Neutralizing antibodies after the third COVID-19 vaccination in healthcare workers with or without breakthrough … – Nature.com
                            February 23, 2024
                            Demographics of and reported breakthrough infections in the    study population    
    This study continued the follow-up of humoral antibody    responses of healthcare workers (HCWs) who received two    BNT162b2 vaccine doses with short three-week interval    (n=230, short group) or two doses of BNT162b2,    mRNA-1273, or ChAdOx1 plus BNT162b2/ mRNA-1273 with a long    12-week (n=202, long group) interval before the third    vaccine dose. We have previously analyzed this cohort up to 3    months after the third vaccine dose7,8,10. The novel data    obtained in this study is the analysis and follow-up of serum    samples up to 9 months after the 3rd vaccine dose. In Finland,    COVID-19 vaccinations were first carried out with a short    three-week interval, and later in the spring of 2021 the    interval was lengthened to 12 weeks. Thus, the vaccinees in the    short interval group received their third dose before those in    the long interval group. Our analysis included serum samples    collected before the first vaccination and before the third    vaccination up to nine months after the third vaccine dose    (short and long interval groups) (Figs.1a    and 2a). The age range of    the participants at the time of the first vaccine dose ranged    from 20 to 65 years (mean 42.7 and median 41.2 years) in the    short interval group and 2267 years (mean 45.7 and median 46.3    years) in the long interval group (Table1).    Eighty-nine percent of the study participants were females.  
    Six of the vaccinees in the short interval group and fifteen in    the long interval group had had a SARS-CoV-2 infection    (confirmed by PCR) before the first vaccination. The number of    PCR/antigen test-confirmed SARS-CoV-2 infections increased in    the study population (and in Finland) after the emergence of    the Omicron variants. The majority of the vaccinees had    received their third dose by the end of 2021, and thus, the    breakthrough infections occurred mostly after the third vaccine    dose: HCWs in the short interval group reported 98 infections    after the third dose and HCWs in the long interval group    reported 10 infections after two doses and 80 after three    vaccine doses (Table1).  
    To estimate the changes in humoral immunity after vaccination    with three doses of COVID-19 mRNA vaccines and potential    exposure to circulating SARS-CoV-2 variants, we analyzed the    changes in SARS-CoV-2 spike protein subunit 1 (S1) and    nucleoprotein (N) specific IgG antibody levels in the sera of    HCWs in the short interval group (Fig.1,    the timeline of the vaccinations, serum collections and    circulating variants is shown in Fig.1a). The third    vaccination induced strong S1-specific IgG responses, which    peaked at 3 weeks post the vaccination and decreased thereafter    (Geometric mean of antibody levels 128.9 EIA units at 3D3wk,    99.96 EIA units at 3D3mo, 93.19 EIA units at 3D6mo, and 99.73    EIA units at 3D9mo; Fig.1b). The reported (PCR    or antigen test confirmed) or serologically observable    (increase in S1-specific or N-specific antibodies greater than    the cut-off, 4.8 or 8.8 EIA units, respectively) SARS-CoV-2    infections increased the S1-specific and N-specific antibody    levels (Fig.1b, e). Follow-up of the    vaccinees showed that the majority of infected vaccinees had an    increase in anti-S1 and anti-N antibodies after the time period    of a reported infection (red lines in Fig.1c, f).  
    Five vaccinees in the short interval group had SARS-CoV-2    N-specific antibodies prior to vaccination8    (Fig.1e): Two of these had    had a PCR test confirmed SARS-CoV-2 infection before the    vaccination while the other three had elevated but stable    anti-N antibody levels without a sign of antibody decline.    Grouping of the vaccinees based on their infection status    (Fig.1d, g)    showed that the anti-S1 and anti-N levels were significantly    different between HCWs with or without a breakthrough infection    at 6 months after the third vaccine dose (non-infected 72 EIA    units vs. infected 112 EIA units for S1, p<0.0001    and 1.4 EIA units vs. 22 EIA units for N,    p<0.0001) after the time point of three months    after the third vaccine dose. In some vaccinees, the    infection-induced antibody response was delayed and, therefore,    was detectable only in the later time points, while 13 infected    vaccinees showed no or little changes in S1-/or N-specific    antibodies (Fig.1c, f).  
