Influenza epidemiology in patients admitted to sentinel Australian hospitals in 2016: the Influenza Complications Alert Network (FluCAN)

During the period 1 April to 30 October 2016 (the 2016 influenza season), 1,952 patients were admitted with confirmed influenza to one of 17 FluCAN sentinel hospitals. Of these, 46% were elderly (≥65 years), 18% were children (<16 years), 5% were Aboriginal and Torres Strait Islander peoples, 3% were pregnant and 76% had chronic co-morbidities.

Page last updated: 08 March 2018

Allen C Cheng, Mark Holmes, Dominic E Dwyer, Louis B Irving, Tony Korman, Sanjaya Senanayake, Kristine Macartney, Christopher C Blyth, Simon Brown, Grant W Waterer, Louise Cooley, N Deborah Friedman, Peter Wark, Graham Simpson, John Upham, Simon Bowler, Stephen Brady, Tom Kotsimbos, Paul M Kelly


The Influenza Complications Alert Network (FluCAN) is a sentinel hospital-based surveillance program that operates at sites in all states and territories in Australia. This report summarises the epidemiology of hospitalisations with laboratory-confirmed influenza during the 2016 influenza season.

In this observational study, cases were defined as patients admitted to one of the sentinel hospitals with an acute respiratory illness with influenza confirmed by nucleic acid detection. Data are also collected on a frequency matched sample of influenza negative patients admitted with acute respiratory infection as a control group.

During the period 1 April to 30 October 2016 (the 2016 influenza season), there were 1,952 patients admitted with confirmed influenza to one of 17 FluCAN sentinel hospitals. Of these, 46% were elderly (≥65 years), 18% were children (<16 years), 5% were Aboriginal and Torres Strait Islander Peoples, 3% were pregnant and 76% had chronic co-morbidities. A small proportion were due to influenza B (7%). Estimated vaccine coverage was 73% in the elderly (≥65 years), 51% in non-elderly adults with medical comorbidities and 15% in children (<16 years) with medical comorbidities. The estimated vaccine effectiveness in the target population was 13% (95% confidence interval (CI): -5% to 27%).

There were a large number of hospital admissions detected with confirmed influenza in this national observational surveillance system in 2016 with case numbers similar to that reported in 2014 and 2015.


Influenza affects up to 5-10% of the population each year.1 Because infection with influenza virus is relatively widespread, the incidence of hospitalisation from influenza is of public health significance, although the risk of hospitalisation is low.2 In this report, we describe the epidemiology of hospitalisation with laboratory-confirmed influenza in the 2016 season in Australia.


The Influenza Complications Alert Network (FluCAN) is a national hospital-based sentinel surveillance system.3 Since 2011, the participating sites have been Canberra Hospital (ACT), Calvary Hospital (ACT), Westmead Hospital (NSW), John Hunter Hospital (NSW), Children’s Hospital at Westmead (NSW), Alice Springs Hospital (NT), Royal Adelaide Hospital (SA), Mater Hospital (QLD), Princess Alexandra Hospital (QLD), Cairns Base Hospital (QLD), Royal Hobart Hospital (TAS), The Alfred Hospital (VIC), Royal Melbourne Hospital (VIC), Monash Medical Centre (VIC), University Hospital Geelong (VIC), Royal Perth Hospital (WA), and Princess Margaret Hospital (WA). Ethical approval has been obtained at all participating sites and at Monash University. Hospital bed capacity statistics were obtained from each participating hospital, and national bed capacity was obtained from the last published Australian Institute of Health and Welfare report.4

An influenza case was defined as a patient admitted to hospital with influenza confirmed by nucleic acid testing (NAT). Surveillance is conducted from early April to end October (with follow up continuing to the end of November) each year. Admission or transfer to an intensive care unit (ICU) included patients managed in a high dependency unit (HDU). The onset date was defined as the date of admission except for patients where the date of the test was more than 7 days after admission, where the onset date was the date of the test. The presence of risk factors and comorbidities was ascertained from the patient’s medical record. Restricted functional capacity was defined as those who were not fully active and not able to carry out all activities without restriction prior to the acute illness.5

We examined factors associated with ICU admission using multivariable regression. Factors independently associated with ICU admission were determined using a logistic regression model with no variable selection process, as all factors were plausibly related to ICU admission.

Vaccine coverage was estimated from the proportion of vaccinated individuals in each age group, stratified by the presence of chronic comorbidities. Vaccine effectiveness was estimated from the odds ratio of vaccination in cases versus controls using the formula, with the odds ratio calculated from a conditional logistic regression, stratified by site and adjusted for age group, the presence of chronic comorbidities, pregnancy and Aboriginal or Torres Strait Islander ethnicity.


