FluWatch annual report: 2019-2020 influenza season

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Organization: Public Health Agency of Canada

Published: 2021-03-25

ISSN: 2562-9018

Cat.: HP57-9E-PDF

Pub.: 200478

Summary

  • The public health measures instituted to reduce the impact of the COVID-19 pandemic also greatly impacted the 2019-2020 influenza season in Canada.
  • Nationally, the 2019-2020 influenza season in Canada began on week 47 (November 17 to 23, 2019), peaked in late January (week 5) and ended early and abruptly on week 13 (March 22 to 28, 2020), eight weeks earlier than the average end of season.
  • Record low numbers of reported influenza detections, hospitalizations, and outbreaks were observed from mid-March to the end of the season; this pattern was observed for all influenza surveillance indicators presented in this report.
  • During the active influenza season (mid-November to mid-March), all seasonal influenza types and subtypes (A(H1N1), A(H3N2) and B/Victoria) circulated concurrently, resulting in higher than average numbers of influenza detections and hospitalizations being reported during that time period.
  • Overall, influenza A was the dominant influenza type (59% of detections) and A(H1N1) the dominant sub-type (68% of sub-typed influenza A).
  • Influenza A affected all age groups, with influenza A(H3N2) primarily affecting adults 65 years of age and older and influenza A(H1N1) primarily affecting individuals under 65 years of age. Influenza B primarily affected younger people, with detections predominantly reported in individuals 5 years of age and under.
  • Overall, influenza vaccine coverage in the 2019-2020 season (42%) was similar to the previous season. Coverage was estimated at 34% for adults aged 18 to 64 years and 70% among seniors (65 and older).
  • Vaccine effectiveness (VE) studies in the outpatient setting demonstrated moderate protection for influenza A(H1N1), at 43%, and good protection against influenza A(H3N2) and influenza B, at 50% and 65% respectively. In the adult inpatient setting, moderate protection (42%) was observed for influenza A(H1N1), but low effectiveness was observed against influenza B (20%), with the confidence limits including 0% (no effectiveness).

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About the FluWatch annual report

FluWatch is Canada's national surveillance system that monitors the spread of the flu and other flu-like illnesses on an ongoing basis using data supplied to the FluWatch program from its pan-Canadian network of labs, hospitals, doctor's offices, individual Canadians and provincial and territorial (PT) ministries of health.

FluWatch reports are based on weekly data that are published throughout the influenza surveillance season which goes from epidemiological week 35 to 34 of the following year. This annual report is a summary of Canada's 2019-2020 influenza season (August 25, 2019 to August 22, 2020) and provides a comparison of core surveillance indicators to those observed in the previous five seasons.

Overview of the 2019-2020 influenza season, based on laboratory-confirmed influenza detections

Data on laboratory-confirmed influenza detections are provided by all 10 provincial laboratories, as well as six hospital laboratoriesFootnote 1 in Ontario. Laboratory-confirmed influenza detections in the Territories are provided by provincial or hospital laboratories in British Columbia, Alberta and Ontario. During the 2019-2020 season a total of 55,379 influenza detections were reported.

The national influenza season started in mid-November (week 47); the start of the influenza season begins when the percentage of tests positive for influenza crosses above 5%. Influenza activity remained at peak levels (above 25% positive detections) between the end of December and February (weeks 52 to 9) with the highest percentage of tests positive for influenza, 30%, being reported at the end of January (week 5).

The influenza season ended abruptly at the end of March (week 13) when public health measures were implemented to reduce the impact of the COVID-19 pandemic in Canada (Figure 1). The end of the influenza season is marked when the percentage of tests positive for influenza crosses below 5%. In 2019-2020, the end of the influenza season occurred eight weeks earlier than the average end of season based on the previous 5 seasons. A similar abrupt decline in seasonal influenza activity during this period was observed in other countries across the Northern Hemisphere.

The sharp decline in influenza detections at the end of March 2020 was not due to a decrease in influenza testing, which continued at above-average levels throughout the spring and summer 2020 (as shown in Figure 1). Rather, the abrupt end to the influenza season at the end of March 2020 corresponds with the implementation of stringent and coordinated public health measures across the country to limit the spread of COVID-19, which included widespread public health recommendations for hand washing, mandated mask wearing, social distancing, provincial school closures and stay-at-home orders.

Figure 1: The percentage of tests positive (left) and number of influenza tests (right) as compared to previous seasons by week, Canada, season 2019-2020

figure 1

The shaded area represents the maximum and minimum percentage of tests positive (a) or number of influenza tests (b) reported by week from seasons 2014-2015 to 2018-2019. Changes in laboratory testing practices as a result of the public health response to the COVID-19 pandemic may affect the comparability of data to previous weeks during the 2019-2020 season and to previous seasons. During the 2019-2020 season one new laboratory reported compared to previous seasons, but the contribution of this data did not affect national trends.

