Low 2012–13 Influenza Vaccine Effectiveness Associated with Mutation in the Egg-Adapted H3N2 Vaccine Strain Not Antigenic Drift in Circulating Viruses

<div><p>Background</p><p>Influenza vaccine effectiveness (VE) is generally interpreted in the context of vaccine match/mismatch to circulating strains with evolutionary drift in the latter invoked to explain reduced protection. During the 2012–13 season, however, detailed genotypic and phenotypic characterization shows that low VE was instead related to mutations in the egg-adapted H3N2 vaccine strain rather than antigenic drift in circulating viruses.</p><p>Methods/Findings</p><p>Component-specific VE against medically-attended, PCR-confirmed influenza was estimated in Canada by test-negative case-control design. Influenza A viruses were characterized genotypically by amino acid (AA) sequencing of established haemagglutinin (HA) antigenic sites and phenotypically through haemagglutination inhibition (HI) assay. H3N2 viruses were characterized in relation to the WHO-recommended, cell-passaged vaccine prototype (A/Victoria/361/2011) as well as the egg-adapted strain as per actually used in vaccine production. Among the total of 1501 participants, influenza virus was detected in 652 (43%). Nearly two-thirds of viruses typed/subtyped were A(H3N2) (394/626; 63%); the remainder were A(H1N1)pdm09 (79/626; 13%), B/Yamagata (98/626; 16%) or B/Victoria (54/626; 9%). Suboptimal VE of 50% (95%CI: 33–63%) overall was driven by predominant H3N2 activity for which VE was 41% (95%CI: 17–59%). All H3N2 field isolates were HI-characterized as well-matched to the WHO-recommended A/Victoria/361/2011 prototype whereas all but one were antigenically distinct from the egg-adapted strain as per actually used in vaccine production. The egg-adapted strain was itself antigenically distinct from the WHO-recommended prototype, and bore three AA mutations at antigenic sites B [H156Q, G186V] and D [S219Y]. Conversely, circulating viruses were identical to the WHO-recommended prototype at these positions with other genetic variation that did not affect antigenicity. VE was 59% (95%CI:16–80%) against A(H1N1)pdm09, 67% (95%CI: 30–85%) against B/Yamagata (vaccine-lineage) and 75% (95%CI: 29–91%) against B/Victoria (non-vaccine-lineage) viruses.</p><p>Conclusions</p><p>These findings underscore the need to monitor vaccine viruses as well as circulating strains to explain vaccine performance. Evolutionary drift in circulating viruses cannot be regulated, but influential mutations introduced as part of egg-based vaccine production may be amenable to improvements.</p></div

Three-dimensional model of antigenic-site differences between circulating H3N2 viruses and the 2012–13 egg-adapted A/Victoria/361/2011 IVR-165 high growth reassortant vaccine strain.

<p>One HA1 monomer is shown with five previously defined antigenic site residues of A–E colored in light green, dark green, light blue, dark blue and purple, respectively, mapped onto a related crystal structure (A/X-31(H3N2), PDB, 1HGG) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092153#pone.0092153-Sauter1" target="_blank">[27]</a> using PyMOL <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092153#pone.0092153-The1" target="_blank">[28]</a>. The most prevalent antigenic site amino acid differences between circulating clade 3C viruses in Canada relative to the egg-adapted A/Victoria/361/2011 IVR-165 vaccine reassortant strain are shown in red and labelled with coloured font representing their antigenic sites, viewed from the front (A) or side (B). Three amino acid differences (Q156H, V186G and Y219S) are owing to mutation in the egg-adapted IVR-165 vaccine strain rather than circulating viruses which instead share identity with the MDCK-passaged WHO reference prototype at these positions. RBS indicates approximate location of the receptor-binding site.</p

Haemagglutinin antigenic site differences in circulating H3N2 viruses relative to the 2012–13 egg-adapted A/Victoria/361/2011 IVR-165^a high growth reassortant vaccine strain.

