VARIATION IN CONSERVATION AMONG DIFFERENT GENES WITHIN THE HERPES SIMPLEX VIRUS TYPE 1, AND ITS CORRELATION WITH FUNCTION Samantha Nadeau & Kerri Callahan.

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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

INTRODUCTION o Most research done on comparison between HSV-1 vs. HSV-2 o Compared dN/dS values o Chose three genes/gene complexes  UL20  UL49  UL15; UL28; UL33

BACKGROUND o Three main morphological regions to virion o Each gene involves a different region  UL20  UL49  UL15; UL28; UL33

HYPOTHESIS o UL20 gene will be least conserved (greatest dN/dS value) o Null: dN=dS

METHODS o Partial genome of strains CJ394, CJ360, CJ311, CJ790, OD4, and TFT401 o Genes UL15, UL20, UL28, UL33, UL49 o 3 sequence alignments: 1.UL20 2.UL15; UL28; UL33 3.UL49

METHODS: ANALYSIS o Codon-based-z-test of selection o Selection at codons via HyPhy o Pairwise distance estimates o Maximum likelihood trees o Null: dN=dS

RESULTS: CODON-BASED-Z-TEST OF SELECTION GeneZ-Statistic HA: dN>dS Prob UL UL15; UL28; UL UL

RESULTS: CODON-BASED-Z-TEST OF SELECTION GeneZ-Statistic HA: DN=/=DS Prob UL UL15; UL28; UL UL

RESULTS: CODON-BASED-Z-TEST OF SELECTION GeneZ statistic HA: dN<dS Prob UL UL15; UL28; UL UL

RESULTS: CODON SELECTION ESTIMATE (HYPHY) GenedN/dS value UL UL15; UL28; UL33 complex0.972 UL

RESULTS: PAIRWISE DISTANCE MATRICES

UL20 MAXIMUM LIKELIHOOD TREE

UL15; UL28; UL33 TREE

UL49 MAXIMUM LIKELIHOOD TREE

TAKE HOME MESSAGE o Can’t compare UL15, UL28, and UL33 against each other to test conservation o UL20 is less highly conserved than UL49 o UL49 is most highly conserved