ENHANCED EPIDEMIOLOGICAL SUMMARY
COVID-19 Regional Incidence and Time to Case
Notification in Ontario
Contents
Contents ........................................................................................................................................................ 1
Purpose ......................................................................................................................................................... 3
Ontario ...................................................................................................................................................... 4
Toronto ..................................................................................................................................................... 8
Central East ............................................................................................................................................. 12
Central West ........................................................................................................................................... 16
Eastern .................................................................................................................................................... 20
North ....................................................................................................................................................... 24
South West .............................................................................................................................................. 28
GTA .......................................................................................................................................................... 32
Non-GTA .................................................................................................................................................. 36
Algoma Public Health .............................................................................................................................. 40
Brant County Health Unit ........................................................................................................................ 44
Chatham-Kent Public Health ................................................................................................................... 48
City of Hamilton Public Health Services .................................................................................................. 52
Durham Region Health Department ....................................................................................................... 56
Eastern Ontario Health Unit.................................................................................................................... 60
Grey Bruce Health Unit ........................................................................................................................... 64
Haldimand-Norfolk Health Unit .............................................................................................................. 68
Haliburton, Kawartha, Pine Ridge District Health Unit ........................................................................... 72
Halton Region Public Health ................................................................................................................... 76
Hastings Prince Edward Public Health .................................................................................................... 80
Huron Perth Public Health ...................................................................................................................... 84
Kingston, Frontenac and Lennox & Addington Public Health ................................................................. 88
Lambton Public Health ............................................................................................................................ 92
Leeds, Grenville & Lanark District Health Unit........................................................................................ 96
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Middlesex-London Health Unit ............................................................................................................. 100
Niagara Region Public Health ................................................................................................................ 104
North Bay Parry Sound District Health Unit .......................................................................................... 108
Northwestern Health Unit .................................................................................................................... 112
Ottawa Public Health ............................................................................................................................ 116
Peel Public Health ................................................................................................................................. 120
Peterborough Public Health .................................................................................................................. 124
Porcupine Health Unit ........................................................................................................................... 128
Public Health Sudbury & Districts ......................................................................................................... 132
Renfrew County and District Health Unit ............................................................................................. 136
Simcoe Muskoka District Health Unit ................................................................................................... 140
Southwestern Public Health.................................................................................................................. 144
Thunder Bay District Health Unit .......................................................................................................... 148
Timiskaming Health Unit ....................................................................................................................... 152
Toronto Public Health ........................................................................................................................... 156
Waterloo Public Health and Emergency Services ................................................................................. 160
Wellington-Dufferin-Guelph Public Health ........................................................................................... 164
Windsor-Essex County Health Unit ....................................................................................................... 168
York Region Public Health ..................................................................................................................... 172
Methods .................................................................................................................................................... 176
Limitations ................................................................................................................................................ 178
References ................................................................................................................................................ 179
Disclaimer.................................................................................................................................................. 179
Citation ...................................................................................................................................................... 179
For Further Information ............................................................................................................................ 179
Public Health Ontario ................................................................................................................................ 179

This report reflects cases that have been publicly reported up to 2020-07-06.
This report includes the most current information available from iPHIS and other local case
management systems (iPHIS plus).
Full french translation is available upon request.

