Last week I presented on "SARS-CoV-2 evolutionary dynamics" at the VIDD departmental seminar at . Slides are available here: bedford.io/talks/sars-cov and a recording is available at youtube.com/watch?v=VErVD_.
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Hey, can you explain what the X-axis is on the slide labeled “Consistent reductions in variant-specific Rt from vaccination”?
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Each state has a series of Rt values estimated across time and across variants. Here Marlin fit a mixed effects model to predict Rt based on vaccination coverage as proportion of population (0 to 1). X-axis shows reduction in Rt going from 0% vaccination to 100% vaccination.
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TY for this. Apologies for a terse question (Twitter limits). On the slide “Estimation of variant-specific Rt through time using state-level data”, the sudden appearance of Delta on the Rt chart seemed to suggest insufficient surveillance. Just an artifact of the chart?
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We can only estimate Rt reliably once a variant reaches ~0.1% frequency. Here estimates for Delta when rarer than 0.1% (generally before April) are censored. Knowledge of Delta’s increased transmissibility should have come from UK data before this and India before that.
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Thank you so much for sharing this talk! I’d love to hear your view - as this evolution continues, what are some of the unlikely things ahead (including tail risks) that could surprise us/catch us off guard?
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From seasonal influenza, we expect that antigenic drift will cause newly evolved strains to replace old strains. However, rapid enough evolution could result in diversification into multiple co-circulating types that would each need vaccinating against. bedford.io/talks/sars-cov
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Thanks; really interesting; really appreciate all the hard work you and the others have done!
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