During the period 1 April to 30 October 2016 (the 2016 influenza season), there were 1,952 patients admitted with laboratory-confirmed influenza to one of 17 FluCAN sentinel hospitals. The peak weekly number of admission was in mid-August (week 35) (Figure 1). The majority of cases were due to influenza A (93%). The proportion due to influenza B was higher in the West Australian hospitals (46/180 26%; Princess Margaret Hospital 34/105 32%; Royal Perth Hospital 12/75 16%) compared to all other jurisdictions (5.0%).

Figure 1: Date of admission in patients hospitalized with confirmed influenza

Figure 1: This graph shows the number of cases at the sentinel hospitals by epidemiological week. It shows influenza activity rose from week 27 to a peak of 220 cases in week 35, before declining until the end of surveillance in week 43. The majority of c

Text version of the Figure (TXT 1 KB)

By week beginning on listed date; representing date of admission (or date of influenza diagnosis if acquired >7 days in hospital)

Of these 1,952 patients, 904 (46%) were >65 years of age, 359 (18%) were children (<16 years), 101 (5%) were Aboriginal and Torres Strait Islander peoples, and 1492 (76%) had chronic co-morbidities (table 1; table 2). There were 50 pregnant women which represented 21% of the 243 female patients aged 16-49, or 3% of the total. Of the 1,599 patients (82%) where influenza vaccination status was ascertained, 752 (47%) had been vaccinated.

Table 1: Demographic characteristics of hospitalized patients with confirmed influenza

Table 1: This table presents the characteristics of patients admitted to the sentinel hospitals, including age, sex, pregnancy status, Indigenous status and jurisdiction, with confirmed influenza, by influenza type and subtype
  Influenza type/subtype Total
  A/H1 A/H3 A/unknown B  
Number of cases 139 256 1422 135 1952
Age group          
<16 years 32 (23%) 1 (0%) 258 (18%) 60 (44%) 351 (18%)
16-49 years 44 (32%) 47 (18%) 279 (20%) 27 (20%) 397 (20%)
50-64 years 32 (23%) 40 (16%) 211 (15%) 17 (13%) 300 (15%)
65-79 years 25 (18%) 78 (31%) 337 (24%) 18 (13%) 458 (24%)
80+ years 6 (4%) 90 (35%) 337 (24%) 13 (7%) 446 (23%)
Female* 67 (48%) 144 (56%) 726 (51%) 54 (40%) 991 (51%)
Pregnant 5 (4%) 3 (1%) 42 (3.0%) 0 (0.0%) 50 (3%)
Aboriginal or Torres Strait Islander peoples 6 (4%) 9 (4%) 76 (5%) 10 (7%) 101 (5%)
ACT 22 (16%) 78 (31%) 152 (11%) 16 (12%) 268 (14%)
NSW 14 (10%) 14 (6%) 450 (32%) 24 (18%) 502 (26%)
NT 0 (0.0%) 0 (0.0%) 43 (3%) 3 (2%) 46 (2%)
QLD 7 (5.0%) 21 (8%) 125 (9%) 12 (9%) 165 (9%)
SA 0 (0.0%) 6 (2%) 165 (12%) 7 (5%) 178 (9%)
TAS 65 (47%) 31 (12%) 29 (2%) 4 (3%) 129 (7%)
VIC 14 (10%) 50 (20%) 397 (28%) 23 (17%) 484 (25%)
WA 17 (12%) 56 (22%) 61 (4%) 46 (34%) 180 (10%)
*Sex missing for 2 patients; reported as number and percentage of patients with type/subtype

Table 2: Risk factors, severity and outcomes in hospitalized adult patients with confirmed influenza

