Fig. 3: Emergence and transmission of SARS-CoV-2 in a large university cluster.

a Time-scaled phylogenetic tree of largest university cluster (cluster 1) derived from the BDSKY model implemented in BEAST 2.6 (Fig. 5). The left-sided heatmap is coloured by case location, and the right-sided heatmap is coloured by student college affiliation, highlighting the top nine colleges by cluster 1 prevalence. Cluster 1 was widely dispersed across the university with limited transmission into the community. b Frequency of Lineage B.1.160.7 (to which cluster 1 belongs) in each region of the UK and the University of Cambridge. Regions are defined as ‘Nomenclature of territorial units for statistics’ (NUTS) regions, where the UK has 9 regions. It is visible that the lineage B.1.160.7 was first sequenced in Wales, and then in the neighbouring South West of England, before becoming prevalent within the University of Cambridge. The lineage remained infrequently detected in the community populating the wider surrounding region (Cambridgeshire, East Anglia, Bedfordshire and Hertfordshire, and Essex, making up East of England) throughout the university term. c A continuous transmission chain of SARS-CoV-2 infections in cluster 1 commenced with a single introduction. Relationships between individuals in cluster 1 were calculated within A2B-COVID. Colours denote potential transmission events from the donor (vertical axis) to the recipient (horizontal axis) that are consistent with transmission¹² or which are borderline possibilities (yellow). The plot shows that the data are consistent with a continuous transmission chain of SARS-CoV-2 infections in cluster 1 occurring via a single introduction; there are multiple potential networks of transmission events between these individuals for which each event would be consistent with a statistical model of direct transmission. We note that individuals in this plot are ordered by the date of the first positive COVID test. Source data are provided as a Source Data file.