Text description
a) Percentage of tests positive for influenza, 2019-20 compared to previous seasons
Surveillance Week  Percentage of tests positive, 2019-20 Maximum Percentage of Tests Positive Minimum Percentage of Tests Positive Average  Percentage of Tests Positive
35 1.26% 1.87% 0.11% 0.73%
36 1.09% 2.28% 0.30% 1.14%
37 1.03% 1.78% 0.40% 0.98%
38 0.95% 2.35% 0.55% 1.37%
39 0.98% 2.95% 0.67% 1.85%
40 1.23% 2.33% 1.08% 1.79%
41 1.54% 3.02% 1.32% 1.76%
42 1.87% 3.40% 0.87% 2.24%
43 1.94% 5.32% 0.84% 3.01%
44 2.17% 8.55% 1.20% 4.01%
45 2.86% 10.10% 1.39% 4.99%
46 4.06% 14.11% 1.51% 6.45%
47 4.98% 15.36% 1.44% 8.25%
48 8.05% 18.20% 0.84% 11.12%
49 9.40% 19.71% 1.64% 13.73%
50 15.64% 27.02% 2.36% 17.06%
51 21.06% 29.09% 3.30% 19.92%
52 27.77% 34.54% 4.28% 23.82%
1 26.08% 31.66% 5.85% 22.87%
2 25.15% 29.10% 7.06% 22.58%
3 26.48% 30.07% 12.24% 23.06%
4 27.90% 29.45% 15.89% 23.17%
5 29.68% 30.62% 19.60% 23.94%
6 29.68% 32.39% 17.89% 24.07%
7 28.33% 32.51% 16.28% 24.40%
8 27.92% 32.87% 17.45% 24.58%
9 25.51% 34.28% 16.80% 24.41%
10 20.16% 35.99% 16.05% 23.83%
11 14.05% 31.41% 16.19% 21.41%
12 7.35% 30.03% 15.03% 20.10%
13 2.48% 28.25% 14.50% 19.56%
14 0.76% 23.16% 12.66% 17.86%
15 0.25% 20.73% 11.95% 16.27%
16 0.09% 18.52% 11.64% 14.48%
17 0.12% 17.30% 9.76% 12.83%
18 0.11% 13.02% 7.88% 10.26%
19 0.09% 11.95% 4.96% 8.98%
20 0.14% 9.13% 3.19% 7.22%
21 0.11% 7.45% 2.97% 5.60%
22 0.09% 4.96% 2.19% 3.86%
23 0.08% 4.39% 0.87% 2.86%
24 0.04% 4.36% 0.81% 2.25%
25 0.06% 3.95% 0.63% 1.88%
26 0.00% 3.08% 0.69% 1.81%
27 0.04% 2.83% 0.42% 1.48%
28 0.04% 1.84% 0.41% 0.91%
29 0.06% 1.55% 0.47% 1.09%
30 0.03% 1.46% 0.46% 0.90%
31 0.02% 1.93% 0.58% 1.11%
32 0.00% 1.19% 0.52% 0.92%
33 0.12% 1.69% 0.40% 0.85%
34 0.02% 1.57% 0.42% 0.92%
b) Number of influenza tests, 2019-20 compared to previous seasons
Surveillance Week  Number of Tests, 2019-20 Maximum Number of Tests Minimum Number of Tests Average  Number of Tests
35 1979 1862 1311 1650
36 2208 1880 1323 1607
37 2631 2235 1778 2036
38 3039 2567 1987 2395
39 3356 2996 2365 2759
40 4078 3384 2443 2945
41 4339 3510 2673 3020
42 4649 4020 2648 3301
43 4996 4470 3084 3635
44 4966 4703 2994 3830
45 5912 5665 3117 4227
46 5589 5449 3176 4359
47 6541 6386 3587 4713
48 7019 7416 3569 5371
49 8108 8559 3836 6031
50 8229 9464 4017 6940
51 10479 11142 3487 8491
52 11305 11338 4272 8759
1 14932 14886 5371 12076
2 15580 16104 5315 12830
3 13750 15001 5270 11434
4 15414 14146 5873 10647
5 16595 14319 6739 10428
6 16121 14687 8324 10382
7 14443 14351 8074 10122
8 13447 14024 7606 10348
9 14520 13316 7507 10244
10 17681 12933 7005 9764
11 23784 12714 6435 9175
12 23640 10431 5976 8238
13 22112 9989 6063 7699
14 22967 8830 4773 7046
15 16699 7836 5090 6527
16 16783 6826 5000 5890
17 16403 6603 4440 5305
18 11771 5640 4143 4780
19 12825 5480 3680 4311
20 12010 5097 3046 3862
21 9992 4001 2577 3197
22 10122 3790 2424 2944
23 8834 3257 1969 2591
24 8248 3120 2034 2449
25 6291 2659 1731 2148
26 6770 2600 1573 1988
27 5700 2163 1554 1833
28 5551 2223 1451 1857
29 6667 2256 1436 1796
30 5878 1950 1463 1664
31 5858 2022 1386 1671
32 5458 1928 1269 1574
33 5187 2089 1251 1671
34 5027 2098 1374 1698

Geographic spread of influenza/influenza-like illness (ILI) activity

All provinces and territories reported activity level data for each week of the 2019-2020 influenza season. Like in previous seasons, flu levels peaked first in Western Canada (mid-December), followed by Central Canada (early January), and lastly in Eastern Canada (early February) (Figure 2).

Figure 2: Number of regions reporting localized or widespread influenza activity by region and week, Canada, season 2019-2020

figure 2

Note: Localized or widespread activity was not reported by any of the territories.