    HCWs with a long vaccine interval received two doses of    BNT162b2, mRNA-1273, or a combination of ChAdOx1 and    BNT162b2/mRNA-1273 as the first two doses    (Table1). Sequential serum    samples were collected before the vaccination and at regular    intervals after each vaccine dose and analyzed for S1- and    N-specific IgG antibody levels (Fig.2, the timeline of the    vaccinations, serum collections and circulating variants is    shown in Fig.2a). The first vaccine    dose induced a wide range of S1-specific antibody levels, and    substantially higher levels in previously infected HCWs    (Fig.2b, c, black dots).    While the second and the third doses increased S1-specific    antibody levels higher, follow-up of the antibody levels of    each vaccinee showed increases also before the third dose and    after the first time point post the third vaccine dose    (Fig.2c). A vast majority of    these increases coincided with a reported SARS-CoV-2 infection    (PCR test or antigen test confirmed) preceding the sampling and    most of these HCWs also had an increase in N-specific    antibodies at the same time (Fig.2e, f).  
    A separate analysis of antibody responses in individuals that    had or had not contracted an infection (PCR or antigen test    confirmed, or serologically observable) showed a decrease    (Geometric mean 115.4 EIA units at 3D3wk vs 32.94 EIA units at    3D9mo) in anti-S1 antibody levels prior to the next vaccine    dose in case there was no infection (p<0.0001;    Fig.2d). A SARS-CoV-2    breakthrough infection increased the S1-specific antibody    levels when responses of infected and uninfected were compared    three and six months, respectively, after the third dose    (Geometric mean 82.30 EIA units at 3D3mo vs 130.6 EIA units at    3D3mo infected, 55.02 EIA units at 3D6mo vs 130.6 EIA units at    3D6mo infected) p<0.0001; Fig.2d). Also, the    N-specific antibody levels were induced by an infection,    although the N-specific response was absent or low in 25 of the    infected vaccinees (Fig.2eg). A decline in    N-specific antibodies was observed in the sequential samples    from participants infected pre-vaccination or post-vaccination    while a few vaccinees had relatively high basal N-antibody    levels without an indication of a decline in antibody (blue    dots above cutoff value, Fig.2f).  
    Of the 412 HCWs who had serum samples available after the third    COVID-19 vaccine dose, 44% (182/412) reported a positive    COVID-19 test (PCR or antigen) post third vaccine dose.    Furthermore, 95% (173/182) of the COVID-19 test-positive HCWs    showed a serological indication of infection, defined as a    diagnostic increase in either S1- or N-specific antibodies    (increase greater than cut-off, 4.8 EIA units for S1 after the    time point of 3D3wk, and 8.8 EIA units for N after the third    dose; Table2). Of the COVID-19    test negative (or untested) HCWs, 13% (30/246) had a    serological indication of infection by S1- or N-specific    antibody levels, making the proportion of HCWs with a    breakthrough infection, confirmed either by COVID-19 test or    serology, after three vaccine doses 51% (212/412). Of note,    measuring only S1 or N-specific antibodies was less sensitive    at detecting infected individuals, since only 64% (117/182) of    the COVID-19 test-positive HCWs had an increase in both anti-S1    and anti-N antibodies. Thus, serological detection of past    infection was most accurate when IgG antibodies for both S1 and    N antigens were positive.  
    We also examined the antibody levels of HCWs and compared those    to their COVID-19 test and serological status. We found that    infection soon after a COVID-19 vaccination was more likely to    lead into lack of serological indication of infection.    Seventeen per cent (10/60) of the HCWs who had a short interval    between the third COVID-19 vaccine dose and a positive COVID-19    test (vaccination less than three months before a positive    COVID-19 test, Supplementary Fig.1) had no serological    indication of an infection. Only 5% of the HCWs with a longer    vaccine interval between COVID-19 vaccination and infection    lacked serological indication of an infection (vaccination    three to six months before a positive COVID-19 test,    Supplementary Fig.2).  
