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Eurosurveillance, Volume 18, Issue 5, 31 January 2013
Rapid communications
Interim estimates of influenza vaccine effectiveness in 2012/13 from Canada’s sentinel surveillance network, January 2013
  1. British Columbia Centre for Disease Control, Vancouver, Canada
  2. University of British Columbia, Vancouver, Canada
  3. Institut National de Santé Publique du Québec (National Institute of Health of Quebec), Québec, Canada
  4. Laval University, Quebec, Canada
  5. Centre Hospitalier Universitaire de Québec (University Hospital Centre of Quebec), Québec, Canada
  6. University of Calgary, Calgary, Canada
  7. Public Health Ontario, Toronto, Canada
  8. Winnipeg Regional Health Authority, Winnipeg, Canada
  9. University of Manitoba, Winnipeg, Canada
  10. University of Toronto, Toronto, Canada
  11. Alberta Provincial Laboratory, Calgary, Canada
  12. Cadham Provincial Laboratory, Winnipeg, Canada
  13. National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada

Citation style for this article: Skowronski DM, Janjua NZ, De Serres G, Dickinson JA, Winter A, Mahmud SM, Sabaiduc S, Gubbay JB, Charest H, Petric M, Fonseca K, Van Caeseele P, Kwindt TL, Krajden M, Eshaghi A, Li Y. Interim estimates of influenza vaccine effectiveness in 2012/13 from Canada’s sentinel surveillance network, January 2013. Euro Surveill. 2013;18(5):pii=20394. Available online:
Date of submission: 21 January 2013

The 2012/13 influenza season in Canada has been characterised to date by early and moderately severe activity, dominated (90%) by the A(H3N2) subtype. Vaccine effectiveness (VE) was assessed in January 2013 by Canada’s sentinel surveillance network using a test-negative case–control design. Interim adjusted-VE against medically attended laboratory-confirmed influenza A(H3N2) infection was 45% (95% CI: 13–66). Influenza A(H3N2) viruses in Canada are similar to the vaccine, based on haemagglutination inhibition; however, antigenic site mutations are described in the haemagglutinin gene.


The 2012/13 influenza season in North America has shown moderately severe activity, spiking over the December/January holiday period, with influenza A(H3N2) viruses predominating among typed/subtyped viruses to date in both Canada (about 90%) and the United States (US) (about 70%) [1,2].

The updated 2012/13 A(H3N2) reference strain recommended by the World Health Organization as vaccine component for the northern hemisphere (A/Victoria/361/2011-like) is antigenically distinct from that recommended for the previous season (A/Perth/16/2009-like) [3], with 11 amino acid (AA) residue differences at antigenic sites of the haemagglutinin (HA) surface protein [4].

Vaccine effectiveness (VE) in Canada was assessed by the country’s sentinel surveillance network in January 2013. Here we report the interim 2012/13 VE estimates against the dominant circulating influenza A(H3N2) subtype in the context of antigenic and genetic characterisation of circulating strains.

Estimating influenza vaccine effectiveness

As previously described [5-11], a test-negative case–control design was used to estimate VE, whereby a patient presenting with influenza-like illness (ILI) testing positive for influenza virus was considered a case and a person testing negative was considered a control.

Several hundred community-based practitioners in sentinel surveillance sites across participating provinces (British Columbia, Alberta, Manitoba, Ontario and Quebec) may offer nasal or nasopharyngeal swabbing to any patient presenting within seven days of symptom onset of ILI – defined as acute onset of respiratory illness with fever and cough and one or more of the following: sore throat, arthralgia, myalgia or prostration.

The VE analysis period included specimens collected from 1 November 2012 (week 44: 28 October 2012–3 November 2012) to 23 January 2013 (week 4: 20–26 January 2013), taking into account onset of influenza activity (Figure 1) and an immunisation campaign that started in October. Epidemiological information was obtained from consenting patients or their parents/guardians using a standard questionnaire at the time of specimen collection, before testing. Ethics review boards in each participating province approved this study.