Text description
Surveillance Week Overall Western Central East
Localized Widespread Localized Widespread Localized Widespread Localized Widespread
35 0 0 0 0 0 0 0 0
36 0 0 0 0 0 0 0 0
37 0 0 0 0 0 0 0 0
38 1 0 1 0 0 0 0 0
39 1 0 0 0 0 0 0 0
40 3 0 2 0 0 0 0 0
41 2 0 2 0 0 0 0 0
42 1 0 1 0 0 0 0 0
43 0 0 0 0 0 0 0 0
44 0 0 0 0 0 0 0 0
45 3 0 1 0 1 0 1 0
46 4 0 2 0 2 0 0 0
47 4 0 2 0 2 0 0 0
48 7 0 4 0 3 0 0 0
49 10 0 5 0 5 0 0 0
50 11 0 5 0 5 0 1 0
51 21 0 8 0 11 0 2 0
52 21 1 10 1 11 0 0 0
1 22 1 9 1 12 0 1 0
2 21 5 6 2 12 3 2 0
3 22 3 5 2 14 1 2 0
4 29 1 10 0 13 1 6 0
5 21 1 6 1 8 0 6 0
6 29 1 8 0 12 1 9 0
7 29 1 8 0 11 1 10 0
8 25 1 4 1 10 0 11 0
9 29 2 6 2 12 0 11 0
10 24 2 6 1 8 1 10 0
11 24 2 7 2 9 0 8 0
12 22 0 7 0 9 0 6 0
13 13 0 3 0 6 0 4 0
14 8 0 2 0 6 0 0 0
15 2 0 0 0 2 0 0 0
16 2 0 0 0 2 0 0 0
17 0 0 0 0 0 0 0 0
18 0 0 0 0 0 0 0 0
19 1 0 0 0 1 0 0 0
20 0 0 0 0 0 0 0 0
21 0 0 0 0 0 0 0 0
22 0 0 0 0 0 0 0 0
23 0 0 0 0 0 0 0 0
24 0 0 0 0 0 0 0 0
25 0 0 0 0 0 0 0 0
26 0 0 0 0 0 0 0 0
27 0 0 0 0 0 0 0 0
28 0 0 0 0 0 0 0 0
29 0 0 0 0 0 0 0 0
30 0 0 0 0 0 0 0 0
31 0 0 0 0 0 0 0 0
32 0 0 0 0 0 0 0 0
33 0 0 0 0 0 0 0 0
34 0 0 0 0 0 0 0 0

Influenza types and subtypes observed during the 2019-2020 influenza season

During the 2019-2020 season, all seasonal influenza types and subtypes circulated (Figure 3). Among the 55,379 laboratory detections of influenza reported, 95% were reported between end of August and early March (weeks 35 to 11).

Figure 3: Number of positive influenza tests and percentage of positive tests by type, subtype and week, Canada, season 2019-2020

figure 3

The shaded area indicates weeks where the positivity rate was at least 5% and a minimum of 15 positive tests were observed, signaling the period of seasonal influenza activity.

Text description
Surveillance Week A(Unsubtyped) A(H3N2) A(H1N1) Influenza B Percent Positive A  Percent Positive B
35 10 16 0 2 1.3 0.1
36 11 13 2 2 1.1 0.1
37 5 17 2 5 0.9 0.2
38 11 15 3 6 1.0 0.2
39 11 21 2 3 1.0 0.1
40 34 9 1 2 1.2 0.1
41 34 18 0 5 1.4 0.1
42 54 12 1 14 1.6 0.3
43 44 13 7 17 1.6 0.3
44 43 23 16 17 1.8 0.3
45 57 57 20 39 2.2 0.7
46 82 43 23 77 2.7 1.4
47 118 49 33 124 3.1 1.9
48 225 67 42 223 4.9 3.2
49 281 79 41 336 5.3 4.1
50 463 100 73 654 7.7 8.0
51 794 149 169 1094 10.6 10.4
52 1223 267 197 1439 15.0 12.7
1 1620 261 431 1533 15.8 10.3
2 1690 165 493 1463 15.8 9.4
3 1575 139 417 1418 16.2 10.3
4 1727 133 370 1952 15.2 12.7
5 1983 97 440 2269 16.0 13.7
6 1970 75 344 2265 15.6 14.1
7 1741 76 321 1851 15.5 12.8
8 1768 74 255 1559 16.3 11.6
9 1928 58 303 1287 16.7 8.9
10 1772 81 399 1152 13.6 6.5
11 1552 70 354 1015 9.8 4.3
12 832 38 154 595 4.8 2.5
13 185 19 39 269 1.3 1.2
14 48 5 11 97 0.3 0.4
15 14 1 7 19 0.1 0.1
16 1 0 3 11 0.0 0.1
17 5 1 0 14 0.0 0.1
18 4 0 0 9 0.0 0.1
19 0 0 0 12 0.0 0.1
20 6 0 0 11 0.1 0.1
21 1 0 1 9 0.0 0.1
22 5 0 0 4 0.1 0.0
23 2 0 3 2 0.1 0.0
24 1 0 0 2 0.0 0.0
25 3 0 0 1 0.1 0.0
26 0 0 0 0 0.0 0.0
27 1 0 1 0 0.0 0.0
28 1 0 0 1 0.0 0.0
29 1 0 0 3 0.0 0.0
30 0 0 0 2 0.0 0.0
31 0 0 0 1 0.0 0.0
32 0 0 0 0 0.0 0.0
33 2 0 1 3 0.1 0.1
34 0 0 0 1 0.0 0.0

Detailed information on age and influenza type/subtype was received for 42,541 laboratory-confirmed influenza cases; 24,347 influenza A and 18,194 influenza B. Among all influenza detections, the proportion of influenza A and B varied by age group. Similarly, among influenza A detections where subtype was identified (5,797), subtype distribution varied by age group.

Figure 4: Proportion of positive influenza specimens by age group and type/subtype reported through case-based laboratory reporting, Canada, season 2019-2020

figure 4

Text description
a) Proportion of influenza A and B by age-group
Age Group Proportion of Influenza A Proportion of Influenza B Total Number Influenza Detections
0 to 4 48.4% 51.6% 7848
5 to 19 31.4% 68.6% 8737
20 to 44 48.3% 51.7% 10811
45 to 64 81.3% 18.7% 6194
65+ 84.3% 15.7% 8951
b) Proportion of subtyped influenza A(H1N1) and A(H3N2) by age-group 
Age Group Proportion of A(H1N1) Proportion of A(H3N2) Total Number of Subtyped  Influenza Detections
0 to 4 67.4% 32.6% 654
5 to 19 53.3% 46.7% 559
20 to 44 74.4% 25.6% 1292
45 to 64 76.4% 23.6% 1288
65+ 52.7% 47.3% 2004

Syndromic / influenza-like illness (ILI) surveillance

Healthcare practitioners sentinel syndromic surveillance

During the 2019-2020 season, an average of 89 healthcare practitioners/centres across the country participated each week in  influenza-like illness (ILI) surveillance for the FluWatch program (Figure 5). On a weekly basis, these sentinel healthcare practitioners report the proportion of patients in their practice who had ILI based on the FluWatch definition:

Sudden onset of flu symptoms with fever and cough and with one or more of the following: sore throat, joint pain, muscle aches, or fatigue which is likely due to the flu.

