Table 1.
Clade/Varianta | Unvaccinated, n (%) | Vaccinated,b n (%) | P Valuec |
---|---|---|---|
A. 2016–2017 full season analysis (1 November 2016 to 30 April 2017)d | |||
Clade 3C.2a | 100 (23) | 30 (22) | .85 |
+ N31S + D53N + R142G + S144R + N171K + I192T + Q197H | 1 (0) | 0 (0) | 1.00e |
+ N121K + S144K | 31 (7) | 10 (7) | .91 |
+ T131K + R142K + R261Q | 61 (14) | 20 (15) | .82 |
Other substitutions | 7 (2) | 0 (0) | .21e |
Clade 3C.2a1 | 320 (73) | 103 (76) | .54 |
Other substitutions without N121K | 28 (6) | 10 (7) | .69 |
+ N121K + K92R + H311Q | 61 (14) | 12 (9) | .12 |
+ N121K + R142G | 66 (15) | 26 (19) | .26 |
+ N121K + T135K + HA2:G150E | 67 (15) | 26 (19) | .29 |
+ N121K + I140M + HA2:G150E | 3 (1) | 4 (3) | .06e |
+ N121K + R142G + I242V + HA2:G150E | 89 (20) | 24 (18) | .49 |
N121K + other substitutions | 6 (1) | 1 (1) | 1.00e |
Clade 3C.3a | 18 (4) | 3 (2) | .43e |
Total | 438 (100) | 136 (100) | |
B. 2017–2018 mid-season analysis (5 November 2017 to 13 January 2018)f | |||
Clade 3C.2a | 142 (93) | 71 (93) | .86 |
+ N31S + D53N + R142G + S144R + N171K + I192T + Q197H | 3 (2) | 0 (0) | .55e |
+ N121K + S144K | 4 (3) | 2 (3) | 1.00e |
+ T131K + R142K + R261Q | 135 (88) | 69 (91) | .56 |
Clade 3C.2a1 | 11 (7) | 4 (5) | .78e |
+ N121K + K92R + H311Q | 9 (6) | 3 (4) | .76e |
+ N121K + T135K + HA2:G150E | 2 (1) | 1 (1) | 1.00e |
Clade 3C.3a | 0 (0) | 1 (1) | .33e |
Total | 153 (100) | 76 (100) |
aSpecimens were tested for influenza viruses using reverse-transcriptase polymerase chain reaction at provincial public health reference laboratories as previously described [5, 7]. Genetic characterization of the hemagglutinin was attempted on all influenza-positive original specimens collected from Canadian Sentinel Practitioner Surveillance Network patients using Sanger sequencing. Phylogenetic analysis was conducted based on nucleotide sequence using the approximate likelihood method to determine clade distribution and identify major genetic clusters (or “parent” groups) in conjunction with published reports. See Supplementary Materials for more details and references related to sequence analysis.
bVaccination status ascertained as per usual based on patient self-report and sentinel practitioner documentation. Patients who self-reported receipt of ≥1 dose of the current season’s influenza vaccine ≥2 weeks before onset of influenza-like illness (ILI) were considered vaccinated; those vaccinated <2 weeks before ILI onset were excluded.
c P values based on χ2 test comparing the proportion of viruses within the specified clade/variant vs all other clades/variants among vaccinated vs unvaccinated participants.
dMethods as per [5], but including viruses with specimen collection dates spanning up to 30 April 2017. Associated GenBank sequence numbers for 564 of 574 included viruses are KY583507 to KY583727, MH216203–MH216328, MH216331–MH216445, and MH216447–MH216548. Ten sequences were of insufficient quality for GenBank submission but were sufficient for clade/variant determination based on clade-defining amino acid substitutions.
eFisher’s exact test used where >25% of expected cell counts were <5.