RNA virus evolution and the predictability of next year's flu

RNA viruses like HIV of influenza virus evolve rapidly and thereby evade human immunity. We have performed whole genome deep sequencing of longitudinal samples spanning 5-10 years from acute to chronic HIV infection. From these data, we estimate the landscape of fitness costs at every nucleotide in the genome and characterize the the complex dynamics of immune escape and reversion. Similarly, influenza viruses change their antigenic properties rapidly and the seasonal influenza vaccine needs to be updated whenever the viruses change antigenically. We show how sequence data can be used predict which influenza virus variants are most likely to succeed and circulate in future seasons. These predictions use theoretical insights into the structure of genealogies of rapidly adapting populations and are provided in near real-time at nextflu.org.