2
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Purpose
This report provides a summary of the regional case counts of COVID-19, likely source of acquisition, and
the timeliness of testing and investigation in Ontario. These regional measures provide important
information to support and monitor re-opening across Ontario.
A brief description of the measures included in this report are summarized below. Additional details are
outlined in the Methods section, found toward the end of this document.
Case count
We measured the daily number of COVID-19 cases according to the date a case was publicly reported
(i.e., the date the public health unit [PHU] reported the case to Public Health Ontario [PHO] plus one day
to account for the delay in public reporting) and produced an epidemic curve using these counts over
time. Examination of these epidemic curves can be used to determine the current trajectory of the
epidemic in each region.
Reproduction number
The reproduction number is the average number of secondary cases of infection generated by each
person infected with COVID-19. A reproduction number greater than one means that the epidemic is
growing in a region, while a reproduction number less than one means the epidemic is coming under
control in a region.
Likely source of acquisition
COVID-19 cases have been examined to determine whether a case travelled, was associated with an
outbreak, was a contact of a case, had no known epidemiological link (sporadic community
transmission), or where information was pending or missing. Tracking the number of cases with no
known epidemiologic link provides insight into how well we are able to ascertain where cases are
coming from and may reflect the effectiveness and timeliness of the contact tracing process, as well as
indicate adherence to public health guidance by individuals who are asked to isolate.
Timeliness of case presentation, testing, and investigation
To halt transmission, it is crucial that potential cases are rapidly identified, tested, reported, and
managed (which includes contact tracing). We examined three timeliness metrics. First, the proportion
of cases that have a specimen collected for testing within 2 days of symptom onset. Second, the
proportion of cases that had a positive result reported to the PHU within 1 day of specimen collection.
Third, the proportion of cases for which case management began within 1 day of a positive result
reported to the PHU.

Flow diagram of case presentation, testing, and investigation

3
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Ontario
Epidemic Curve: Ontario

Data Source: iPHIS plus

4
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Ontario

Data Source: iPHIS plus

5
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Ontario

Data Source: iPHIS plus

6
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Ontario

Data Source: iPHIS plus

7
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Toronto
Epidemic Curve: Toronto

Data Source: iPHIS plus

8
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Toronto

Data Source: iPHIS plus

9
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Toronto

Data Source: iPHIS plus

10
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Toronto

Data Source: iPHIS plus

11
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Central East
Epidemic Curve: Central East

Data Source: iPHIS plus

12
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Central East

Data Source: iPHIS plus

13
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Central East

Data Source: iPHIS plus

14
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Central East

Data Source: iPHIS plus

15
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Central West
Epidemic Curve: Central West

Data Source: iPHIS plus

16
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Central West

Data Source: iPHIS plus

17
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Central West

Data Source: iPHIS plus

18
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Central West

Data Source: iPHIS plus

19
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Eastern
Epidemic Curve: Eastern

Data Source: iPHIS plus

20
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Eastern

Data Source: iPHIS plus

21
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Eastern

Data Source: iPHIS plus

22
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Eastern

Data Source: iPHIS plus

23
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 North
Epidemic Curve: North

Data Source: iPHIS plus

24
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: North

Data Source: iPHIS plus

25
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: North

Data Source: iPHIS plus

26
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: North

Data Source: iPHIS plus

27
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 South West
Epidemic Curve: South West

Data Source: iPHIS plus

28
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: South West

Data Source: iPHIS plus

29
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: South West

Data Source: iPHIS plus

30
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: South West

Data Source: iPHIS plus

31
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 GTA
Epidemic Curve: GTA

Data Source: iPHIS plus

32
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: GTA

Data Source: iPHIS plus

33
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: GTA

Data Source: iPHIS plus

34
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: GTA

Data Source: iPHIS plus

35
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Non-GTA
Epidemic Curve: Non-GTA

Data Source: iPHIS plus

36
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Non-GTA

Data Source: iPHIS plus

37
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Non-GTA

Data Source: iPHIS plus

38
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Non-GTA

Data Source: iPHIS plus

39
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Algoma Public Health
Epidemic Curve: Algoma Public Health

Data Source: iPHIS plus

40
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Algoma Public Health

Data Source: iPHIS plus

41
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Algoma Public Health

Data Source: iPHIS plus

42
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Algoma Public Health

Data Source: iPHIS plus

43
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Brant County Health Unit
Epidemic Curve: Brant County Health Unit

Data Source: iPHIS plus

44
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Brant County Health Unit

Data Source: iPHIS plus

45
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Brant County Health Unit

Data Source: iPHIS plus

46
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Brant County Health Unit

Data Source: iPHIS plus

47
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Chatham-Kent Public Health
Epidemic Curve: Chatham-Kent Public Health

Data Source: iPHIS plus

48
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Chatham-Kent Public Health

Data Source: iPHIS plus

49
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Chatham-Kent Public Health