    To determine the comparative efficiency of BNT162b2 and    mRNA-1273 as the third dose, S1-specific antibody responses    were analyzed after the third vaccine dose in uninfected HCWs.    In both short and long-interval groups, the vaccine-induced    antibody responses had similar kinetics, with the S1 antibody    level peaking at 3 weeks after vaccination, followed on an    average by a 25 EIA unit decline in subsequent samples    (Fig.3a, b). The mRNA-1273    vaccine as the third dose provided significantly higher    S1-specific antibody responses in both interval groups    (p<0.0423 in the short interval group and    p<0.0300 in the long interval group). The    difference between the groups receiving BNT162b2 or mRNA-1273    as the third dose in the long interval group was observable    already prior to the third dose (a result of different vaccine    combinations before the third dose, different vaccine    combination groups marked with different colors in    Fig.3b), and the difference    in antibody levels remained observable also after the third    dose (Fig.3b).  
            SARS-CoV-2 S1-specific IgG antibody responses induced            by Bnt162b2 or mRNA-1273 (triangles) as the third            vaccine dose were compared in the sera of uninfected            vaccinees who received a two doses of Bnt162b2            with a short, three-week dose interval or b two            doses of Bnt162b2 (orange), mRNA-1273 (violet), or            ChAdOx1 + Bnt162b2/mRNA-1273 (green) with a long dose            interval before the third vaccine dose. SARS-CoV-2            S1-specific IgG antibody responses were analyzed by EIA            in serum samples collected before the third dose (2D6mo            or 2D8mo) and after the third vaccine dose (3D3wk,            3D3mo, 3D6mo, and 3D9mo). Geometric means geometric            standard deviations of antibody levels, and number of            samples in each time point are shown. Dashed lines            indicate the cut-off values for seropositivity.          
    Our study included HCWs aged 19 to 67 years at the time of the    first vaccine dose. To examine whether age affects humoral    immune responses induced by COVID-19 vaccines, we analyzed    anti-S1 IgG antibody levels in relation to age from uninfected    HCWs (Supplementary Fig.3). Some decrease in    antibody levels was observed by increasing age, but a higher    age did not prevent the induction of high antibody levels.    Although the oldest age group, 5567-year-olds, had, on    average, the lowest antibody levels at 3 and 6 months after the    third vaccine dose the antibody levels were relatively equal    between all age groups (Supplementary Fig.4).  
    Neutralizing capacity of the sera against SARS-CoV-2 variants    was first examined in the short interval group by randomly    selecting a subset of 41 HCWs (no prior PCR-confirmed    SARS-CoV-2 infection). MNT was used to analyze in vitro    neutralizing antibody titers against the ancestral D614G    variant and the five recent SARS-CoV-2 Omicron variants, BA.1,    BA.2, BA.5, BQ.1.1, and XBB.1.5 in serum samples collected at    six months after the second vaccine dose (2D) and 3 weeks    (3wk), three months (3mo), and six months (6mo) after the third    booster dose (3D). (Fig.4al).  
            HCWs received two doses of BNT162b2 with a three-week            interval and a third dose of BNT162b2 (circle) or            mRNA-1273 (triangle) eight months later.            af Serum samples were collected 6 months            after the second vaccine dose (2D6mo, n=41), 3            weeks (3D3wk, n=40), 3 months (3D3mo,            n=41), and 6 months (3D6mo, n=39)            after the third dose and analyzed with MNT for            neutralizing antibodies against SARS-CoV-2 D614G and            Omicron BA.1, BA.2, BA.5, BQ.1.1 (BA.5 subvariant), and            XBB.1.5 (BA.2 subvariant) variants. HCWs with confirmed            SARS-CoV-2 infection between three and six months after            third dose (n=12) were separated (red dots and            triangles; infected 3D6mo). Half-maximal inhibitory            dilutions (ID50) were calculated, and titers            <10 were marked as 5. Geometric mean titers for            vaccine groups are indicated above each time point and            shown as lines with geometric SDs. gl            Sequential serum samples of each individual are            connected with lines. Red lines indicate where a            vaccinee has had a PCR or antigen test confirmed            SARS-CoV-2 infection. mq Top and side            views of trimeric SARS-CoV-2 spike protein structure            (PDB: 7WK2) show amino acid differences of Omicron            BA.1, BA.2, BA.5, BQ.1.1, and XBB.1.5 compared to Wuhan            Hu-1 sequence as amino-acid substitutions (orange) and            deletions (red).          
