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. 2021 Sep 2;7(2):veab073. doi: 10.1093/ve/veab073

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© The Author(s) 2021. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 1. — Background spatiotemporal heterogeneity in sampling fractions and effective reproductive number R_e of SARS-CoV-2 in the US. (A) Sampling fractions estimated based on the number of full viral genomes deposited to GISAID relative to the estimated number of total COVID infections in each region and time interval. (B) Effective reproductive number R_e estimates from the ML SARS-CoV-2 phylogeny. A regional transmission effect was estimated for each region and time interval, which was then used to rescale the estimated base transmission rate to compute R_e. The base transmission rate was estimated to be 0.184 per day, which assuming a constant recovery/removal rate of 0.14 per day yields an estimated time-averaged $Inline graphic$ . States are grouped into the geographic regions designated by the US Department of Health and Human Services.

Inline graphic — Background spatiotemporal heterogeneity in sampling fractions and effective reproductive number R_e of SARS-CoV-2 in the US. (A) Sampling fractions estimated based on the number of full viral genomes deposited to GISAID relative to the estimated number of total COVID infections in each region and time interval. (B) Effective reproductive number R_e estimates from the ML SARS-CoV-2 phylogeny. A regional transmission effect was estimated for each region and time interval, which was then used to rescale the estimated base transmission rate to compute R_e. The base transmission rate was estimated to be 0.184 per day, which assuming a constant recovery/removal rate of 0.14 per day yields an estimated time-averaged $Inline graphic$ . States are grouped into the geographic regions designated by the US Department of Health and Human Services.