Beginning in mid-March (week 11), lower than usual percent of visits for ILI were reported to the FluWatch program through the spring and summer months, due to changes in healthcare seeking behavior of individuals, the implementation of non-pharmaceutical public health measures to reduce COVID-19, and a decreasing number of sentinel healthcare practitioners reporting to FluWatch. From weeks 35 to 10, an average of 9,751 patients were seen by an average of 98 sentinels; from weeks 11 onwards, an average of 6,268 patients were seen by an average of 76 sentinels. Although a decrease in reporting is expected during the summer months, the decrease was greater this season compared to the previous season. In the 2018-2019 season, from weeks 35 to 10, an average of 9,164 patients were seen by an average of 113 sentinels; from week 11 onwards, average of 7,919 patients were seen from an average of 97 sentinels.

Figure 5: Percentage of visits for ILI reported by sentinels by week, Canada, season 2019-2020

figure 5

The shaded area represents the maximum and minimum percentage of visits for ILI reported by week from seasons 2013-2014 to 2018-2019

Text description
Surveillance Week 2019-2020 Average  Min Max
35 0.6% 0.6% 0.4% 0.9%
36 0.4% 0.6% 0.4% 0.9%
37 0.7% 0.7% 0.5% 1.0%
38 1.1% 0.7% 0.6% 1.0%
39 0.8% 0.9% 0.5% 1.2%
40 1.0% 1.2% 0.8% 1.7%
41 0.9% 1.7% 0.8% 2.8%
42 1.1% 1.6% 1.2% 2.1%
43 0.7% 1.2% 0.8% 1.7%
44 0.9% 1.2% 0.7% 1.7%
45 0.7% 1.2% 0.9% 1.5%
46 1.1% 1.4% 1.2% 1.8%
47 1.2% 1.6% 1.1% 2.2%
48 0.9% 1.5% 1.1% 2.2%
49 1.0% 1.7% 1.0% 2.8%
50 1.4% 1.5% 1.1% 1.7%
51 1.1% 1.9% 1.4% 2.7%
52 2.5% 2.0% 1.0% 3.1%
1 2.9% 3.4% 1.9% 5.4%
2 1.5% 3.4% 1.8% 5.7%
3 1.8% 2.3% 1.3% 3.7%
4 1.4% 2.0% 1.1% 2.9%
5 1.5% 2.1% 1.4% 3.1%
6 1.7% 2.4% 1.4% 4.0%
7 1.3% 2.4% 0.9% 3.5%
8 1.4% 2.3% 0.8% 3.4%
9 1.3% 2.3% 0.9% 3.1%
10 1.4% 2.0% 1.0% 2.8%
11 1.7% 1.9% 1.1% 2.8%
12 0.9% 1.6% 0.6% 2.6%
13 0.9% 1.6% 1.1% 2.6%
14 0.7% 1.7% 1.1% 3.0%
15 1.0% 1.3% 0.9% 1.9%
16 0.6% 1.2% 0.8% 1.7%
17 0.5% 1.2% 0.7% 1.7%
18 0.5% 1.3% 0.5% 2.0%
19 0.3% 0.9% 0.6% 1.3%
20 0.5% 1.1% 0.6% 1.5%
21 0.3% 0.9% 0.5% 1.3%
22 0.4% 0.7% 0.3% 1.0%
23 0.2% 0.8% 0.6% 1.0%
24 0.2% 0.7% 0.6% 1.0%
25 0.2% 0.6% 0.4% 0.8%
26 0.1% 0.8% 0.5% 1.4%
27 0.2% 0.6% 0.5% 0.7%
28 0.3% 0.7% 0.5% 1.3%
29 0.1% 0.9% 0.6% 1.7%
30 0.2% 0.6% 0.2% 0.9%
31 0.3% 0.4% 0.2% 0.6%
32 0.4% 0.8% 0.3% 1.2%
33 0.2% 0.7% 0.4% 1.3%
34 0.2% 0.7% 0.4% 1.5%

FluWatchers

FluWatchers are volunteers across Canada who report whether they have had symptoms of ILI in the preceding week, via a weekly online questionnaire. FluWatchers surveillance for the 2019-2020 season started in October (week 40) and due to the COVID-19 pandemic, continued to the end of the season in August (week 34) instead of ceasing in week 18, as was done in the previous three seasons.

Between weeks 40 and 13 (September 29 to October 5 and March 22 to March 28), an average of 3,139 participants reported each week. The average number of weekly participants increased to 10,280 between weeks 14 and 34, due to FluWatchers spring recruitment activities in response to the COVID-19 pandemic. Overall, a total of 16,681 participants reported at least once this season, resulting in 297,520 completed questionnaires.

The percentage of FluWatchers reporting ILI, as defined by fever and cough, peaked at the start of January (week 1) at 4.3% (Figure 6). Peak ILI activity within the FluWatchers program coincided with laboratory influenza activity which remained at peak levels (above 25% positive detections) between weeks 52 to 9. A downward trend of ILI among FluWatchers was observed starting in week 11 onwards, despite the influx of new participants.

Non-pharmaceutical public health measures were widely implemented across Canada during mid-March (week 11), after which, reports of cough and fever among FluWatchers markedly decreased and remained at low levels (<0.30%) through the spring and summer months. This trend was consistent with other influenza indicators.