    Six months after the second vaccine dose, 95% of the vaccinees    (39/41) neutralized the D614G and 44% (18/41), 76% (31/41), 90%    (37/41), 5% (2/41), and 0% (0/41) neutralized Omicron BA.1,    BA.2, BA.5, BQ.1.1, and XBB.1.5 variants, respectively    (Fig.4af). The third    vaccine dose increased neutralizing antibodies against all    variants, although the levels against BQ.1.1 and XBB.1.5    variants remained lowest. Despite the gradual decrease in the    levels of neutralizing antibodies after the third dose, the    geometric mean titers (GMT) were 4.47.2x higher six months    after the third dose in comparison to 6 months after the second    dose, (80 vs 364 for D614G, 9 vs 47 for Omicron BA.1, 24v. 173    for BA.2, and 26 vs 125 for BA.5; p<0.0001 for each    pair). For Omicron BQ.1.1 and XBB.1.5 variants, the GMTs were    2.0x and 2.4x higher (5 vs. 12 for Omicron BQ.1.1,    p=0.0003, and 5 vs. 10 for Omicron XBB.1.5;    p=0.0001). Six months after the third dose only two    samples had titers below the detection limit for Omicron BA.1,    one sample for BA.2, 12 samples for BQ.1.1 and 17 samples for    XBB.1.5. The results suggest that the neutralization efficiency    of the induced antibodies is still reasonably high against the    earlier Omicron variants, but is strongly reduced against    BQ.1.1 and XBB.1.5 variants, with the number of samples below    the detection limit increasing at the 3D6mo time point.  
    Twelve of the 41 vaccinees reported a PCR-confirmed SARS-CoV-2    breakthrough infection between the sampling of three and six    months after the third dose. The breakthrough infection    increased the levels of neutralizing antibodies, and the GMTs    were 625x higher compared to non-infected participants (364 in    non-infected vs. 2239 in infected at 3D6mo for D614G, 47 vs.    644 for Omicron BA.1, 173 vs. 997 for BA.2, and 125 vs. 910 for    BA.5, 5 vs.126 for BQ.1.1, and 5 vs. 109 for XBB.1.5;    p=0.0002 for D614G and Omicron BA.2,    p<0.0001 for Omicron BA.1 and BA.5, and    p
    To study differences in neutralizing antibody titers elicited    by different vaccine combinations and vaccine dose intervals    against D614G and Omicron BA.1. BA.2, BA.5, BQ.1.1, and XBB.1.5    sera from a representative number of HCWs (with two BNT162b2    with a short (n=41) or with a long vaccine dose    interval (n=35), two mRNA-1273 (n=31), or    ChAdOx1 and BNT162b2 or mRNA-1273 (n=45) before the    third dose of BNT162b2 or mRNA-1273) were analyzed with MNT    (Fig.5). At 6 months after    the second vaccine dose, the majority of vaccinees in each    vaccine combination group had neutralizing antibodies against    D614G variant and Omicron BA.2 and BA.5, whereas all vaccine    combination groups had lower or undetectable levels of    neutralizing antibodies against Omicron BA.1, BQ.1.1, and    XBB.1.5. Interestingly, 2 x mRNA-1273 induced higher    neutralizing antibody titers at 2D6mo against all variants,    before the administration of the third vaccine dose. The third    vaccine dose increased neutralizing antibody titers in all    vaccine groups resulting in neutralizing antibody titers above    the detection limit against all Omicron variants, leaving only    four vaccinees below the detection limit against BQ.1.1 and ten    against XBB.1.5. Interestingly, in Omicron variants 3 weeks    after the third dose, the short interval 2 x BNT162b2 vaccine    group had the highest GMT, even 1.11.9x higher than in the 2 x    mRNA-1273 group (Fig.5).  