Figure 1. Laboratory detection of influenza by week and virus subtype, Canada, 2012/13 sentinel surveillance system (n=833)

Specimens were tested for influenza viruses A (to subtype level) and B at provincial reference laboratories by real-time reverse-transcription polymerase chain reaction according to provincial protocols [4,11]. Odds ratios (OR) for influenza vaccination among cases versus controls were estimated by multivariable logistic regression. VE against medically attended laboratory-confirmed influenza was calculated as [1 – OR] × 100. Patients for whom the timing of vaccination was unknown or was less than two weeks before symptom onset were excluded from the primary VE analysis but explored in sensitivity analyses. Those with unknown comorbidity were included and further explored in sensitivity analyses.

Genetic characterisation of sentinel influenza A(H3N2) viruses

Sequencing of the HA1 gene of a convenience sample (n=82) of available influenza A(H3N2) viruses, spanning the season so far but with emphasis on more recent activity, was undertaken for each province to identify AA substitutions within the 131 residues of antigenic sites A–E [11,12]. These were expressed as percentage identity and relatedness compared with the vaccine reference strain (A/Victoria/351/2011). Pairwise identities were calculated from alignments of translated protein sequences generated in Geneious Pro v4.8.5 using a MUSCLE multiple sequence alignment algorithm. The approximate likelihood method was used to generate the phylogenetic tree of aligned nucleotide sequences in Geneious Pro v4.8.5.

HA sequences from reference strains used in the phylogenetic analysis were obtained from the EpiFlu database of the Global Initiative on Sharing Avian Influenza Data (GISAID) (Table 1).

Table 1. Reference haemagglutinin sequences used in phylogenetic analysis, Canada, 2012/13 sentinel surveillance, January 2013

Interim estimates of influenza vaccine effectiveness

A total of 939 specimens were submitted from sentinel surveillance sites between 1 November 2012 and 23 January 2013. After exclusion criteria were applied (Figure 2), 739 participants contributed to overall VE analysis: their profile was similar to that seen in VE analyses of previous seasons [4,8,9,11]. Those aged 20–49 years contributed most to the analysis (43%) and the median interval between symptom onset and specimen collection was three days (Table 2).

Figure 2. Specimen exclusion for interim influenza vaccine effectiveness analysis, Canada, 2012/13 sentinel surveillance system

Table 2.
Profile of participants included in primary analysis, interim 2012/13 influenza vaccine effectiveness evaluation, Canada

About half (355/739) of the specimens were positive for influenza, of which 86% (287/334) of subtyped viruses were A(H3N2) (Table 3), a predominance similar to that noted elsewhere for Canada (Figure 1) [1]. The 2012/13 vaccine was received by 27% (108/402) controls (i.e. test-negative) and 17% (61/365) cases (i.e. test-positive) (p<0.001) (Table 2). Of those with information available for both 2011/12 and 2012/13 (n=682), 136/150 (91%) of those immunised in 2012/13 were also immunised in 2011/12. The proportion of controls reporting immunisation for 2012/13 and earlier seasons was comparable to that in previous sentinel and other survey reports for Canada (about 30%) [4,7-9,11,14] and was also similar for influenza A(H1N1)pdm09 immunisation: 48% compared with previous Canadian surveys (41%) [11]. The proportion of samples from patients with comorbidity was comparable to previous sentinel system estimates (14–23%) and other reports for Canada (15–20%) [4,7-11,15].

Table 3. Laboratory profile of specimens included in primary analysis, interim 2012/13 influenza vaccine effectiveness evaluation, Canada

The overall crude (unadjusted) VE against influenza A(H3N2) virus was 39% (95% CI: 10–59) and against any influenza was 45% (95% CI: 20–63) (Table 4). Fully adjusted VEs were 45% (95% CI: 13–66) for A(H3N2) and 52% (95% CI: 25–69) overall. The overall VE estimate reflects the predominance of influenza A(H3N2) virus, with little contribution from influenza B or A(H1N1) viruses, precluding reliable estimates for those components.

Table 4. Interim 2012/13 influenza A(H3N2) and overall influenza vaccine effectiveness, Canada

Virus characterisation

All influenza A(H3N2) isolates to date this season characterised in Canada by the haemagglutination inhibition assay have been considered antigenically similar to the 2012/13 vaccine component, although characterisation so far includes few (n=3) of the sentinel viruses described here [1]. HA1 sequences of a subset of 82 (29%) sentinel A(H3N2) viruses were thus assessed for substitutions potentially contributing to suboptimal VE (Figure 3, Table 5). Sequencing was based on original specimens from British Columbia (n=15), Alberta (n=25), Manitoba (n=4) and Ontario (n=11) and virus isolates from Quebec (n=27).

