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Phylogeographic Analysis Gives Insight Into Omicron Spread in England

The introduction and spread of the Omicron lineage of SARS-CoV-2 in England reflects human mobility patterns, a new phylogeographic analysis in Science reports. A University of Oxford-led team analyzed 115,622 SARS-CoV-2 Omicron BA.1 genomes, of which about 42 percent were from England, that were sampled between early November 2021 and late January 2022. They identified about 6,500 independent importation events, though most led to single cases, and traced the earliest importation event to early November 2021. They note that six of the eight largest Omicron lineages in England were already present when travel restrictions from southern African countries — where the lineage was first reported — were put into place and continued to arrive from secondary sources. In additional analyses, the researchers traced local Omicron transmission, finding it was first concentrated in Greater London and moved with travel from there. "UK travel restrictions were intended to delay the expansion of BA.1 locally while offering additional vaccinations to at-risk individuals," the researchers write. "However, Omicron had likely already spread internationally by the time it was detected in late November 2021, allowing the establishment of secondary locations of exportation. Therefore, any proposed global systems that aim to rapidly detect and respond to new [variants of concern] (and emerging infectious diseases in general) should be designed around the connection structure of human mobility networks."

The Scan

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