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BACKGROUND o Three main morphological regions to virion o Each gene involves a different region UL20 UL49 UL15; UL28; UL33
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VARIATION IN CONSERVATION AMONG
DIFFERENT GENES WITHIN THE HERPES SIMPLEX VIRUS TYPE 1, AND ITS CORRELATION WITH FUNCTION
Samantha Nadeau& Kerri Callahan
INTRODUCTIONoMost research done on comparison between HSV-1 vs. HSV-2oCompared dN/dS valuesoChose three genes/gene complexesUL20 UL49UL15; UL28; UL33
BACKGROUNDoThree main morphological regions to virionoEach gene involves a different regionUL20UL49UL15; UL28; UL33
HYPOTHESISoUL20 gene will be least conserved (greatest dN/dS value)oNull: dN=dS
METHODSoPartial genome of strains CJ394, CJ360, CJ311, CJ790, OD4, and TFT401oGenes UL15, UL20, UL28, UL33, UL49o3 sequence alignments:
1. UL202. UL15; UL28; UL333. UL49
METHODS: ANALYSISoCodon-based-z-test of selectionoSelection at codons via HyPhyoPairwise distance estimatesoMaximum likelihood treesoNull: dN=dS
RESULTS: CODON-BASED-Z-TEST OF SELECTION
Gene Z-StatisticHA: dN>dS
Prob
UL20 -2.572 1.0UL15; UL28; UL33
-1.895 1.0
UL49 -1.794 1.0
RESULTS: CODON-BASED-Z-TEST OF SELECTIONGene Z-Statistic
HA: DN=/=DSProb
UL20 -3.017 0.003
UL15; UL28; UL33
-1.764 0.080
UL49 -1.780 0.078
RESULTS: CODON-BASED-Z-TEST OF SELECTION
Gene Z statistic HA: dN<dS
Prob
UL20 2.669 .004
UL15; UL28; UL33 1.798 .037
UL49 1.73 .043
RESULTS: CODON SELECTION ESTIMATE (HYPHY)Gene dN/dS value
UL20 0.749
UL15; UL28; UL33 complex 0.972
UL49 0.306
RESULTS: PAIRWISE DISTANCE MATRICES
RESULTS: PAIRWISE DISTANCE MATRICES
RESULTS: PAIRWISE DISTANCE MATRICES
UL20 MAXIMUM LIKELIHOOD TREE Human herpesvirus 1 strain CJ394 partial genome
Human herpesvirus 1 strain CJ360 partial genome
Human herpesvirus 1 strain CJ311 partial genome
Human herpesvirus 1 strain TFT401 partial genome
Human herpesvirus 1 strain OD4 partial genome
Human herpesvirus 1 strain CJ970 partial genome
10093
750.0000
0.0000
0.0000
0.0369
0.0022
0.00000.0047
0.03480.0045
0.0023
0.005
UL15; UL28; UL33 TREE Human herpesvirus 1 strain CJ394 partial genome
Human herpesvirus 1 strain CJ360 partial genome
Human herpesvirus 1 strain TFT401 partial genome
Human herpesvirus 1 strain CJ970 partial genome
Human herpesvirus 1 strain CJ311 partial genome
Human herpesvirus 1 strain OD4 partial genome
99
100
100
0.0082
0.0084
0.0000
0.0054
0.0000
0.0000
0.6869
0.7299
0.3706
0.0401
0.1
UL49 MAXIMUM LIKELIHOOD TREE
Human herpesvirus 1 strain TFT401 partial genome
Human herpesvirus 1 strain CJ970 partial genome
Human herpesvirus 1 strain CJ394 partial genome
Human herpesvirus 1 strain CJ311 partial genome
Human herpesvirus 1 strain OD4 partial genome
Human herpesvirus 1 strain CJ360 partial genome
67
0.0018
0.0035
0.0017
0.0000
0.0000
0.0000
0.0000
0.0018
0.0005
TAKE HOME MESSAGEoCan’t compare UL15, UL28, and UL33 against each other to test conservationoUL20 is less highly conserved than UL49oUL49 is most highly conserved