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Fig. 1 | Genome Medicine

Fig. 1

From: SARS-CoV-2 population dynamics in immunocompetent individuals in a closed transmission chain shows genomic diversity over the course of infection

Fig. 1

Transmission chain of SARS-CoV-2 between 16 participants (y axis) following potential introductions of the virus succeeded by a mass spreading event (at day 0) with 70 people in attendance. The initial positive RT-qPCR test is shown as a pentagon with the only negative test reported shown as a blue circle (Participant 06, who later tested positive). A pentagon with no fill shows a positive test that was not sequenced, and therefore has no associated lineage data (Participant 08 was sequenced but there was not enough sequencing coverage to define a lineage). Symptomatic periods of the individuals are shown in a thick grey line, isolation period in a black line, direct contacts through a solid arrow and participants who came into contact with other participants whilst mixing generally (including living and working together) is shown with a dashed arrow. Subsequent SARS-CoV-2 positive samples from the initial test are shown as smaller circles. Isolation of infected individuals in this cohort only began once population testing had occurred, and those SARS-CoV-2 positive by RT-qPCR were moved to a quarantine location. Participant 06 was the last to test positive, was asymptomatic and was last to isolate during this outbreak recording a negative RT-qPCR test at day 8. Participants in contact at the same time are shown via a bracket, e.g. participants 02, 13 and 04 were all direct contacts of participants 16, 12 and 07. Arrows that begin prior to the spreading event indicate individuals who were in contact with each other on a day-to-day basis i.e. through work and living environment. Lineage information from viral sequences extracted, sequenced and classified using Pangolin are colour-coded: B.1, black; B.1.36, red; B.1.36.1, orange. Note, for consistency, all timepoints are referenced to the mass spreading event and should be considered as days post this event. This figure was created using Biorender

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