The molecular evolution of proteins and viruses

Rapid evolution is a defining feature of many of the most medically problematic viral diseases, including influenza. Although this rapid evolution is usually bad from the perspective of public health, it offers a unique vantage from which to study a range of important questions in biology. For instance, consider the figure below, which summarizes the evolution of the human and swine descendants of the 1918 influenza pandemic. It took less than 90 years for these two viral lineages to become as different at the protein level as humans and pigs themselves – and the full sequences of many of the evolutionary intermediates are known. Furthermore, this is just one example of the many viral evolutionary histories that can be reconstructed in remarkable detail. We apply a combination of experimental and computational approaches to use the information in such histories to address questions such as:

Selected Publications:

Bargavi Thyagarajan and Jesse D. Bloom. "The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin." eLife. doi: 10.7554/eLife.03300 (2014) | pdf

Jesse D. Bloom. "An experimentally determined evolutionary model dramatically improves phylogenetic fit." Molecular Biology and Evolution. 31:1956-1978 (2014) | pdf

L. Ian Gong, Marc A. Suchard, Jesse D. Bloom. "Stability-mediated epistasis constrains the evolution of an influenza protein." eLife. 2:e00631 (2013) | pdf

Kathryn A. Hooper and Jesse D. Bloom. "A mutant influenza virus that uses an N1 neuraminidase as the receptor-binding protein." Journal of Virology. 87:12531-12540 (2013) | pdf