
NamePart (type = given)
Cody Andrew
NamePart (type = date)
1995-
DisplayForm
Cody Wain
Role
RoleTerm (authority = RULIB)
author
Name (type = personal)
NamePart (type = family)
Duffy
NamePart (type = given)
Siobain
DisplayForm
Siobain Duffy
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
chair
Name (type = corporate)
NamePart
Rutgers University
Role
RoleTerm (authority = RULIB)
degree grantor
Name (type = corporate)
NamePart
School of Graduate Studies
Role
RoleTerm (authority = RULIB)
school
TypeOfResource
Text
Genre (authority = marcgt)
theses
OriginInfo
DateCreated (encoding = w3cdtf); (qualifier = exact)
2019
DateOther (encoding = w3cdtf); (qualifier = exact); (type = degree)
2019-05
CopyrightDate (encoding = w3cdtf); (qualifier = exact)
2019
Language
LanguageTerm (authority = ISO 639-3:2007); (type = text)
English
Abstract
Rubella is an infection caused by rubella virus. Rubella virus belongs to the Togaviridae family and is a single stranded positive sense RNA virus of about 9,762 nucleotides. Rubella, once known as German Measles, causes an iconic red rash all over the body and the teratogenic congenital rubella syndrome in pregnant women. Due to Measles-Mumps-Rubella vaccination rates falling throughout the developed world and measles and mumps becoming resurgent, the evolution of rubella virus is important to study prior to its potential resurgence. The E1 gene of the rubella virus is responsible for interaction with the human immune system, and it is the antigen to which antibodies are formed. The evolutionary rate of E1 along with the full rubella genome was determined using phylodynamic analysis. Both the whole genome and the E1 gene were evolving in a clocklike manner, and the evolution of both were successfully analyzed with BEAST2 software. A difference between the best-fitting priors between the two datasets was the kind of molecular clock preferred: the whole genome was best fit by a relaxed molecular clock, while the E1 gene preferred the strict molecular clock. This difference had some impact on the results, with the estimated evolutionary rate for the E1 gene from the strict clock being lower than the whole genome, but still within the 95% highest posterior density range at 1.08 x 10-3 substitutions per site per year (ssy) while the whole genome had an evolutionary rate of 1.60 x 10-3 ssy with a 95% Highest Posterior Density (HPD) of 1.06 x 10-3 to 2.18 x 10-3 ssy. Reconducting the E1 analysis with a relaxed molecular clock resulted in a similar evolutionary rate as the whole genome of 1.51 x 10-3 ssy with a 95% HPD of 1.23 x 10-3 to 1.80 x 10-3 ssy. This is one of the first cases where there was a statistically significant difference in substitution rate (non-overlapping HPDs) between analyses of the same dataset calculated with different clock priors. The relaxed clock estimates of nucleotide substitution rate are higher than has been estimated for rubella virus in the past and agrees with the more rapid rate of evolution seen in a single decade in China. These results suggest that rubella evolves faster than expected, though it is not undergoing substantial positive selection, and that choice of clock model is a more significant determinant of substitution rate than previously considered.
Subject (authority = ETD-LCSH)
Topic
Rubella -- Genetic aspects
Subject (authority = RUETD)
Topic
Microbial Biology
Subject (authority = ETD-LCSH)
Topic
Viruses -- Evolution
RelatedItem (type = host)
TitleInfo
Title
Rutgers University Electronic Theses and Dissertations
Identifier (type = RULIB)
ETD
Identifier
ETD_9812
PhysicalDescription
Form (authority = gmd)
InternetMediaType
application/pdf
InternetMediaType
text/xml
Extent
1 online resource (viii, 45 pages) : illustrations
Note (type = degree)
M.S.
Note (type = bibliography)
Includes bibliographical references
RelatedItem (type = host)
TitleInfo
Title
School of Graduate Studies Electronic Theses and Dissertations
Identifier (type = local)
rucore10001600001
Location
PhysicalLocation (authority = marcorg); (displayLabel = Rutgers, The State University of New Jersey)
NjNbRU
Identifier (type = doi)
doi:10.7282/t3-x29f-jf11
Genre (authority = ExL-Esploro)
ETD graduate
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RightsDeclaration (ID = rulibRdec0006)
The author owns the copyright to this work.
RightsHolder (type = personal)
Name
FamilyName
Wain
GivenName
Cody
MiddleName
Andrew
Role
Copyright Holder
RightsEvent
Type
Permission or license
DateTime (encoding = w3cdtf); (qualifier = exact); (point = start)
2019-04-11 21:05:44
AssociatedEntity
Name
Cody Andrew Wain
Role
Copyright holder
Affiliation
Rutgers University. School of Graduate Studies
AssociatedObject
Type
License
Name
Author Agreement License
Detail
I hereby grant to the Rutgers University Libraries and to my school the non-exclusive right to archive, reproduce and distribute my thesis or dissertation, in whole or in part, and/or my abstract, in whole or in part, in and from an electronic format, subject to the release date subsequently stipulated in this submittal form and approved by my school. I represent and stipulate that the thesis or dissertation and its abstract are my original work, that they do not infringe or violate any rights of others, and that I make these grants as the sole owner of the rights to my thesis or dissertation and its abstract. I represent that I have obtained written permissions, when necessary, from the owner(s) of each third party copyrighted matter to be included in my thesis or dissertation and will supply copies of such upon request by my school. I acknowledge that RU ETD and my school will not distribute my thesis or dissertation or its abstract if, in their reasonable judgment, they believe all such rights have not been secured. I acknowledge that I retain ownership rights to the copyright of my work. I also retain the right to use all or part of this thesis or dissertation in future works, such as articles or books.
Copyright
Status
Copyright protected
Availability
Status
Open
Reason
Permission or license
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windows xp
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1.7
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DateCreated (point = end); (encoding = w3cdtf); (qualifier = exact)
2019-04-24T00:38:43
DateCreated (point = end); (encoding = w3cdtf); (qualifier = exact)
2019-04-24T00:38:43
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