Figure 6: Percentage of participants reporting fever and cough by week, Canada, season 2019-2020

figure 6

FluWatchers surveillance is active from weeks 40 to 18 during a typical season. Historical data is unavailable between weeks 19 and 34.

Text description
Surveillance Week 2019-2020 Average  Min Max
35 N/A N/A N/A N/A
36 N/A N/A N/A N/A
37 N/A N/A N/A N/A
38 N/A N/A N/A N/A
39 N/A N/A N/A N/A
40 2.18% 2.68% 2.18% 2.71%
41 1.81% 2.31% 1.81% 2.57%
42 1.71% 1.83% 1.61% 2.03%
43 2.18% 1.76% 1.49% 2.18%
44 1.63% 1.55% 1.39% 1.78%
45 1.42% 1.97% 1.42% 2.32%
46 1.22% 2.04% 1.22% 2.15%
47 1.50% 2.07% 1.44% 2.39%
48 1.67% 2.69% 1.67% 3.35%
49 2.17% 2.69% 1.97% 3.16%
50 2.12% 3.17% 2.12% 3.79%
51 2.56% 3.39% 2.53% 3.95%
52 4.15% 3.93% 2.81% 5.38%
1 4.26% 3.70% 2.85% 4.76%
2 3.13% 2.88% 1.90% 3.93%
3 3.30% 3.24% 2.35% 4.84%
4 3.06% 3.14% 2.13% 4.23%
5 3.39% 3.12% 2.62% 3.59%
6 3.03% 3.61% 2.76% 4.28%
7 2.65% 3.36% 2.58% 3.79%
8 2.70% 3.22% 2.54% 3.65%
9 2.38% 2.96% 2.38% 3.53%
10 2.12% 2.73% 2.12% 3.11%
11 2.46% 2.33% 1.89% 2.63%
12 1.50% 2.60% 2.46% 2.82%
13 0.87% 2.48% 1.99% 3.06%
14 0.50% 2.13% 1.35% 2.58%
15 0.27% 1.78% 1.60% 1.93%
16 0.28% 2.00% 1.47% 2.44%
17 0.16% 1.73% 1.40% 2.31%
18 0.23% 1.50% 1.19% 2.09%
19 0.26% N/A N/A N/A
20 0.20% N/A N/A N/A
21 0.15% N/A N/A N/A
22 0.16% N/A N/A N/A
23 0.15% N/A N/A N/A
24 0.09% N/A N/A N/A
25 0.12% N/A N/A N/A
26 0.06% N/A N/A N/A
27 0.09% N/A N/A N/A
28 0.11% N/A N/A N/A
29 0.12% N/A N/A N/A
30 0.10% N/A N/A N/A
31 0.11% N/A N/A N/A
32 0.20% N/A N/A N/A
33 0.16% N/A N/A N/A
34 0.23% N/A N/A N/A

Influenza outbreak surveillance

Influenza and ILI outbreak activity reports were provided by all provinces and territories each week this season, in the following settings: long term care facilities (LTCF), acute care facilities, school and/or daycares, and settings categorized as “other” (i.e. retirement homes, correctional facilities, personal care homes, work camps and workplaces). Settings under surveillance vary by province and territory.

A total of 978 laboratory-confirmed influenza outbreaks were reported (Figure 7).

In addition to the laboratory-confirmed influenza outbreaks, a total of 175 outbreaks of ILI were reported; 172 occurred in schools and/or daycares and three occurred in settings categorized as “other”.

Figure 7: Number of influenza outbreaks by type, subtype and week, Canada, season 2019-2020

figure 7

Text description
Surveillance Week H1N1 H3N2 AUnS B All Outbreaks
35 0 0 0 0 0
36 0 0 0 0 0
37 0 0 0 0 0
38 0 0 1 0 2
39 0 1 0 0 1
40 0 1 1 0 2
41 0 2 0 0 3
42 0 1 0 0 1
43 0 0 0 1 1
44 0 0 1 0 1
45 1 4 0 0 6
46 0 2 3 0 5
47 0 0 1 3 4
48 1 5 3 2 11
49 0 4 8 1 16
50 2 6 8 2 20
51 5 14 10 3 32
52 8 25 30 3 67
1 31 25 63 10 143
2 34 17 64 16 141
3 15 8 34 9 75
4 16 15 34 9 107
5 8 1 26 2 86
6 6 5 31 12 80
7 12 2 21 10 58
8 6 2 26 8 63
9 12 2 23 4 48
10 1 1 17 3 39
11 4 4 34 5 61
12 7 1 10 7 25
13 3 2 8 5 18
14 3 0 3 4 10
15 0 0 2 1 3
16 0 0 0 2 2
17 0 0 0 0 0
18 0 0 0 0 1
19 0 0 0 1 1
20 0 0 0 0 0
21 0 0 0 0 0
22 0 0 0 0 0
23 0 0 0 0 0
24 0 0 0 1 1
25 0 0 0 0 0
26 0 0 0 0 0
27 0 0 0 0 0
28 0 0 0 0 0
29 0 0 0 0 0
30 0 0 0 0 0
31 0 0 0 0 0
32 0 0 0 0 0
33 0 0 0 0 0
34 0 0 0 0 0

Severe outcomes influenza surveillance

Data on severe outcomes associated with influenza in Canada are reported by participating provincial and territorial ministries of health (PT-SOS) as well as two sentinel hospital networks: the Immunization Monitoring Program Active (IMPACT) network and the Canadian Immunization Research Network's Serious Outcome Surveillance Network (CIRN-SOS).

PT-SOS comprises of both pediatric and adult influenza hospitalizations from acute care hospitals in nine province and territoriesFootnote 2. CIRN-SOS reports adult (16 years of age and older) influenza hospitalizations and deaths while IMPACT reports pediatric (16 years of age and under) influenza hospitalizations. CIRN-SOS network consist of nine hospitals across four provincesFootnote 3 and the IMPACT network consists of 12 pediatric hospitals across eight provincesFootnote 4.

