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Hill numbers at the edge of a pandemic: rapid SARS-COV2 surveillance without alignments or trees

2022-06-23 epidemiology Title + abstract only
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The COVID-19 pandemic has highlighted the critical role of genomic surveillance for guiding policy and control strategies. Timeliness is key, but rapid deployment of existing surveillance is difficult because most approaches are based on sequence alignment and phylogeny. Millions of SARS-CoV-2 genomes have been assembled, the largest collection of sequence data in history. Phylogenetic methods are ill equipped to handle this sheer scale. We introduce a pan-genomic measure that examines the infor...

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