Table 2: this table presents risk factors, including pregnancy, medical co-morbidities, residence in nursing home and influenza vaccine status, in patients admitted to ICU.
  Not admitted to ICU Admitted to ICU Total
Number of cases 1738 214 1952
Pregnancy 43 (3%) 7 (3%) 50 (3%)
Medical comorbidities 1316 (76%) 176 (82%) 1492 (76%)
Chronic respiratory illness 515 (30%) 71 (33%) 586 (30%)
Chronic cardiac disease 567 (33%) 70 (33%) 637 (32%)
Diabetes 383 (22%) 46 (22%) 429 (22%)
Chronic liver disease 74 (4%) 15 (7.0%) 89 (5%)
Chronic neurological illness 280 (16%) 31 (15%) 311 (16%)
Chronic renal disease 219 (13%) 28 (13%) 247 (13%)
Immunocompromised 260 (15%) 33 (15%) 293 (15%)
Malignancy 187 (11%) 25 (12%) 212 (11%)
Obesity 198 (11%) 33 (15%) 231 (12%)
Nursing home resident 152 (9%) 4 (2%) 156 (8%)
Received influenza vaccine 693/1431 (48%) 59/168 (35%) 752/1599 (47%)
Influenza type/subtype      
A/H1 126 (7%) 13 (6%) 139 (7%)
A/H3 231 (13%) 25 (12%) 256 (13%)
A/unknown 1260 (73%) 162 (76%) 1422 (73%)
B 121 (7.0%) 14 (7%) 135 (7%)
In hospital mortality 40/1692 (2%) 25/207 (12%) 65/1899 (3%)

Incidence of hospital admissions with influenza

Overall, the peak incidence of admissions with confirmed influenza was 3.2 per 100 hospital beds (in epidemiological week 35), but varied from 0.54 per 100 hospital beds at Princess Alexandra Hospital (QLD) to a 9.7 per 100 hospital beds at Westmead Hospital (NSW).

Presentation and management

For 1,759 patients with laboratory-confirmed influenza where the duration of symptoms was known, the median duration of symptoms prior to admission was 2 days (interquartile range (IQR): 1, 4 days). Of all cases, 65 cases (3%) were diagnosed more than 7 days after admission and therefore were likely to be hospital-acquired. Radiological evidence of pneumonia was present in 363 patients (19%).

Of all cases, 214 patients were admitted to ICU, including 180 patients (9%) were initially admitted to ICU and a further 34 (2%) subsequently transferred to ICU after initial admission to a general ward. The elderly (>65 years) and residents of nursing homes were less likely to be admitted to intensive care. There were no statistically significant differences in the risk of admission to ICU by influenza type in patients admitted to hospital with influenza.


The mean length of hospital stay for all patients was 5.6 days. Admission to ICU was associated with a mean hospital length of stay of 11.1 days compared to those not admitted to ICU (4.9 days). Of the 1,899 patients where hospital mortality status was documented, 65 patients died (3%), which included 25 patients in ICU. Case fatality was higher in the elderly (51/864; 6%) than in non-elderly adults and children (14/1,035; 1%). Of the 65 deaths, 62 (95%) occurred in patients with comorbidities. The case fatality of influenza-associated pneumonia was 8% (29/359).

Vaccine coverage and effectiveness

Vaccination status was ascertained in 1,599 of 1,952 cases (82%) and 1,386 of 1,715 test negative control patients (81%). Estimated vaccine coverage was 73% (467/636) in the elderly (≥65 years), 51% (212/414) in non-elderly adults with medical comorbidities and 15% (18/116) in children (<16 years) with medical comorbidities. In the target population, the crude odds ratio of vaccination in cases versus controls was 0.87 (95% confidence interval (CI): 0.73 to 1.02) and the adjusted odds ratio of vaccination was 0.87 (95% CI: 0.73 to 1.05). The estimated vaccine effectiveness in the target population was therefore 13% (95% CI: -5%to 27%). In the elderly (>65 years), there was no evidence of vaccine effectiveness (estimated VE -19%, 95% CI: -52% to 8.0%)


In the 2016 season, we have documented more than 1,900 cases of influenza, which represents a similar number of admissions as 2014 (n=2,097) and 2015 (n=2,070). Based on the bed capacity of sentinel hospitals, this is likely to represent around 14,000 admissions with confirmed influenza nationally. However, as influenza testing is not performed on all patients with acute respiratory presentations, and influenza may also trigger delayed respiratory presentations (e.g. secondary bacterial pneumonia) and non-respiratory complications (e.g. acute myocardial infarction), this should be regarded as a minimum estimate.

The 2016 year was the first season in which the use of quadrivalent vaccine (containing two influenza A and two influenza B strains) was funded under the National Immunisation Program. However, in comparison with the 2015 season, where more than half of admissions were due to influenza B and both Victorian and Yamagata lineages circulated, the incremental benefit of the quadrivalent vaccine would be expected to be minimal in 2016 as influenza B activity was low. Influenza vaccine effectiveness was noted to be low in the target population in this season in comparison to previous years (and absent in the elderly). Further work is being performed to explore this issue further. Vaccine effectiveness in the elderly has generally been found to be lower than in younger age groups, but a study from the United States found influenza vaccine to be cost-effective in the elderly over four seasons.6

