TABLE 4.

Comparing contact tracing and genomic epidemiology in studying the outbreak^a

Ward or no. of events or cases	Contact tracing	Genomic epidemiology
Ward A	No. of cases: 23	No. of cases sequenced: 9 All B.1.564.1 lineage
	First case: 3 December 2020 Last case: 31 December 2020	First case: 3 December 2020 Last case: Earliest 22 December 2020
	Physiotherapist moving between wards A and B (directionality unknown) Source: unclear if it is ward B
Ward B	No. of cases: 3	No. of cases sequenced: 3 All B.1.564.1 lineage
	First case: 3 December 2020 Last case: 4 December 2020
	Physiotherapist moving between wards A and B (directionality unknown) Source: unclear if it is ward A
Ward C	No. of cases: 19	No. of cases sequenced: 11 B.1.564.1 (n = 7) likely spread from ward A to ward C B.1 (n = 1) and B.1.1.32 (n = 1) are likely community importations
	First case: 4 December 2020 Last case: 29 December 2020	First case: 6 December 2020 (date of first B.1.564.1 case) Last case: Earliest, 20 December 2020 (date of last B.1.564.1 case)
	No community importations	At least 2 community importations
	Four patients in ward C were exposed to two COVID-positive patients in ward A Source: ward A
Ward D	No. of cases: 9 One of the two earliest cases had no direct epidemiological link to other cases	No. of cases sequenced: 8 B.1.564.1 lineage (n = 6) B.1 lineage (n = 1) Since the two earliest cases were B.1.564.1 and B.1, it suggests that B.1 sample is the one that has no direct epidemiological link to other cases.
	First case: 10 December 2020 Last case: 22 December 2020	First case: 10 December 2020 Last case: Earliest, 17 December 2020 (last B.1.564.1 case)
	No community importation	At least 1 community importation
	Source: unclear
Ward E	No. of cases: 4 All patients exposed to one COVID positive HCW	No. of cases sequenced: 3 B.1.564.1 lineage (n = 2) B.1.231 lineage (n = 1) Case with B.1.231 lineage is likely due to community importation or exposure to different patient or HCW
	First case: 10 December 2020 Last case: 20 December 2020	First case: 19 December 2020 (first B.1.564.1 case) Last case: 20 December 2020 (last B.1.564.1 case)
	No community importations	At least 1 community importation
	Source: COVID-positive HCW
No. of cases in the outbreak	All cases (n = 106)	At least all sequenced B.1.564.1 lineage (n = 55)
Index case	Unknown
No. of importations into hospital	At least 1	At least 9 (1 from each lineage in Table 3)
No. of within-room transmission events	15	5
No. of neighboring room-to-room transmission events	Ward A: 5 Ward B: 1 Ward C: 7 Ward D: 1 Ward E: 2	Ward A: 3 Ward B: 1 Ward C: 2 Ward D: 0 Ward E: 1

^aConcordances and differences between contract tracing and genomic epidemiology are indicated by merged and split cells, respectively. One within-room transmission event in contact tracing is counted as at least two COVID-positive patients in one room with positive tests within a 20-day transmission range. We observed whether genomic epidemiology supports these contact tracing room transmission events by establishing the number of events where lineage assignment was B.1.564.1. Similarly, we counted neighboring room-to-room transmission contact tracing events as adjacent rooms with at least two COVID-positive patients within a 20-day transmission range. Last, we identified support for neighboring room-to-room transmission contact tracing events if the lineage for these sequences was B.1.564.1. All of the contact tracing transmission events that could not be supported by genomics was attributed to not sequencing all patient samples.