Phylogenetic trees are at the center of genomic epidemiology because they allow us to visualize and evaluate how genome sequences representing a given pathogen relate to each other. However, phylogenetic tree building takes time. CZ GEN EPI offers access to a tool that can place sequences onto existing, pre-calculated trees rather than building trees from scratch with your data, with comparable accuracy. This approach is known as phylogenetic placement and its main advantage is speed (takes minutes!). Below we summarize when it might be useful to place your samples onto a global SARS-CoV-2 phylogeny using the Ultrafast Sample placement on Existing tRees (UShER) tool.
Benefits of phylogenetic placement using UShER
UShER places your samples onto a regularly updated global SARS-CoV-2 phylogenetic tree with such speed that is actually considered a ‘real-time’ phylogenetic placement analysis. In addition to ultra-fast analysis, UShER is designed to enable easy visualization of subtrees containing newly placed sequences through the Nextstrain platform. The quick turn around time of phylogenetic placements allows users to answer questions related to pathogen transmission dynamics in a timely manner. Some common questions that can be explored with UShER phylogenetic placements include:
- Is this the first time we have detected a given lineage in my jurisdiction?
- What sequences are most closely related to my sample?
- Could the outbreak in my community be linked to an outbreak in another jurisdiction?
- My sample came from an individual with a recent travel history. Are there samples from the travel destination that are similar in genotypes, that may potentially suggest travel acquired infections?
Learn how to use UShER here.