VARIATION IN CONSERVATION AMONG DIFFERENT GENES WITHIN THE HERPES SIMPLEX VIRUS TYPE 1, AND ITS...

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

UL20 MAXIMUM LIKELIHOOD 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 OD4 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






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







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

VARIATION IN CONSERVATION AMONG DIFFERENT GENES WITHIN THE HERPES SIMPLEX VIRUS TYPE 1, AND ITS...

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