Journal of Antivirals & Antiretrovirals
Open Access
ISSN: 1948-5964
ISSN: 1948-5964
R. Burke Squires, Brett Pickett, Jyothi Noronha, Victoria Hunt and Richard H. Scheuermann
Posters: JAA
The fi rst pandemic of the 21st century arose in March of 2009 but it was not until December of that yearthat a vaccine for the pandemic strain was available to the general public. Th e nine-month time frame for vaccine production is not restricted to pandemic outbreaks. In fact, every year a new vaccine must be produced for seasonal fl u infection, which takes the same length of time to prepare. Th e infl uenza vaccine has to be reproduced each year due to the virus mutating in an eff ort to evade host immune response, a process known as antigenic drift . A signifi cant challenge is to predict which infl uenza strains will be prevalent in the human population when the vaccine is ready. In an eff ort to create a vaccine that minimizes or eliminates the eff ect of antigenic drift , we have developed a method to elucidate conserved epitope regions (CER) within eachfl u protein. CERs are regions with minimal polymorphic activity that also possess strong epitope activity in the form of T-cell and B-cell activity. Utilizing the pre-computed polymorphism analysis data from the Infl uenza Research Database (IRD) (www.fl udb.org), we determined the rate of polymorphism across all 10 proteins of human H1N1 subtype infl uenza viruses. Th e polymorphism score was calculated using a sliding 5-mer window to obtain an average polymorphism score for the region. Epitope coverage for each amino acid position was computed using custom scripts and experimentally determined epitopes from the Immune Epitope database (IEDB) (www.immuneepitope.org). Th e two datasets were then plotted along the length of each protein and CERs were selected that represented minimal polymorphism scores with increased epitope coverage. Comparing CERs to experimentally determined cross-reactive epitopes validated the CERs. Specifi cally, experimentally determined antibody binding regions are covered by one or more CERs. Finally, the CERs for HA also include all four highly cross-reactive predicted epitopes and are found to be conserved in both seasonal H1N1 and the pandemic H1N1 2009 viruses.