Baseline characteristics
In 2020, 637 HCW were recruited across 6 sites, of whom 24 opted not to be vaccinated in 2020 and were therefore not considered in this analysis. Pre-vaccination and post-vaccination blood samples were available for 595 vaccinated HCWs (586 with both visits), and end-of-season blood samples were available for 564. The median time between vaccination and post-vaccination blood draw was 15 days (IQR: 14, 18) and the median time between vaccination and end-of-year blood draw was 174 days (IQR: 165, 188) (Supplementary Figure 1). In 2021, the number newly recruited was 759, while 339 recruited in 2020 (including 2 who were unvaccinated in 2020), were vaccinated in 2021 and continued follow up. Eighteen of the HCWs newly recruited in 2021 were unvaccinated and not considered further. Pre-vaccination blood samples were available for 1070 vaccinated HCWs, post-vaccination samples for 1031 and end-of-season samples for 1002. The median time between vaccination and post-vaccination blood draw was 15 days (IQR: 14, 19) and the median time between vaccination and end-of-year blood draw was 165 days (QR: 154,184). See Figure 1 for the STROBE flowchart detailing patient recruitment and follow-up and Supplementary Figure 1 for a summary of follow-up times.
Demographic and workplace characteristics are presented in Table 1 by study year. HCW were a median of 39 years at recruitment (39y in 2020; 40y in 2021) and predominantly female (81% in 2020; 85% in 2021). In both study years, most HCW were full-time employed (57% in 2020; 62% in 2021) and around half were in clinical roles (53% in 2020; 46% in 2021). Fourteen percent had at least one high risk condition (13% in 2020; 15% in 2021).
A(H1N1)pdm09 antibody titres over the course of vaccination
The A(H1N1)pdm09 vaccine antigens included in egg-based vaccines in 2020 and 2021 were from genetically distinct subgroups, with A/Brisbane/02/2018 in 6B.1A.1 subgroup, and A/Victoria/2570/2019 in the 6B.1A.5a.2 subgroup. Vaccine antigens for the 5 years prior to 2020 were also genetically distinct, being an A/Michigan/45/2015 6B.1 virus in 2017-19 and A/California/7/2009 in 2015-16 (Supplementary Figure 2).
In both 2020 and 2021, pre-vaccination GMTs against both cell and egg-grown antigens were lowest among HCWs with 0-prior vaccinations at around 10-20, with the group with 5+ prior vaccinations having the next lowest pre-vaccination GMTs (Supplementary Table 1, Supplementary Figure 3A). In contrast, day 14 post-vaccination GMTs were higher in the 0-prior group compared with the 5-prior group. There was also a statistically significant trend towards increased post-vaccination titres with lower number of prior vaccinations in both 2020 and 2021, with an average decrease of at least 0.79 with each additional prior vaccination (Table 2). Post-vaccination titres were also dependent on the pre-vaccination titre (Figure 2A; Supplementary Figure 4A). Predicted post-vaccination GMTs from the model were adjusted for pre-vaccination titre (centred at 5), vaccine brand, age in decades (centred at 18 years), sex, BMI, and presence of any pre-existing health conditions and continued to show an inverse association with both number of prior vaccinations as well as a positive association with pre-vaccination titre (Figure 2B; Supplementary Table 2). Age and vaccine brand were also important predictors against egg-, but not cell-grown, antigens (Supplementary Table 2).
Pre-vaccination seropositivity was lowest for the 0-prior vaccination group, but those with 5-prior vaccinations had the next lowest seropositivity and this group remained lowest post-vaccination (Supplementary Table 1). For all vaccination groups seropositivity increased to above 50% post-vaccination for cell-grown antigens and was even higher for egg-grown antigens (above 85%), and seropositivity was sustained above pre-vaccination levels 6 months post-vaccination. There was a clear trend of decreasing seropositivity with increasing numbers of prior vaccinations in 2021 but not 2020 (Supplementary Figure 3B); however, a clearer trend emerged after adjustment for pre-vaccination titre (Figure 2B; Supplementary Figure 6).