In recent seasons, there has been ongoing concern about mismatches between the A/H3N2 vaccine and circulating strains, due in part to antigenic change associated with egg adaptation as well as growing genetic diversity within circulating A/H3N2 strains, with North American data suggesting a higher vaccine effectiveness against 3C.3b than 3C.3a and 3C.2a clades.7, 8 Additionally, work has suggested that the effectiveness of influenza vaccines against A/H1N1pdm may be poorer in a middle aged cohort born before 1980, who were exposed to 163Q A/H1N1/USSR types.9

The peak incidence of confirmed influenza provides a measure of the impact of influenza. We chose to use acute hospital beds as a denominator because the number of admissions are not readily available in a timely manner, and bed numbers provide a “hard limit” of hospital capacity. The proportion of hospital beds occupied by patients with confirmed influenza can be estimated from the incidence and mean duration of stay – at Westmead Hospital in 2016, a peak weekly incidence of 9.7 per 100 beds roughly equates to 9% of the hospital bed capacity (9.7 admissions per 700 bed days x 5.6 days).

We found that around half of the influenza cases were unvaccinated. Our estimates of vaccine coverage are similar to that of previous years, where around 70-80% of the elderly, around 60% of non-elderly adults with comorbidities and around 20% in children with comorbidities.10-13 Our estimates of influenza vaccine coverage in the elderly are consistent with recent estimates from a meta-analysis of vaccine coverage in the Australian elderly population collected by a variety of methods, providing reassurance about the validity of hospital controls for this purpose.14 Additionally, we have recently compared vaccine coverage estimates from hospital, primary care and community-based systems and found them to be broadly consistent.15

The systematic review also found an increase in coverage associated with public funding of influenza vaccine since 1999; however, our findings reinforce the need to improve coverage particularly in younger populations with medical comorbidities where publicly funded vaccine has been available since 2010. We found that 93% of admissions with influenza in the elderly occurred in patients with medical comorbidities; this proportion was 71% in non-elderly adults and 44% in children. This suggests that even with an effective influenza vaccine, the current policy of vaccinating only younger individuals with comorbidities would not be expected to provide protection to more than half of children admitted to hospital.

There are several limitations to this surveillance system. There may be under-ascertainment of influenza due to poor quality sample collection or the lack of use of influenza laboratory tests, despite the diagnosis of influenza having implications for infection control and antiviral use in hospitals. Delayed presentations or secondary bacterial pneumonia may be associated with false negative influenza tests as the influenza infection may be cleared by the time of presentation. Ascertainment in tropical regions is limited by sampling in the winter/dry season only.

In summary, we detected a large number of hospital admissions with laboratory-confirmed influenza in a national observational study in 2016 comparable to 2014 and 2015 but much higher than in prior years. A consistent finding over several years is that a high proportion of patients with severe influenza, and almost all deaths, occurred in patients with chronic comorbidities.


We thank Neela Joshi Rai, Ristilla Ram, Jo-Anne Thompson, Janette Taylor (Westmead Hospital), Cazz Finucane, Camille Gibson (Princess Margaret Hospital; Telethon Institute), Janine Roney, Jill Garlick, Virginia Cable, Nigel Pratt, Jess Costa (The Alfred Hospital), Kristof Boot, Megan Martin (Mater Hospital), Michelle Thompson, Casey McLeod, Adam Kadmon, Stewart Duncum, Gerri Shandler, Sarah Mclean (Royal Melbourne Hospital), Jocelynne McRae, Laura Rost, Nicole Dinsmore Gemma Saravanos, Kathy Meredith (Children’s Hospital at Westmead), Wendy Beckingham, Sandra Root, Gabriela Defries, Kris Farrelly (Canberra and Calvary Hospitals), Stella Green, Sue Richmond (Cairns Base Hospital), Irene O’Meara, Ingrid Potgeiter (Alice Springs Hospital; Menzies School of Health Research), Tina Collins, Michelle Towers (Princess Alexandra Hospital), Susan Wagg (Royal Hobart Hospital), Kate Ellis (University Hospital Geelong, Barwon Health), Doug Dorahy, Lorissa Hopkins, Jasmine Wark (John Hunter Hospital), Jenny McGrath, Louise Milazzo, Sarah Richards, Cathy Short, Cate Green, Mary McAlister, Eve Boxhall, Ashleigh Richardson, Catriona Doran, Nicole Gurrey, Sophie Whitehead,Jiayas Lin, Rebecca Glover, Segun Kandel, Monima Pamang, Kate Shelton (Royal Adelaide Hospital), Ellen MacDonald, Sophie Damianopoulos, Fiona Seroney (Royal Perth Hospital). We acknowledge the support of the Australian Government Department of Health for funding this system.