Hospitalizations

During the 2019-2020 influenza season, 2,493 influenza-associated hospitalizations were reported by participating provinces and territories, which corresponds to an annual seasonal hospitalization incidence of 31 hospitalizations per 100,000 population in the 2019-2020 season (Table 1a).

Table 1a: Estimated annual seasonal incidence of influenza hospitalizations (per 100,000 population) by age group, Canada, seasons 2014-2015 to 2019-2020
Age groups (years) Influenza season (predominant influenza A subtype)
2014-15
(H3N2)
2015-16
(H1N1)
2016-17
(H3N2)
2017-18
(H3N2)
2018-19
(H1N1)
2019-20
(H1N1)
0 to 4 46 96 42 69 97 75
 5 to 19 16 16 10 17 22 16
20 to 44 13 16 6 12 14 14
45 to 64 16 37 22 41 40 23
≥65 207 68 143 268 132 79
Overall 45 34 34 64 45 30
Table 1b: Estimated annual seasonal incidence of influenza hospitalizations (per 100,000 population) by age group, type and subtype, Canada, seasons 2014-2015 to 2019-2020
Age groups (years) Influenza type and subtype
H1N1 H3N2 A B Overall
0 to 4 17 9 41 34 75
 5 to 19 2 2 5 11 16
20 to 44 3 2 8 6 14
45 to 64 7 4 18 4 23
≥65 16 27 64 15 79
Overall 7 7 21 10 30

Influenza-associated hospitalizations are reported by N.L., P.E.I, N.S., N.B., Man., Alta., Y.T. and N.W.T. Data provided by Saskatchewan is not included in these rates as only hospitalizations that require intensive medical care are reported by Sask. The annual seasonal hospitalization rate for a given season is calculated using the population by age group in participating province and territories.

Bolded values indicate the age group with the highest rate during the season.

Figure 8: Number of influenza-associated hospitalizations reported by CIRN-SOS (left) and IMPACT (right) networks by week of admission, Canada, season 2019-2020

figure 8

Text description
CIRN
Surveillance Week Total Influenza
35 N/A
36 N/A
37 N/A
38 N/A
39 N/A
40 N/A
41 N/A
42 0
43 0
44 0
45 0
46 2
47 4
48 8
49 11
50 13
51 31
52 75
1 102
2 72
3 61
4 46
5 51
6 72
7 49
8 57
9 60
10 35
11 19
12 14
13 11
14 3
15 2
16 0
17 2
18 2
19 1
20 0
21 0
22 0
23 0
24 0
25 N/A
26 N/A
27 N/A
28 N/A
29 N/A
30 N/A
31 N/A
32 N/A
33 N/A
34 N/A
IMPACT
Surveillance Week 2019-2020 Average  Min Max
35 0 0.4 0 1
36 2 0.2 0 1
37 0 0.6 0 2
38 0 0.8 0 2
39 1 1.2 0 3
40 0 0.6 0 2
41 2 1.4 0 3
42 2 2.8 0 7
43 1 5 2 11
44 3 6.4 1 21
45 4 9.8 2 36
46 5 13 1 37
47 11 12 1 35
48 22 18.6 2 46
49 27 21 3 41
50 39 30 4 54
51 59 40.6 5 82
52 108 55 14 94
1 112 53 21 90
2 90 40.2 12 65
3 79 44.6 27 62
4 89 51.2 34 87
5 118 47 25 67
6 112 49.4 15 79
7 65 57.8 17 118
8 79 61.6 25 134
9 60 56.6 12 151
10 49 55 17 135
11 44 50.6 16 118
12 23 39.2 13 87
13 4 32.2 15 66
14 2 28.6 12 56
15 0 25 11 56
16 0 23 11 41
17 0 19.2 9 37
18 1 16.2 8 28
19 0 11 5 19
20 1 10 0 18
21 0 6.4 4 9
22 0 6 1 9
23 0 3.2 1 7
24 1 2.8 1 6
25 0 1.8 0 5
26 0 1.4 0 3
27 0 1 0 2
28 0 1 0 2
29 1 0.6 0 3
30 0 0.6 0 1
31 0 0 0 0
32 0 0 0 0
33 0 0.4 0 2
34 0 0.6 0 2

Figure 9: Number and percentage of hospitalizations reported by CIRN-SOS (left) and IMPACT (right) network by age group and type, Canada, season 2019-2020

figure 9

Proportions may not add correctly due to rounding.

Text description
CIRN
Age Group (Years) Influenza A Influenza B Influenza A/B Co-Infection All Influenza % by Age Group
16 to 34 33 46 0 79 10%
35 to 49 50 12 1 53 8%
50 to 64 121 24 1 146 18%
65 to 79 223 41 1 265 33%
80 + 196 47 0 243 31%
IMPACT
Age Group (Years) Influenza A Influenza B Influenza A/B Co-Infection All Influenza % by Age Group
< 2 264 188 5 457 38%
2 to 4 180 154 2 336 28%
5 to 9 112 155 2 269 22%
10 to 16 69 85 0 154 13%

ICU admissions and deaths

A total of 306 ICU admissions and 120 deaths were reported this season by participating province and territories.

The CIRN-SOS and IMPACT data offer additional surveillance indicators on the severity of influenza in hospitalized patients.

CIRN-SOS

IMPACT

Influenza strain characterizations

From September 1, 2019 to August 31, 2020, the National Microbiology Laboratory (NML) characterized 2,021 influenza viruses received from Canadian laboratories: 760 A(H1N1), 368 A(H3N2), 893 influenza B.
Antigenic characterization is established by hemagglutination inhibition (HI) assay using egg-passaged vaccine reference viruses for A(H1N1) and A(H3N2), and cell-passaged vaccine reference virus for influenza B. Over recent years, circulating strains of A(H3N2) have evolved, and are increasingly difficult to characterize by HI assay. Genetic characterization is established by sequencing the hemagglutinin gene of the influenza viruses to compare their genetic properties.