Data Source: iPHIS plus

50
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Chatham-Kent Public Health

Data Source: iPHIS plus

51
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 City of Hamilton Public Health Services
Epidemic Curve: City of Hamilton Public Health Services

Data Source: iPHIS plus

52
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: City of Hamilton Public Health Services

Data Source: iPHIS plus

53
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: City of Hamilton Public Health Services

Data Source: iPHIS plus

54
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: City of Hamilton Public Health Services

Data Source: iPHIS plus

55
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Durham Region Health Department
Epidemic Curve: Durham Region Health Department

Data Source: iPHIS plus

56
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Durham Region Health Department

Data Source: iPHIS plus

57
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Durham Region Health Department

Data Source: iPHIS plus

58
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Durham Region Health Department

Data Source: iPHIS plus

59
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Eastern Ontario Health Unit
Epidemic Curve: Eastern Ontario Health Unit

Data Source: iPHIS plus

60
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Eastern Ontario Health Unit

Data Source: iPHIS plus

61
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Eastern Ontario Health Unit

Data Source: iPHIS plus

62
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Eastern Ontario Health Unit

Data Source: iPHIS plus

63
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Grey Bruce Health Unit
Epidemic Curve: Grey Bruce Health Unit

Data Source: iPHIS plus

64
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Grey Bruce Health Unit

Data Source: iPHIS plus

65
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Grey Bruce Health Unit

Data Source: iPHIS plus

66
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Grey Bruce Health Unit

Data Source: iPHIS plus

67
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Haldimand-Norfolk Health Unit
Epidemic Curve: Haldimand-Norfolk Health Unit

Data Source: iPHIS plus

68
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Haldimand-Norfolk Health Unit

Data Source: iPHIS plus

69
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Haldimand-Norfolk Health Unit

Data Source: iPHIS plus

70
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Haldimand-Norfolk Health Unit

Data Source: iPHIS plus

71
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Haliburton, Kawartha, Pine Ridge District Health Unit
Epidemic Curve: Haliburton, Kawartha, Pine Ridge District Health Unit

Data Source: iPHIS plus

72
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Haliburton, Kawartha, Pine Ridge District Health Unit

Data Source: iPHIS plus

73
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Haliburton, Kawartha, Pine Ridge District Health Unit

Data Source: iPHIS plus

74
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Haliburton, Kawartha, Pine Ridge District Health Unit

Data Source: iPHIS plus

75
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Halton Region Public Health
Epidemic Curve: Halton Region Public Health

Data Source: iPHIS plus

76
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Halton Region Public Health

Data Source: iPHIS plus

77
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Halton Region Public Health

Data Source: iPHIS plus

78
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Halton Region Public Health

Data Source: iPHIS plus

79
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Hastings Prince Edward Public Health
Epidemic Curve: Hastings Prince Edward Public Health

Data Source: iPHIS plus

80
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Hastings Prince Edward Public Health

Data Source: iPHIS plus

81
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Hastings Prince Edward Public Health

Data Source: iPHIS plus

82
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Hastings Prince Edward Public Health

Data Source: iPHIS plus

83
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Huron Perth Public Health
Epidemic Curve: Huron Perth Public Health

Data Source: iPHIS plus

84
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Huron Perth Public Health

Data Source: iPHIS plus

85
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Huron Perth Public Health

Data Source: iPHIS plus

86
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Huron Perth Public Health

Data Source: iPHIS plus

87
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Kingston, Frontenac and Lennox & Addington Public Health
Epidemic Curve: Kingston, Frontenac and Lennox & Addington Public Health

Data Source: iPHIS plus

88
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Kingston, Frontenac and Lennox & Addington Public Health

Data Source: iPHIS plus

89
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Kingston, Frontenac and Lennox & Addington Public Health

Data Source: iPHIS plus

90
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Kingston, Frontenac and Lennox & Addington Public Health

Data Source: iPHIS plus

91
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Lambton Public Health
Epidemic Curve: Lambton Public Health

