Fig. 2: Genomic diversity of SARS-CoV-2 in the university and community.

a Maximum likelihood tree showing that the majority of lineages from university isolates were distinct from community isolates. The node leaves (branch tips) show case location and global PANGO lineage is illustrated in the vertical bar. b Time-scaled coalescent tree including university members and local community isolates from study period with visible segregation between the two groups. College affiliation is shown for university members in the second set of vertical columns, highlighting the ‘top nine’ colleges by cluster 1 prevalence. c Epidemic curves demonstrating a steeper decline in SARS-CoV-2 cases in the University of Cambridge (i) compared to the local community (ii), with associated lineages. Only cases with available genomes are included. University term ran from the week commencing October 5 to the week commencing November 30. The light blue shaded area reflects a 4-week national lockdown in the UK, which was associated with a large fall in COVID-19 cases in University students. Specific lineages highlighted are the four largest lineages within the University (minimum 20 cases over the study period) and the community (minimum 50 cases over the study period). For (i), weekly individual case ascertainment for staff and students testing positive for SARS-CoV-2 through both symptomatic and asymptomatic testing pathways provided at the University of Cambridge is indicated. For (ii), weekly cases with genomes available from the local community are shown. Source data are provided as a Source Data file.