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Viral genome sequencing places White House COVID-19 outbreak into phylogenetic context

Bedford, T.; Logue, J. K.; Han, P. D.; Wolf, C. R.; Frazar, C. D.; Pelle, B.; Ryke, E.; Lee, J.; Rieder, M. J.; Nickerson, D. A.; Lockwood, C. M.; Starita, L. M.; Chu, H. Y.; Shendure, J.

2020-11-01 epidemiology
10.1101/2020.10.31.20223925 medRxiv
Show abstract

In October 2020, an outbreak of at least 50 COVID-19 cases was reported surrounding individuals employed at or visiting the White House. Here, we applied genomic epidemiology to investigate the origins of this outbreak. We enrolled two individuals with exposures linked to the White House COVID-19 outbreak into an IRB-approved research study and sequenced their SARS-CoV-2 infections. We find these viral sequences are identical to each other, but are distinct from over 190,000 publicly available SARS-CoV-2 genomes. These genomes fall as part of a lineage circulating in the USA since April or May 2020 and detected in Virginia and Michigan. Looking forwards, sequencing of additional community SARS-CoV-2 infections collected in the USA prior to October 2020 may shed further light on its geographic ancestry. In sequencing of SARS-CoV-2 infections collected after October 2020, it may be possible to identify infections that likely descend from the White House COVID-19 outbreak.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.