Data Source: iPHIS plus

92
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Lambton Public Health

Data Source: iPHIS plus

93
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Lambton Public Health

Data Source: iPHIS plus

94
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Lambton Public Health

Data Source: iPHIS plus

95
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Leeds, Grenville & Lanark District Health Unit
Epidemic Curve: Leeds, Grenville & Lanark District Health Unit

Data Source: iPHIS plus

96
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Leeds, Grenville & Lanark District Health Unit

Data Source: iPHIS plus

97
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Leeds, Grenville & Lanark District Health Unit

Data Source: iPHIS plus

98
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Leeds, Grenville & Lanark District Health Unit

Data Source: iPHIS plus

99
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Middlesex-London Health Unit
Epidemic Curve: Middlesex-London Health Unit

Data Source: iPHIS plus

100
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Middlesex-London Health Unit

Data Source: iPHIS plus

101
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Middlesex-London Health Unit

Data Source: iPHIS plus

102
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Middlesex-London Health Unit

Data Source: iPHIS plus

103
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Niagara Region Public Health
Epidemic Curve: Niagara Region Public Health

Data Source: iPHIS plus

104
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Niagara Region Public Health

Data Source: iPHIS plus

105
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Niagara Region Public Health

Data Source: iPHIS plus

106
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Niagara Region Public Health

Data Source: iPHIS plus

107
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 North Bay Parry Sound District Health Unit
Epidemic Curve: North Bay Parry Sound District Health Unit

Data Source: iPHIS plus

108
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: North Bay Parry Sound District Health Unit

Data Source: iPHIS plus

109
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: North Bay Parry Sound District Health Unit

Data Source: iPHIS plus

110
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: North Bay Parry Sound District Health Unit

Data Source: iPHIS plus

111
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Northwestern Health Unit
Epidemic Curve: Northwestern Health Unit

Data Source: iPHIS plus

112
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Northwestern Health Unit

Data Source: iPHIS plus

113
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Northwestern Health Unit

Data Source: iPHIS plus

114
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Northwestern Health Unit

Data Source: iPHIS plus

115
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Ottawa Public Health
Epidemic Curve: Ottawa Public Health

Data Source: iPHIS plus

116
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Ottawa Public Health

Data Source: iPHIS plus

117
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Ottawa Public Health

Data Source: iPHIS plus

118
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Ottawa Public Health

Data Source: iPHIS plus

119
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Peel Public Health
Epidemic Curve: Peel Public Health

Data Source: iPHIS plus

120
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Peel Public Health

Data Source: iPHIS plus

121
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Peel Public Health

Data Source: iPHIS plus

122
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Peel Public Health

Data Source: iPHIS plus

123
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Peterborough Public Health
Epidemic Curve: Peterborough Public Health

Data Source: iPHIS plus

124
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Peterborough Public Health

Data Source: iPHIS plus

125
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Peterborough Public Health

Data Source: iPHIS plus

126
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Peterborough Public Health

Data Source: iPHIS plus

127
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Porcupine Health Unit
Epidemic Curve: Porcupine Health Unit

Data Source: iPHIS plus

128
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Porcupine Health Unit

Data Source: iPHIS plus

129
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Porcupine Health Unit

Data Source: iPHIS plus

130
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Porcupine Health Unit

Data Source: iPHIS plus

131
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Public Health Sudbury & Districts
Epidemic Curve: Public Health Sudbury & Districts

Data Source: iPHIS plus

132
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Public Health Sudbury & Districts

Data Source: iPHIS plus

133
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Public Health Sudbury & Districts

Data Source: iPHIS plus

134
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Public Health Sudbury & Districts

Data Source: iPHIS plus

135
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Renfrew County and District Health Unit
Epidemic Curve: Renfrew County and District Health Unit

Data Source: iPHIS plus

136
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Renfrew County and District Health Unit

Data Source: iPHIS plus

137
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Renfrew County and District Health Unit

Data Source: iPHIS plus

138
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Renfrew County and District Health Unit

Data Source: iPHIS plus

139
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Simcoe Muskoka District Health Unit
Epidemic Curve: Simcoe Muskoka District Health Unit

Data Source: iPHIS plus

140
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Simcoe Muskoka District Health Unit

