Mapping Viral Genotypes Vs Phenotypes through the Sequence Analysis of Emerging Viruses

We will investigate, via viral sequence analysis, that how genetic changes will be mapped into a number of important viral phenotypes in this 3-year project. The subjects to be studied include (1) genetic changes vs antigenic changes (2) amino acid substitutions vs viral replication (co-evolution), and (3) genetic diversity and phenotype-associated signatures.We will be targeting to the influenza viruses, one of the RNA viruses that are likely to emerge into a pandemic threat.We will also analyze enterovirus, in particular to the enterovirus type 71 (EV71) that caused significant morbidity in Taiwan in the past 10 years. Based on how this program was formed in the first place, we (component project #4) will intensively collaborate with the rest of the team, by sharing data, knowledge and methods. For example, due to our long-term working knowledge of these two viruses, we will be helping the others to gather sequence and other information for their tasks.We will need the novel multiple sequence alignment techniques and high-speed parallel computing power supported from component project #5 (Dr. CY Lin) to deal with the tremendous amount of sequence information. To compensate our single amino acid-based investigation into these viral phenotypes, Dr. Tang’s motif-based search from component project #1 will add up the functional pictures of them. Dr. Lu’s secondary structure and reading-frame investigation of the viral RNA from component project #2 would provide insights into these phenotypes from the RNA level, in addition to our view from amino acid residues. And Dr. Peng’s investigation of viral subtypes would definitely correlate to our surface antigenicity analysis. Our co-PI, Dr. Shih, who is also the co-PI of the program project, and is currently leading the Research Center for Emerging Viral Infections at Chang Gung University, will serve as the steering person in the virology aspect.With the team-up of these two important disciplines of bioinformatics, we will, in the end, provide an integrated viral sequence annotation system for rapid identification and characterization of potentially emerging influenza viruses and enteroviruses, that would be in service for the virology community whenever there is a new virus spotted and its genomic sequence generated.

Project ID:PB9709-3577
External Project ID:NSC97-2221-E182-034-MY3