Figure 3. Phylogenetic tree of influenza A(H3N2) viruses, Canada, 2012/13 sentinel surveillance system

Table 5.
Changes in amino acid sequence encoded by haemagglutinin (HA1) gene (antigenic regions)a for subset of 2012/13 Canadian sentinel influenza A(H3N2) strains relative to reference strainsb

Of the 82 sequences, 75 clustered within the European Centre for Disease Prevention and Control (ECDC)-described Clade 3C, which includes the A/Victoria/361/2011 vaccine strain (Figure 3) [16]. There were, however, four to eight AA mutations (93.9–96.9% vaccine identity) in HA1 antigenic sites compared with the A/Victoria/361/2011 vaccine reference strain as follows: 2/82 with four AA mutations (from specimens collected mid-November and mid-December); 19/82 with five (October–January); 22/82 with six (October–January); 29/82 with seven (November–January) and 3/82 with eight mutations (late-December). Of note, the 32/82 viruses with seven or eight AA mutations included loss of glycosylation through T128A substitution in antigenic site B. The remaining seven sentinel sequences (collected mid-November to early January) clustered within ECDC Clade 6 (A/Iowa/19/2010-like) with 6/82 showing 11AA mutations (91.6% vaccine identity) and one exhibiting 12 AA mutations (90.8% vaccine identity) relative to the A/Victoria/361/2011 vaccine strain (Figure 3, Table 5). These Clade 6 viruses also included loss of glycosylation at position N45S, a non-antigenic site mutation.


Mid-season reporting of virus evolution, vaccine relatedness and VE can support real-time risk communication and mitigation. Our interim 2012/13 VE results show that vaccination reduced the risk of medically attended laboratory-confirmed influenza due to the predominant A(H3N2) virus subtype by about half.

Our estimates are comparable to, if somewhat lower than, interim 2012/13 VE estimates recently reported by the US indicating 62% VE overall, 55% for influenza A and 70% for influenza B [17]. The proportion of influenza A viruses contributing to interim VE analysis in the US study setting (57%) is different from the profile for the rest of the US (about 70%) or Canada (about 90%); influenza A(H3N2) viruses have so far predominated in both countries [1,2]. Participant profiles were not presented and multivariable adjustment was also not undertaken in the interim US analysis. Although our own adjusted VE estimates did not substantially differ (less than 5–10%) from our unadjusted VE estimates, assessment of bias and confounding has to be separately undertaken for each dataset. Nevertheless, suboptimal VE for the influenza A(H3N2) component of the vaccine in both Canada and the US is inconsistent with haemagglutination inhibition characterisation indicating good vaccine match to circulating A(H3N2) viruses [1,2]. Such discordance between conventional in vitro characterisation of vaccine match by haemagglutination inhibition and epidemiological measures of VE has been noted in previous seasons’ estimates from our sentinel network [6,7,11], highlighted also in a recent meta-analysis of other studies, including randomised controlled trials [18].

Molecular markers of virus mutation may offer more insight. It has previously been suggested that a change of at least four AA in two or more HA antigenic sites heralds emergence of virus drift, potentially compromising antibody binding [19]. However, HA antigenic-site maps have been updated and more studies are needed to correlate genetic variation in circulating viruses with epidemiological variation in measured VE [12,20]. Not only the number but also the nature and location of AA substitutions are likely to be relevant. Furthermore, hypotheses to explain the variable efficacy of repeat immunisation have included positive and negative interference from pre-existing antibody, with differential effects depending on the antigenic distance across successive vaccine components and circulating strains [21]. We note that a high proportion of participants (91%) who were immunised this season had also received vaccine the previous season. These virological, host and other factors potentially contributing to suboptimal VE warrant more in-depth evaluation.

