Table 2. Phylogenetic Analysis and Epidemiologically Inferred Transmission Clusters.

Phylogenetic Cluster	Sequenced Strains*	No. of Infected Recruits in the Same Platoon without Sequenced Isolate†	No. of Genomes in Cluster	No. of Infected Recruits with an Infected Roommate
	no. of strains (no. in same platoon)
Cluster 1	2 (0)	3	5	0
Cluster 2	6 (6)	3	9	6
Cluster 3	2 (2)	0	2	2
Cluster 4	2 (2)	0	2	0
Cluster 5	5 (4)	4	9	4
Cluster 6	2 (NA)‡	0	2	0
Total	19 (14)	10	29	12

^*A total of 19 genomes belonging to 6 cluster strains were obtained from 18 participants. One participant had 2 different virus strains identified in samples obtained at different times.

^†Values indicate the number of infected study participants or nonparticipants who were assigned to the platoon most associated with the phylogenetically defined transmission cluster. The transmission cluster was defined according to the SARS-CoV-2 strain sequence. Infected recruits in each platoon with the highest proportion of participants infected with a sequenced cluster strain were tentatively assigned to that cluster if no sequenced isolate was obtained from that recruit.

^‡The platoon assignments of these participants were not available.