            Serum samples, collected 6 months after the second dose            (2D6mo), 3 weeks (3D3wk), and 3 months (3D3mo) after            the third vaccine dose from HCWs who received 2x            BNT162b2 with a short vaccine dose interval            (n=41, yellow circles and triangles) or 2x            BNT162b2 (n=35, orange circles and triangles),            2x mRNA-1273 (n=31, purple circles and            triangles), or ChAdOx1+BNT162b2/mRNA-1273            (n=45, green circles and triangles) with a            long vaccine dose interval, and a third dose of            BNT162b2 (circle) or mRNA-1273 (triangle) were compared            for neutralizing antibody responses against D614G and            Omicron variants BA.1, BA.2, BA.5, BQ.1.1, and XBB.1.5.            HCWs with confirmed SARS-CoV-2 infection between the            samplings at 3 weeks and three months after the third            dose (3D3wk and 3D3mo) were separated (3 doses +            infection, n=24, red circles and triangles).            Half-maximal inhibitory dilutions (ID50)            were calculated, and titers <10 were marked as 5.            Geometric mean titers (GMTs) for each vaccine group are            shown as lines with geometric SDs.          
    Three months after the third vaccine dose, the decrease in    neutralizing antibody titers against D614G, and the Omicron    variants was similar in all vaccine combination groups, and the    neutralizing titers remained slightly higher in the 2 x    BNT162b2 and 2 x mRNA-1273 vaccine groups than in the other    groups. The difference in neutralization of Omicron BA.1 and    XBB.1.5 was significant when the titers in short 2 x BNT162b2    group were compared to titers in ChAsOx1+BNT162b2/mRNA-1273    group (GMT 40 vs. 99 against BA.1, p=0.0014; GMT 8 vs.    16 against XBB.1.5, p=0.0024) and 2x mRNA-1273 group    (GMT 8 vs. 16 against XBB.1.5, p=0.040).  
    Between the sampling of 3 weeks and three months after the    third dose, 24 of the HCWs with the long vaccine interval    reported a COVID-19 test-positive SARS-CoV-2 breakthrough    infection (red dots in Fig.5). The neutralizing    antibody titers against the four variants were significantly    higher in infected than in non-infected HCWs. Only one HCW with    three vaccine doses and an infection had neutralizing antibody    titers against Omicron XBB.1.5 below the detection limit.    Altogether, these results indicate that the studied vaccine    combinations elicit high titers of SARS-CoV-2 neutralizing    antibodies against Omicron BA.1, BA.2, and BA.5 variants, while    the titers against the Omicron BQ.1.1 and XBB.1.5 were yet    relatively low. An infection within three months after three    vaccine doses elicits high neutralizing antibody titers against    all Omicron variants.  
    The estimation of neutralization capacity of    COVID-19-vaccinated individuals against different variants is    central in deciding the need for further vaccine doses. Here,    we compared the neutralizing antibody titers of HCWs without    breakthrough infection against D614G and Omicron variants BA.1,    BA.2, BA.5, BQ.1.1, and XBB.1.5 in the order these variants    emerged (Fig.6). Regardless of the    vaccine combination, the neutralizing capacity of the    antibodies was 4.811.5x reduced 3 weeks and 3 months after the    third vaccine dose when moving from D614G variant to Omicron    BA.1, 2.14.6x increased from Omicron BA.1 to BA.2, and    again1.52.3x reduced from Omicron BA.2 to BA.5, and 4.99.9x    further reduced to BQ.1.1 and to XBB.1.5. The only exception    was the 2 x mRNA-1273+BNT162b2/mRNA-1273 group, as in this    group there was no significant difference between the    neutralization capacity against Omicron BA.2 and Omicron BA.5    (GMT 503 vs 359) at 3 weeks after the third dose.  