Post-vaccination geometric mean titre rises (GMRs) were highest for the vaccine-naïve group but were not very different among the 4 vaccine-experienced groups, all with a mean GMR of ~2 in 2020 and ranging from 3-4 against cell antigens and from 6-8 against egg antigens in 2021 (Supplementary Figure 3C; Supplementary Table 1). GMRs decreased with increasing pre-vaccination titre and fell below 4-fold for all prior vaccination groups with pre-vaccination titres exceeding 80 (Supplementary Figure 4C). Effects of prior vaccination remained substantial after adjusting for pre-vaccination titre, age at enrolment and vaccine brand (Supplementary Table 4, Supplementary Figure 7). Similarly, seroconversion was higher among the vaccine-naïve, but not very different among vaccine-experienced groups (Supplementary Table 1; Supplementary Figure 3D). Adjustment for pre-vaccination titre, age and brand reduced the differences in seroconverted proportions between the vaccine-naïve and vaccine-experienced, and, in 2021, revealed no apparent trend of declining seroconversion from 0 to 5-prior vaccinations (Supplementary Table 5, Supplementary Figure 8).
A(H3N2) antibody titres over the course of vaccination
The vaccine administered in 2020 contained an A/South Australia/34/2019-like virus, which fell in the 3C.2a1b.2 genetic subgroup (Supplementary Figure 9). This virus was genetically distinct from the 2021 vaccine virus, A/Hong Kong/2671/2019, which fell in the 3C.2a1b.1b subgroup, and both were distinct from the vaccine viruses used in the 5 years prior to 2020. However, there were some shared epitopes, including the T160K substitution in the egg antigens of 2016-2021 vaccine strains, which is a known egg-acquired adaptation associated with a loss of glycosylation [23]. All vaccine strains apart from A/Hong Kong /2671/2019 contained several other glycosylation sites within antigenic sites A and B that were retained in egg-grown strains (Supplementary Table 6).
As with A(H1N1)pdm09, responses to A(H3N2) antigens exhibited a pattern of declining GMTs by number of prior vaccinations (Supplementary Table 7; Supplementary Figure 10), and increasing GMTs with higher pre-vaccination titres (Figure 3A; Supplementary Figure 11). The trend was more apparent in 2021 than in 2020, with an expected reduction in GMT of 0.93 in 2020 and 0.87 in 2021 (Table 2), which was maintained after adjustment for pre-vaccination titre, vaccine brand, age, sex, BMI and pre-existing health conditions (Figure 3B; Supplementary Table 8, Supplementary Figure 12).
Post-vaccination seropositivity was high and above 65% for cell-grown antigens and above 90% for egg-grown antigens, consistent with higher post-vaccination HI titres against egg compared with cell-grown antigens (Supplementary Table 7; Supplementary Figure 10B). In 2020, the raw data suggested increasing seropositivity from 0 to 4 prior vaccinations; however, after adjustment for pre-vaccination titre, this trend reversed, albeit not monotonically (Figure 3C; Supplementary Table 9, Supplementary Figure 13).
Post-vaccination GMRs were highest for the vaccine-naïve group with a mean rise of 3.3 against cell-grown antigens (compared to mean rises ranging from 1.4 to 2.3-fold for the vaccine-experienced groups (Supplementary Table 6; Supplementary Figure 10C). Correspondingly, around half the vaccine-naïve HCWs seroconverted to cell-grown antigen (56% in 2020 and 47% in 2021), but fewer than half of the vaccine-experienced groups seroconverted, with seroconversion as low as 7.7% for those receiving 3-prior vaccinations in 2020 (Supplementary Table 7; Supplementary Figure 10D). Seroconversions were higher against egg- compared with cell-grown antigens, and for HCWs with lower pre-vaccination titres (Supplementary Figure 11). GMR and seroconversion trends were maintained after adjustment for pre-vaccination titre, age and vaccine brand (Figure 3C-D; Supplementary Tables 10 & 11; Supplementary Figures 14 & 15).