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

2. 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

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

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

5. 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

6. 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

7. RESULTS: CODON-BASED-Z-TEST OF SELECTION GeneZ-Statistic HA: dN>dS Prob UL20-2.5721.0 UL15; UL28; UL33 -1.8951.0 UL49-1.7941.0

8. RESULTS: CODON-BASED-Z-TEST OF SELECTION GeneZ-Statistic HA: DN=/=DS Prob UL20-3.0170.003 UL15; UL28; UL33-1.7640.080 UL49-1.7800.078

9. RESULTS: CODON-BASED-Z-TEST OF SELECTION GeneZ statistic HA: dN<dS Prob UL202.669.004 UL15; UL28; UL331.798.037 UL491.73.043

10. RESULTS: CODON SELECTION ESTIMATE (HYPHY) GenedN/dS value UL200.749 UL15; UL28; UL33 complex0.972 UL490.306

11. RESULTS: PAIRWISE DISTANCE MATRICES

14. UL20 MAXIMUM LIKELIHOOD TREE

15. UL15; UL28; UL33 TREE

16. UL49 MAXIMUM LIKELIHOOD TREE

17. 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