            Comparison of neutralizing antibody titers against            D614G and Omicron variants BA.1, BA.2, BA.5, BQ.1.1,            and XBB.1.5 at 3 weeks (3D3wk) and three months (3D3mo)            after the third vaccine dose of HCWs without SARS-CoV-2            infection within each vaccine combination group (2x            BNT162b2 with a short, n=40 at 3D3wk and at            3D3mo or a long vaccine dose interval, n=34 at            3D3wk and n=27 at 3D3mo; 2x mRNA-1273            n=31 at 3D3wk and n=24 at 3D3mo; or            ChAdOx1+BNT162b2/mRNA-1273, n=44 at 3D3wk            and n=35 at 3D3mo). Half-maximal inhibitory            dilutions (ID50) were calculated, and titers            <10 were marked as 5. Geometric mean titers (GMTs)            for each vaccine group are indicated above bars and            shown as lines with geometric SDs.          
    The follow-up of neutralizing antibodies in HCWs who had a    breakthrough infection showed that the infection boosted the    titers of neutralizing antibodies 1.77.9x against the tested    variants (Fig.7). The fold difference    between the Omicron variants was relatively similar at all time    points (1.52.1x between BA.1 and BA.2, 1.41.5 between BA.2    and BA.5 etc.), while saturation of titers for D614G affected    the measured GMT values (Supplementary Fig.5). The comparable    fold difference between the variants in both pre-infection and    post-infection samples from vaccinees suggests that an Omicron    variant infection equally enhances the existing neutralizing    antibody response against various variants.  
            Neutralizing antibodies against D614G and Omicron            variants BA.1, BA.2, BA.5, BQ.1.1, and XBB.1.5 of            a 12 HCWs with short vaccination interval and            b 23 HCWs with long vaccination interval with a            breakthrough infection were compared. Half-maximal            inhibitory dilutions (ID50) were calculated            before third COVID-19 vaccine dose (2D6mo), and 3 weeks            (3D3wk), 3 months (3D3mo), and 6 months (3D6mo, only            for short vaccine interval group) after receiving the            third COVID-19 vaccine dose. Uninfected individuals are            marked with blue (long interval) or yellow (short            interval) diamonds, infected individuals with red            diamonds. Titers <10 were marked as 5. Titers of            each vaccinee in different time points are connected            with lines. Red line indicates the period of a PCR- or            serology-confirmed infection. Geometric mean antibody            titers with standard deviations are shown as bars and            lines at each time point.          
    To analyze the correlation of the antibody responses induced by    the vaccinations against the Omicron variants BA.1, BA.2, BA.5,    BQ.1.1, and XBB.1.5 and the ancestral D614G variant, the    neutralization efficiency of 499 serum samples from 155    vaccinees was pairwise compared between the six SARS-CoV-2    variants (Supplementary Fig.6). Neutralizing    antibody titers against the D614G variant were higher than    against any of the Omicron variants. Even though the    neutralization efficiency between different variants varied,    they correlated well with each other (r=0.77710.8766,    p<0.0001 for all pairwise comparisons).  
    Parallel examination of neutralizing antibody titers (for BA.5    as an example) and IgG responses for S1 and N showed similar    kinetics following the third vaccine dose and breakthrough    infections in both short and long vaccine interval groups    (Supplementary Fig.7). In the long    vaccine interval group the breakthrough infections    (n=23) occurred closer to the third vaccine dose    (between 3D3wk and 3D3mo) than in the short vaccine interval    group (n=12, between 3D3mo and 3D6mo). Of the 12 short    vaccine group HCWs with a confirmed breakthrough infection 92%    (11/12) had an increase in anti-N and 83% (10/12) in anti-S1    antibodies, and 83% (10/12) had at least a 4x-increase in    Omicron BA.5-specific neutralizing titers. In the long-interval    vaccine group serological evidence for a breakthrough infection    was detectable in anti-N antibodies in 65% (15/23), in anti-S1    antibodies in 78% (18/23), and for Omicron BA.5 neutralizing    titers in 48% (11/23) of infected HCWs. Three HCWs with a    COVID-19 test-positive infection showed no increase in S1- or    N-specific IgG antibodies, however, two of these had their    serum sampling close (810 days) to the positive COVID-19 test    date, and this may have been too early after the infection to    detect newly formed antibodies.  
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Neutralizing antibodies after the third COVID-19 vaccination in healthcare workers with or without breakthrough ... - Nature.com