Real-time analysis of human pathogen evolution requires a diverse collection of bioinformatics tools to infer transmission dynamics and make recommendations to public health officials. These tools must scale with the number of samples and be flexible enough to adapt to a variety of questions and organisms. To meet these needs, we developed Augur, a bioinformatics toolkit designed for phylogenetic analyses of human pathogens.
Published 07 Jan 2021 in JOSS
Rapid mutation of seasonal influenza’s hemagglutinin protein allows viruses to escape our adaptive immunity necessitating regular vaccine updates. We developed a novel framework that forecasts influenza evolution by combining fitness estimates from experimental assays and genomic data. We found that experimental measurements of antigenic drift provide more accurate forecasts than genomic data alone.
Published 02 Sep 2020 in eLife
The high-throughput technique of deep mutational scanning (DMS) has recently made it possible to experimentally measure the effects of all amino-acid mutations to a protein. We developed an interactive visualization tool, dms-view, to enable dynamic exploration of DMS data in linked views with other site-level data and 3D protein structures.
Published 17 Aug 2020 in The Journal of Open Source Science
Understanding the spread and evolution of pathogens is important for effective public health measures and surveillance. To address this need, we developed Nextstrain, a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualisation platform. Nextstrain compiles our current understanding into a single accessible location, publicly available for use by health professionals, epidemiologists, virologists and the public alike.
Published 01 Dec 2018 in Bioinformatics
Most efforts to understand the evolution of seasonal influenza A/H3N2’s surface protein, hemagglutinin (HA), focus on mutations that increase viral fitness by enabling escape from the immune system. We investigated the functional effects of all possible single amino-acid mutations to the HA of a single, recent H3N2 strain in laboratory conditions. We found that mutations with neutral or beneficial effects in the lab were often successful in nature, while mutations with deleterious effects were not.
Published 13 Aug 2018 in PNAS