![]() Thus, our method addresses an important need for maintaining a fully updated reference phylogeny. We demonstrate that our approach greatly improves the speed of phylogenetic placement of new samples and data visualization, making it possible to complete the placements under the constraints of real-time contact tracing. Here, we resolve this challenge by building an efficient tree-based data structure encoding the inferred evolutionary history of the virus. However, because the viral phylogeny is already so large-and will undoubtedly grow many fold-placing new sequences onto the tree has emerged as a barrier to real-time genomic contact tracing. ![]() As the SARS-CoV-2 virus spreads through human populations, the unprecedented accumulation of viral genome sequences is ushering in a new era of ‘genomic contact tracing’-that is, using viral genomes to trace local transmission dynamics.
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