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. 2023 Jan 7;10(2):ofad001. doi: 10.1093/ofid/ofad001

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© The Author(s) 2023. Published by Oxford University Press on behalf of Infectious Diseases Society of America.

This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence (https://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 1. — Genetic diversity of sampled severe acute respiratory syndrome coronavirus 2. (A) We identified household transmission pairs and longitudinal samples by address matching from 4 participants enrolled in studies including a household transmission study, clinical trials of Favipiravir and Lambda, and a mask shedding study. (B) Histogram of pairwise single nucleotide polymorphism distances between consensus sequences from samples longitudinally sampled from the same individual, from different individuals within the same household, and between individuals from different households. (C) A maximum likelihood phylogeny inferred from consensus sequences with IQ-Tree with branches colored by clade. Clade assignments are made with Nextclade [46] through the nf-core viralrecon pipeline [24]. Branch lengths are in distances of substitutions per site. FP, false positive; TP, true positive.