Data Source: iPHIS plus

141
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Simcoe Muskoka District Health Unit

Data Source: iPHIS plus

142
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Simcoe Muskoka District Health Unit

Data Source: iPHIS plus

143
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Southwestern Public Health
Epidemic Curve: Southwestern Public Health

Data Source: iPHIS plus

144
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Southwestern Public Health

Data Source: iPHIS plus

145
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Southwestern Public Health

Data Source: iPHIS plus

146
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Southwestern Public Health

Data Source: iPHIS plus

147
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Thunder Bay District Health Unit
Epidemic Curve: Thunder Bay District Health Unit

Data Source: iPHIS plus

148
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Thunder Bay District Health Unit

Data Source: iPHIS plus

149
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Thunder Bay District Health Unit

Data Source: iPHIS plus

150
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Thunder Bay District Health Unit

Data Source: iPHIS plus

151
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timiskaming Health Unit
Epidemic Curve: Timiskaming Health Unit

Data Source: iPHIS plus

152
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Timiskaming Health Unit

Data Source: iPHIS plus

153
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Timiskaming Health Unit

Data Source: iPHIS plus

154
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Timiskaming Health Unit

Data Source: iPHIS plus

155
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Toronto Public Health
Epidemic Curve: Toronto Public Health

Data Source: iPHIS plus

156
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Toronto Public Health

Data Source: iPHIS plus

157
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Toronto Public Health

Data Source: iPHIS plus

158
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Toronto Public Health

Data Source: iPHIS plus

159
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Waterloo Public Health and Emergency Services
Epidemic Curve: Waterloo Public Health and Emergency Services

Data Source: iPHIS plus

160
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Waterloo Public Health and Emergency Services

Data Source: iPHIS plus

161
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Waterloo Public Health and Emergency Services

Data Source: iPHIS plus

162
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Waterloo Public Health and Emergency Services

Data Source: iPHIS plus

163
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Wellington-Dufferin-Guelph Public Health
Epidemic Curve: Wellington-Dufferin-Guelph Public Health

Data Source: iPHIS plus

164
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Wellington-Dufferin-Guelph Public Health

Data Source: iPHIS plus

165
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Wellington-Dufferin-Guelph Public Health

Data Source: iPHIS plus

166
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Wellington-Dufferin-Guelph Public Health

Data Source: iPHIS plus

167
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Windsor-Essex County Health Unit
Epidemic Curve: Windsor-Essex County Health Unit

Data Source: iPHIS plus

168
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: Windsor-Essex County Health Unit

Data Source: iPHIS plus

169
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: Windsor-Essex County Health Unit

Data Source: iPHIS plus

170
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: Windsor-Essex County Health Unit

Data Source: iPHIS plus

171
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 York Region Public Health
Epidemic Curve: York Region Public Health

Data Source: iPHIS plus

172
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Reproduction Number: York Region Public Health

Data Source: iPHIS plus

173
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Likely Acquisition: York Region Public Health

Data Source: iPHIS plus

174
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Timeliness: York Region Public Health

Data Source: iPHIS plus

175
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 Methods
•

•

The data for this report were based on:


Information extracted from the Ontario Ministry of Health (Ministry) integrated Public
Health Information System (iPHIS) database as of 4 p.m. on the day prior to this report.



Information successfully uploaded to the Ministry from Local Systems: Toronto Public
Health (Coronavirus Rapid Entry System) CORES, The Ottawa Public Health COVID-19
Ottawa Database (The COD) and Middlesex-London COVID-19 Case and Contact
Management Tool (CCMtool) as of 2 p.m. on the day prior to this report.

The date variable used in the figures for the epidemic curve and the reproduction number
throughout this report refers to the date that a case first appeared in the compiled data set + 1
additional day. This corresponds to the “public reporting date” of each case at the provincial level.


In order to account for certain instances when there were long lags between when a case’s
specimen was collected and when their data was entered into iPHIS, CORES, The COD, or
CCMtool, we replaced the public reporting date with the specimen collection date + 3 days
(the mode of the distribution from specimen collection to public reporting date). This
replacement was made for cases whose delay between specimen collection and case
creation was between 7 and 90 days.