Author details

Prof Allen C Cheng, Alfred Health; Monash University

Prof Mark Holmes, University of Adelaide, Royal Adelaide Hospital,

Prof Dominic E Dwyer, University of Sydney, Westmead Hospital,

A/Prof Louis Irving, Royal Melbourne Hospital, University of Melbourne,

A/Prof Tony Korman, Monash Medical Centre; Monash University,

A/Prof Sanjaya Senenayake, Australian National University, The Canberra Hospital,

A/Prof Kristine Macartney, Children’s Hospital at Westmead,

A/Prof Christopher Blyth, Princess Margaret Hospital, University of Western Australia, Telethon Kids Institute,

Prof Simon Brown, University of Western Australia, Royal Perth Hospital,

Prof Grant Waterer, University of Western Australia, Royal Perth Hospital,

Dr Louise Cooley, Royal Hobart Hospital

Dr N. Deborah Friedman, University Hospital Geelong,

Prof Peter Wark, University of Newcastle, John Hunter Hospital,

Dr Graham Simpson, Cairns Base Hospital,

Prof John Upham, Princess Alexandra Hospital, University of Queensland,

Dr Simon Bowler, Mater Hospitals,

Dr Stephen Brady, Alice Springs Hospital,

A/Prof Tom Kotsimbos, Alfred Health; Monash University

Adjunct Prof Paul Kelly, ACT Government Health Directorate; Australian National University Medical School

Corresponding author: Prof Allen Cheng, Department of Epidemiology and Preventive Medicine, Monash University, Commercial Road, Melbourne VIC 3004. Email:


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  16. Annual report

Table 3: Factors associated with admission to intensive care in patients hospitalised with confirmed influenza

Table 3: This table presents the results of a logistic regression looking at factors independently associated with admission to intensive care, including age, medical co-morbidities, Indigenous status, pregnancy, nursing home residence and influenza type/subtype.
Variable Crude OR p Adjusted OR* p
<16 years 0.9 (0.6, 1.4) 0.713 1.1 (0.7, 1.8) 0.685
16-64 years 1   1  
65+ years 0.6 (0.5, 0.9) 0.007 0.7 (0.5, 0.9) 0.017
Medical comorbidities 1.5 (1.0, 2.1) 0.035 1.9 (1.3, 2.9) 0.001
Aboriginal or Torres Strait Islander peoples 1.6 (0.9, 2.7) 0.11 1.3 (0.7, 2.3) 0.369
Pregnancy 1.3 (0.6, 3.0) 0.488 1.0 (0.4, 2.4) 0.935
Restricted functional status 1.1 (0.8, 1.5) 0.426 1.0 (0.7, 1.4) 0.912
Nursing home resident 0.2 (0.1, 0.5) 0.002 0.2 (0.1, 0.6) 0.003
Influenza type/subtype        
A/H1 0.9 (0.4, 2.0) 0.778 0.9 (0.4, 1.9) 0.701
A/H3 0.9 (0.5, 1.9) 0.85 1.1 (0.5, 2.3) 0.761
B 1   1  
A/unk 1.1 (0.6, 2.0) 0.72 1.2 (0.7, 2.2) 0.561
* all variables included in multivariate model

Figure 2: Incidence of confirmed influenza (per 100 hospital beds) by week and year

Figure 2: This graph shows the rate of cases at the sentinel hospitals, expressed per 100 hospital beds, by week, in comparison with previous seasons since 2011. It shows that the timing and peak of the influenza season (3 cases per 100 hospital beds) was

Text version of the Figure (TXT 1 KB)

Figure 3: Peak incidence of confirmed influenza (per 100 hospital beds) by hospital

Figure 3: This graph compares the peak number of cases per 100 hospital beds at each sentinel site. It shows that after adjusting for hospital size, Westmead Hospital (NSW) had very high influenza activity (10 cases per 100 hospital beds per week); Canber

Text version of the Figure (TXT 1 KB)

RM: Royal Melbourne; MM: Monash Medical Centre, GL: University Hospital Geelong, WE: Westmead Hospital, JHH: John Hunter Hospital, CA: Canberra and Calvary Hospitals, RA: Royal Adelaide, RP: Royal Perth Hospital, RH: Royal Hobart Hospital, MA: Mater Hospital, PA: Princess Alexandra Hospital, CB: Cairns Base Hospital, AS: Alice Springs Hospital, CHW: Children’s Hospital at Westmead, PMH: Princess Margaret Hospital ]