Influenza A(H3N2)

The influenza A(H3N2) component of the 2019-2020 Northern Hemisphere influenza vaccine was an A/Kansas/14/2017 -like virus which belongs to the genetic group 3C.3a.

Antigenic characterization

Among the 109 influenza A(H3N2) viruses antigenically characterized during the 2019-2020 season, the majority (n=86, 79%) showed reduced titer by HI assay to A Kansas/14/2017 using antiserum raised against egg-propagated A Kansas/14/2017. Twenty-three viruses were characterized as A Kansas/14/2017-like (Figure 12a).

Genetic characterization

Nearly all (n=353, 96%) of the 368 A(H3N2) viruses genetically characterized during the 2019-2020 season belonged to genetic group 3C.2a1b based on sequence analysis of the HA gene. Fifteen viruses belonged to the genetic group 3C.3a (Figure 13).

Group 3C.2a1b viruses analysed represent:

Table 2: Genetic and antigenic characterization among characterized A(H3N2) viruses, Canada, season 2019-2020 (n=648)
Genetic clade Genetic characterization only Antigenic characterization: Total A(H3N2)
Similar to
A Kansas/14/2017-like
Reduced titer to
A Kansas/14/2017-like
Subclade 3C.2a1 259 9 85 353
Clade 3C.3a 0 14 1 15
Total 259 23 86 368

Influenza A(H1N1)

The influenza A(H1N1) component of the 2019-2020 Northern Hemisphere influenza vaccine was an A/Brisbane/02/2018-like virus.

Among the 760 A(H1N1) viruses characterized during the 2019-2020 season, 50% (n=382) were antigenically similar to A/Brisbane/02/2018 by HI testing using antiserum raised against egg-propagated A/Brisbane/02/2018 (Figure 12b).

Influenza B

Antigenic characterization

Among the 184 influenza B viruses antigenically characterized during the 2019-2020 season, the vast majority (181) belonged to the B/Victoria lineage. Three viruses were antigenically characterized as similar to B/Phuket/3073/2013 (B/Yamagata lineage).

The majority (90%, 162) of B/Victoria lineage viruses showed reduced titer by HI assay to B/Colorado/06/2017 using antiserum raised against cell culture-propagated B/Colorado/06/2017 (Figure 12c).

Sequence analysis of B/Victoria lineage viruses with reduced titre to B/Colorado/06/2017 showed that 100% (n=162) had a three amino acid deletion (162-164) in the HA gene and belong to the genetic subclade V1A.3.

Genetic characterization

During the 2019-2020 season, 100% (709) of influenza B/Victoria viruses genetically characterized had a three amino acid deletion (162 to 164) in the HA gene and belong to the genetic subclade V1A.3. (Figure 13b). Viruses in this genetic subclade are antigenically distinct from the vaccine strain B/Colorado/06/2017, which belongs to genetic subclade V1A.1 that has a two amino acid deletion (162 to 163) in the HA gene. No circulating viruses were identified during the 2019-2020 season which belonged to the same subclade as the vaccine virus (V1A.1).

Figure 10: Distribution of antigenic phenotypes among characterized influenza viruses, Canada, season 2019-2020

figure 10

Text description
A) Antigenic phenotypes among influenza A(H3N2) viruses
Number of viruses characterized:  109
Antigenic phenotype of A(H3N2) virus Number of viruses Percentage
A/Kansas/14/2017-like 23 21%
Reduced titer to A/Kansas/14/2017 86 79%
B) Antigenic phenotypes among influenza A(H1N1) viruses
Number of viruses characterized:  760
Antigenic phenotype of A(H1N1) virus Number of viruses Percentage
A/Brisbane/02/2018-like 378 50%
Reduced titer to A/Brisbane/02/2018 382 50%
C) Antigenic phenotypes among influenza B viruses
Number of viruses characterized:  184
Antigenic phenotype of influenza B virus Number of viruses Percentage
B/Colorado/06/2017-like 19 10%
Reduced titer to B/Colorado/06/2017 162 88%
B/Phuket/3073/2013-like 3 2%

Figure 11: Distribution of genetic clades among characterized influenza viruses, Canada, season 2019-2020

figure 11

Text description
A) Distribution of genetic clades among characterized A(H3N2) viruses 
Number of viruses sequenced:  368
Genetic Clade of A(H3N2) virus Number of viruses Percentage
Subclade 3C.2a1b 353 96%
Clade 3C.3a 15 4%
B) Distribution of genetic clades among characterized influenza B/Victoria viruses
Number of viruses sequenced:  871
Genetic Clade of influenza B/Victoria virus Number of viruses Percentage
Subclade V1A.3 (3Del) 871 100%
Subclade V1A.1 (2Del) 0 0%

Antiviral resistance

The National Microbiology Laboratory (NML) also tests influenza viruses received from Canadian laboratories for antiviral resistance. From September 1, 2019 to August 31, 2020:

Vaccine monitoring

Vaccine monitoring refers to activities related to the monitoring of influenza vaccine coverage and effectiveness. The quadrivalent vaccines used in the 2019-2020 northern hemisphere influenza season contained:

The B/Colorado/06/2017-like virus was included in both the trivalent and quadrivalent vaccines.

Vaccine monitoring refers to activities related to the monitoring of influenza vaccine coverage and effectiveness.

Vaccine coverage

The Seasonal Influenza Immunization Coverage Survey is an annual telephone survey conducted between January and February that collects information from Canadians on whether they received the annual seasonal influenza vaccine that season. Vaccine coverage is measured as the percentage of people who received the influenza vaccine in a specific influenza season.

