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. 2021 Apr 21;7(1):veab041. doi: 10.1093/ve/veab041

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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 Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 3. — Transmission dynamics of shared within-host variants between CH1 outbreak samples. Each plot shows shared iSNVs between putative donor (red)/recipient (blue) pairs as evidence for transmission. (A) The presence of shared iSNVs between P3 and P5, (B) between P3 and P7. P7 further infected X1 (L) and P23 (C). P3 also sustained a transmission chain through HW4 (I) who infected P11 (F). Finally, P3 infected and transmitted iSNVs to P22 (D), P21(E), P10 (G), P13 (H), P20 (J) and P29 (L). Variants with frequency greater than 0.5 fixed as SNVs in the recipient.