In rare circumstances when this delay was more than 90 days, we did not make the date
replacement.

•

The date variable used in the figures for the likely acquisition and the timeliness metrics refers to
the case reported date, which is the date the case was reported to the public health unit.

•

Due to smaller case counts, we have combined the North West and North East regions into a single
region in this report.

•

The PHUs were categorized into regions as follows:


Toronto: Toronto Public Health



Central East: Durham Region Health Department, Haliburton, Kawartha, Pine Ridge District
Health Unit, Peel Public Health, Simcoe Muskoka District Health Unit, and York Region
Public Health



Central West: Brand County Health Unit, City of Hamilton Public Health Services,
Haldimand-Norfolk Health Unit, Halton Region Public Health, Niagara Region Public Health,
Region of Waterloo Public Health and Emergency Services, and Wellington-DufferinGuelph Public Health



Eastern: Ottawa Public Health, Eastern Ontario Health Unit, Hastings Prince Edward Public
Health, Kingston, Frontenac and Lennox & Addington Public Health, Leeds, Grenville &
Lanark District Health Unit, and Renfrew County and District Health Unit

176
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 

Northern: Northwestern Health Unit, Thunder Bay District Health Unit, Algoma Public
Health, North Bay Parry Sound District Health Unit, Porcupine Health Unit, Public Health
Sudbury & Districts, and Timiskaming Health Unit



South West: Chatham-Kent Public Health, Grey Bruce Health Unit, Huron Perth Public
Health, Lambton Public Health, Middlesex-London Health Unit, Southwestern Public
Health, and Windsor-Essex County Health Unit



GTA health units include: Durham Region Health Department, Peel Public Health, Toronto
Public Health, and York Region Public Health.

•

With the exception of the time from case reported date to investigation start date, orientation of
case counts by geography is based on the diagnosing health unit (DHU). DHU refers to the case’s
public health unit of residence at the time of illness onset and not necessarily the location of
exposure. For the time from case reported date to investigation start date, responsible public
health unit was used in order to align with the process for case management. Cases for which the
responsible health unit was reported as the Ministry of Health (MOH) (to signify that the PHU is
not responsible for case management, such as cases that are not residents of Ontario) have been
excluded from the analyses.

•

Epidemic curve: smoothed epidemic curves were estimated using generalized additive models of
the daily number of cases.

•

Reproduction number: the reproduction number was measured using the EpiEstim package in R.1
The procedure uses daily reported case counts and a 7-day rolling window for estimation. The
mean serial interval was set at 4.5 days with a standard deviation of 2.5 days, as adapted from
published esimates.2,3 EpiEstim uses a Markov Chain Monte Carlo sampling procedure, and the
median represents the middle of the distribution of most probable values of the reproduction
number. The reproduction number of a region was only calculated when there were at least 12
cases in that region in the last 7 days.

•

Likely source of acquisition is determined by examining the exposure and risk factor fields from
iPHIS and local systems to determine whether a case travelled, was associated with an outbreak,
was a contact of a case, had no known epidemiological link (sporadic community transmission) or
where information was pending or missing. Cases with multiple exposures or risk factors were
assigned to a single likely acquisition source group which was determined hierarchically in the
following order:


For cases with an episode date on or after April 1, 2020: Outbreak-associated > close
contact of a confirmed case > travel > no known epidemiological link > information missing
or unknown



For cases with an episode date before April 1, 2020: Travel > outbreak-associated > close
contact of a confirmed case > no known epidemiological link > information missing or
unknown.



Data for the three days prior to the extract date are not shown for this graph due to lags in
data entry.

177
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 •

Timeliness of reporting: smoothed curves were estimated using generalized additive models of the
proportion of cases that were reported within the stated time frame. The dots in the graph
represent the individual proportions for a given reported date. The duration elapsed from
reporting to investigation was only measured from May 1st onwards, as this is the date that the
directive to enter investigation start date was issued. Cases with missing or pending dates have
been excluded from the denominator in this analysis.