Limitations of this surveillance approach to VE estimation have been described previously [6-11]. For our interim analysis, we draw particular attention to small sample size, resulting in wide confidence intervals and variability around the point estimate. Age-specific VE analyses (e.g. children and elderly people) would be of additional important interest – our estimates primarily reflect the prominent contribution of adults 20–49 years of age. However, stratification of VE analysis by age would further reduce the statistical power and precision of estimates in this interim report. The slightly higher VE with restriction to participants without comorbidity (Table 4) may similarly reflect such variability. End-of-season analysis will further expand upon these interim findings and may better support stratified analyses. Although we have assessed vaccine relatedness through gene sequencing of community-based sentinel viruses available from each province and across the season to date, in this interim assessment the sampling frame for specimen selection was not random or systematic. Bias may result from the preferential inclusion of specimens that demonstrate low cycle threshold values (high RNA levels) or successful virus isolation. These, however, are issues for all laboratory-based influenza surveillance. Finally, in reviewing participant profiles, we identified no obvious signals of bias and in our analysis we adjusted for recognised potential confounders, but ultimately, given the observational design, we cannot rule out other unrecognised influences on the VE estimates.

In summary, our interim findings indicate that the 2012/13 vaccine shows a substantial but suboptimal protection. As such, adjunct protective measures (e.g. antivirals) may be warranted for those at high risk of influenza complications, whether they are vaccinated or not. Interim virus monitoring and VE results may also inform vaccine reformulation for subsequent seasons. Ultimately, however, better understanding of the factors affecting annual influenza VE is needed for improved product development and immunisation programme acceptance in the long term.

The authors gratefully acknowledge the contribution of sentinel sites whose regular submission of specimens and data provide the basis of our analyses. We wish to thank the following for network coordination activities in each province including: Elaine Douglas, Kasim Qureshi (Alberta); Hazel Rona, Tanis Kershaw, Debbie Nowicki, Arielle Goldman-Smith, Alex Henteleff (Manitoba); Romy Olsha, (Ontario); Sophie Auger, Monique Douville Fradet (Quebec). We thank those who provided laboratory support in each province including Virology staff of the British Columbia Public Health Microbiology and Reference, the Alberta Provincial and Public Health Ontario Laboratories and Roy Cole and Kerry Dust of the Cadham Provincial Laboratory (Manitoba) and Joel Ménard and Lyne Désautels of the Laboratoire de santé publique du Québec. We further acknowledge the gene sequencing support provided by Kanti Pabbaraju and Sallene Wong (Alberta), Paul Rosenfeld and Aimin Li (Ontario) and the authors, originating and submitting laboratories of the reference virus sequences from GISAID’s EpiFlu Database ( (see Table 1).

SMM holds a Canada Research Chair in Pharmacoepidemiology and Vaccine Evaluation, and was supported by an establishment grant from the Manitoba Health Research Council and by Great-West Life, London Life and Canada Life Junior Investigator Award from the Canadian Cancer Society (grant number 2011-700644).

Funding was provided by the Canadian Institutes of Health Research, the British Columbia Centre for Disease Control, Alberta Health and Wellness, Public Health Ontario, Ministère de la santé et des services sociaux du Québec and the Institut national de santé publique du Québec.

Conflict of interest
GDS has received research grants from GlaxoSmithKline (GSK) and Sanofi Pasteur and participated in an ad hoc GSK advisory board meeting for an unrelated issue for which travel expenses were reimbursed. SMM has received research grants from GSK, Pfizer and Sanofi Pasteur. JBG has received research grants from GSK and Hoffmann-LaRoche for antiviral resistance studies. MK has received research grants from Roche, Merck, Gen-Probe and Siemens. Salaries of TLK and SS provided by a grant of the Canadian Institutes of Health Research. No other authors have competing interests to declare.

Authors’ contributions
Principal investigator (epidemiology): DMS (National and British Columbia); GDS (Quebec); JAD (Alberta); ALW (Ontario); SMM (Manitoba). Principal investigator (laboratory): JBG (Ontario); HC (Quebec); MPP and MK (British Columbia); KF (Alberta); PVC (Manitoba), YL (national). National database coordination: TLK. Data analysis: NZJ and DMS (epidemiology); SS and AE (phylogenetic). Data interpretation: all. Preparation of first draft: DMS. Draft revision and approval: all.


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