In the 2019-2020 influenza season, coverage was similar to the 2018-19 season, at:

Table 3: Influenza vaccine coverage among adults (n=3,026) by age group, gender and medical conditions, seasonal influenza vaccination coverage survey, Canada, January 2020 – February 2020
Age group (years) All Male Female
N Vaccine coverage % (95% CI) N Vaccine coverage % (95% CI) N Vaccine coverage % (95% CI)
All adults (≥18) 3023 41.8 (39.7-43.9) 1320 37.2 (34.1-40.2) 1691 46.1 (43.2-49.0)
18 to 64 Total 2234 34.1 (31.8-36.5) 1005 29.8 (26.5-33.1) 1218 38.4 (35.1-41.7)
18 to 64 with chronic diseases 668 43.6 (39.0-48.1) 268 38.3 (31.5-45.2) 397 47.9 (41.7-54.0)
18 to 64 without chronic diseases 1558 30.0 (27.3-32.7) 732 26.7 (22.9-30.5) 818 33.5 (29.6-37.3)
≥65 789 70.3 (66.7-73.8) 315 67.2 (61.5-72.9) 473 72.7 (68.3-77.1)
Totals by subgroups do not add up to 3026 because missing gender or chronic medical condition status information.

Vaccine effectiveness

The Canadian Sentinel Practitioner Surveillance Network (SPSN) provides estimates of the effectiveness of the seasonal influenza vaccine in preventing medically-attended illness due to laboratory-confirmed influenza among Canadians.

Based on data collected between November 1, 2019 and March 28, 2020, vaccine effectiveness was estimated to be 53% for any influenza, 43% for influenza A(H1N1), 50% for influenza A(H3N2), and 65% for influenza B. The SPSN mid-season estimates were published and are available in Eurosurveillance; the updated end-of-season estimates are available online on British Columbia's Centre for Disease Control website.

The Serious Outcomes Surveillance (SOS) Network of the Canadian Immunization Research Network (CIRN-SOS) provides estimates of the effectiveness of the seasonal influenza vaccine in preventing hospitalization for laboratory-confirmed influenza in adults.

Based on data collected between November 3, 2019 and February 15, 2020, among adult (16 years of age and older) hospitalized cases of influenza, vaccine effectiveness was estimated to be 29.6% for any influenza, 42.4% for influenza A(H1N1) and 19.6% for influenza B. Vaccine effectiveness estimates for H3N2 were not presented in the CIRN-SOS network interim vaccine effectiveness report.

More information on the CIRN-SOS Network including study methodology and available publications can be viewed on their webpage.

Table 4: Vaccine effectiveness estimates against primary care visits (SPSN - November 1, 2019, to March 28, 2020) and hospitalizations (CIRN-SOS - November 3, 2019 to February 15, 2020)
SPSN (primary care visits)Table 4 Footnote a CIRN-SOS (adult hospitalizations)
VE(%) (CI)Table 4 Footnote b N VE(%) (CI)Table 4 Footnote c N
All influenza 53 (45-60) 4633 29.6 (-0.1-50.4) 593
Influenza A Total 44 (32-54) 3587 33.4 (3.9-53.9) 536
Influenza A H1N1 43 (30-54) 3333 42.4 (-3.5-67.9) 348
Influenza A H3N2 50 (26-66) 2634 n/a n/a
Influenza B 65 (56-73) 3453 19.6 (-66.2-61.1) 331
Table 4 Footnote a

SPSN 2019-2020 estimates are published and available in on British Columbia's Centre for Disease Control website (end-of-season) and Eurosurveillance (interim). CI: confidence interval

Table 4 Return to footnote a referrer

Table 4 Footnote b

adjusted for age (0-8, 9-19, 20-49, 50-64, 65+ years), province, specimen collection interval and calendar time (natural cubic spline with 3 equally spaced knots)

Table 4 Return to footnote b referrer

Table 4 Footnote c

All ages, influenza A, A/H1N1, and influenza B adjusted VE estimates adjusted for age groups, admission from long term care facility, and pregnancy.

Table 4 Return to footnote c referrer

Notes

To learn more about the FluWatch program, see the Overview of influenza monitoring in Canada page. For more information on the flu, see our Flu (influenza) web page.

Thank you to our Fluwatch surveillance partners who participate in the influenza surveillance program!

Footnote 1

Children's Hospital of Eastern Ontario (CHEO), Ottawa; Mount Sinai Hospital, Toronto; Sick Kids Hospital, Toronto; St. Joseph's Health Care, London; St. Joseph's Health Care; Hamilton; Sunnybrook Health Sciences Centre, Toronto.

Return to footnote 1 referrer

Footnote 2

Influenza-associated hospitalizations are reported by N.L., P.E.I, N.S., N.B., Man., Alta., Y.T. and N.W.T. Sask. only reports  hospitalizations that require intensive medical care are reported by Sask.

Return to footnote 2 referrer

Footnote 3

B.C:Surrey Memorial Hospital; Ont: Mount Sinai Hospital, Hamilton Health Sceinces, Ottawa General, North York General, Health Sciences North; Que:CHUQ/CHUL, CHUS; NS: Dartmouth General, Queen Elizabeth II Health Sciences Centre

Return to footnote 3 referrer

Footnote 4

B.C: B.C. Children's Hospital; Alta: Alberta Children's Hospital, Stollery Children's Hospital; Sask: Royal University Hospital; Ont: CHEO, Sick Kids; Que: Le Centre Mère-Enfant de Québec City, CHU-Sainte-Justine, The Montreal Children's Hospital; NS: IWK Health Centre, Halifax; NL: Eastern Health Janeway Child Health and Rehabilitation Centre

Return to footnote 4 referrer

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