<p>N = number of sentinel viruses with that sequence. Bold font signifies amino acid (AA) substitutions compared with IVR-165. Clade designation, number of antigenic site differences and percent antigenic site pairwise identity are also displayed. Only the 31/131 antigenic site positions showing differences between circulating H3N2 viruses and IVR-165 are displayed. AA sequences at those positions for other recent vaccine viruses are also displayed.</p>a<p>. IVR-165 is the egg-adapted high growth reassortant strain substituted by manufacturers for the MDCK-passaged A/Victoria/361/2011 (H3N2) prototype virus recommended as 2012–13 vaccine component by the World Health Organization (WHO) designated here as A/Victoria/361/2011 (MDCK).</p>b<p>. Number of antigenic site AA differences and percent antigenic site identity relative to IVR-165. Percent identity derived as per <b><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092153#pone.0092153.s009" target="_blank">Text S1</a></b>.</p>c<p>. A/Victoria/210/2009 (X-187) is the egg-adapted high growth reassortant strain used by manufacturers for the 2011–12 influenza vaccine for the northern hemisphere., shown for historic comparison.</p>d<p>. A/Texas/50/2012 (MDCK) and (X-223) are the WHO-recommended prototype and egg-adapted high growth reassortant strains, respectively, for the 2013–14 influenza vaccine for the northern hemisphere, shown for added comparison.</p

Influenza specimens by week and subtype, 2012–13 sentinel surveillance period (N = 1682).

<p>NOTE: excludes specimens from patients failing to meet the influenza-like illness case definition or unknown; specimens collected >7 days after influenza-like illness onset or interval unknown; comorbidity unknown; age unknown or <1 year and influenza test results unavailable or inconclusive on typing. Missing collection dates were imputed as the laboratory accession date minus two days, the average time period between collection date and laboratory accession date for records with valid data for both fields. One specimen diagnosed with both A/H3N2 and A(H1N1)pdm09 in week 2 is not presented in the graph. Vaccine effectiveness analysis spans week 44 to week 18.</p

Specimen exclusion for influenza vaccine effectiveness analysis, Canada, 2012–13 sentinel surveillance system.

<p>NOTE: exclusions shown here in stepwise fashion to arrive at total case and control tally (i.e. those meeting multiple exclusion criteria are counted on the basis of the first exclusion criterion met in the list shown). Missing collection dates were imputed as the laboratory accession date minus two days, the average time period between collection date and laboratory accession date for records with valid data for both fields.</p

Profile of participants included in primary influenza VE analysis, 2012–13, Canada.

<p>TIV = trivalent influenza vaccine; VE = vaccine effectiveness.</p>a<p>. Including any one or more of heart, pulmonary, renal, metabolic, blood, cancer, or conditions that compromise immunity or the management of respiratory secretions, or morbid obesity <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092153#pone.0092153-National3" target="_blank">[20]</a>.</p>b<p>. For the 2012–13 season, of 319 participants reporting vaccine receipt ≥2 weeks before symptom onset, 298 reported this was given through injection, 5 through nasal spray (all children except one) with route of administration unspecified for 16.</p>c<p>. Children <2 years of age in 2012–13 were excluded from 2011–12 vaccine uptake analysis as they may not have been vaccine-eligible during the fall 2011–12 immunization campaign on the basis of age <6 months.</p>d<p>. Children <3 years of age in 2012–13 were excluded from 2010–11 vaccine uptake analyses.</p>e<p>. In Canada, AS03-adjuvanted monovalent A(H1N1)pdm09 vaccine comprised >95% of doses distributed <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092153#pone.0092153-Skowronski6" target="_blank">[17]</a>.</p>f<p>. Children <4 years of age in 2012–13 were excluded from monovalent A(H1N1)pdm09 vaccine uptake analyses.</p

Primary and restricted analysis - influenza vaccine effectiveness based on sentinel system in Canada 2012–13 season.

<p>BC = British Columbia, AB = Alberta, MB = Manitoba, ON = Ontario, QC = Québec; d = days; NE = not estimable owing to sparse data.</p>a<p>. Adjusted for age (1–8, 9–19, 20–49, ≥50 years), province, interval, week.</p>b<p>. Adjusted for age (1–8, 9–19 years), comorbidity, province, interval, week; except B/Yamagata not adjusted for province.</p>c<p>. Adjusted for comorbidity, province, interval, week; except B/Victoria not adjusted for province.</p>d<p>. Adjusted for age (50–64, ≥65 years), province, interval, week; except A(H1N1)pdm09, influenza B, B/Victoria, B/Yamagata not adjusted for province.</p