For the time from case reported date to investigation start date, cases with a disposition
status of referred to the First Nations and Inuit Health Branch (FNIHB), lost to follow up, or
untraceable were excluded from the analyses.



If there were no cases within 7 days of the case reported date, the smoothed curve for the
proportion meeting the target is not shown.



Data for the three days prior to the extract date are not shown for this graph due to lags in
data entry.

Limitations
•

This report includes confirmed cases of COVID-19 as per the Ontario Ministry of Health case
definition, which may change over time. Case detection is strongly influenced by the provincial
testing strategy, which may also influence the time elapsed between various steps in the testing
and notification process.

•

iPHIS and iPHIS plus (which includes iPHIS, CORES, The COD, and COVID-19 CCMtool) are dynamic
disease reporting systems, which allow ongoing updates to data previously entered. As a result,
data extracted represent a snapshot at the time of extraction and may differ from previous or
subsequent reports.

•

The data only represent cases reported to public health units and recorded in iPHIS plus. As a
result, all counts will be subject to varying degrees of underreporting due to a variety of factors,
such as disease awareness and medical care seeking behaviours, which may depend on severity of
illness, clinical practice, changes in laboratory testing, and reporting behaviours.

•

The public reporting date lags the infection date; as such, public reporting dates likely represent
infections that occurred approximately 10 days earlier.

•

For reproduction number analyses, all cases since initial importation were presumed to be locally
transmitted. Further, the estimates of the reproduction number are influenced by the choice of
serial interval. As such, the reported estimates in the analysis are subject to change as additional
data on the estimated serial interval are published.

•

The epidemic curves in this report will not align with the curves provided in other reports due to
the date chosen. In monitoring trends over time, the public reporting date was specifically chosen
in order to identify early signals of increasing cases, which is challenging when using episode date
or reported date due to lags in data entry and therefore the need for caution when reviewing case
data for more recent days. As such, numbers from the epidemic curve should not be compared
between this regional report and the daily/weekly epidemiologic summary.

178
COVID-19 Regional Incidence and Time to Case Notification in Ontario

 References
1.

Cori A, Ferguson NM, Fraser C, Cauchemez S. A new framework and software to estimate timevarying reproduction numbers during epidemics. American Journal of Epidemiology 2013;
178(9):1505–1512. Available from: https://doi.org/10.1093/aje/kwt133

2.

Nishiura H, Linton NM, Akhmetzhanov AR. Serial interval of novel coronavirus (COVID-19)
infections. Int J Infect Dis 2020; 93:284–286. Available from:
https://doi.org/10.1016/j.ijid.2020.02.060

3.

Du Z, Xu X, Wu Y, Wang L, Cowling BJ, Ancel Meyers L. Serial interval of COVID-19 among publicly
reported confirmed cases. Emerg Infect Dis. 2020; 26(6):1341-1343. Available from:
https://doi.org/10.3201/eid2606.200357

Disclaimer
This document was developed by Public Health Ontario (PHO). PHO provides scientific and technical
advice to Ontario’s government, public health organizations and health care providers. PHO’s work is
guided by the current best available evidence at the time of publication.
The application and use of this document is the responsibility of the user. PHO assumes no liability
resulting from any such application or use.
This document may be reproduced without permission for non-commercial purposes only and provided
that appropriate credit is given to PHO. No changes and/or modifications may be made to this document
without express written permission from PHO.

Citation
Ontario Agency for Health Protection and Promotion (Public Health Ontario). COVID-19 regional
incidence and time to case notification in Ontario. Toronto, ON: Queen’s Printer for Ontario; 2020.

For Further Information
For more information, email epir@oahpp.ca.

Public Health Ontario
Public Health Ontario is an agency of the Government of Ontario dedicated to protecting and promoting
the health of all Ontarians and reducing inequities in health. Public Health Ontario links public health
practitioners, front-line health workers and researchers to the best scientific intelligence and knowledge
from around the world.
For more information about PHO, visit publichealthontario.ca.

179
COVID-19 Regional Incidence and Time to Case Notification in Ontario