Baseline characteristics of the cohorts
The Omicron variant continues to evolve under immune selection and serial novel sub-variants emerged with substantial mutations in the spike protein, resulting in different antigenicity and immune evasion ability (Extended Data Fig. 1A). In this study, a total of 194 participants confirmed for naive or breakthrough infections with Omicron BA.5 (unvaccinated, N = 13; booster vaccination, N = 41), BF.7 (regular vaccination, N = 10; booster vaccination, N = 29) and XBB (unvaccinated, N = 30; regular vaccination, N = 13; booster vaccination, N = 58) variants between August 2022 and June 2023, were enrolled and measured the plasma neutralizing profiles against WT, BA.1, BA.2, BA.2.75.2, BA.4/5, BF.7, BQ.1.1, XBB.1.16, XBB.1.5 and XBB.1.9 variants using SARS-CoV-2 pseudovirus neutralization assays. The detailed baseline characteristics of these participants are shown in Table 1. In the cohort of XBB infection, there are 48 participants (unvaccinated, N = 15; booster vaccination, N = 33) were re-infection patients, with the first infection of BA.5/BF.7 variants and the second XBB variant. For these participants, the median age is 57 (interquartile range (IQR): 38-74.5), and 60.4% of patients had underlying health conditions. The median days between the last vaccination and first infection, the last vaccination and the second infection were 466 (IQR: 345.5–540) and 523 (IQR: 449–617), respectively. Of note, the median days between first infection and re-infection was 146 (IQR:140.3–151). Moreover, 25.7%, 61.4% and 12.9% showed mild, moderate and severe diseases, respectively. Based on the infected variants, status of vaccination and number of infections, these 194 participants were divided into five cohorts for the further analyses (Extended Data Fig. 1B). All the plasma samples were collected at least 7 days post illness onset/laboratory confirmation with a median of 10 (IQR: 8–14) (Table 1 and Fig. 1B).
Table 1
Baseline characteristics of SARS-CoV-2 infections included in this study.
Characteristic
|
SARS-CoV-2 infected cases
|
P values
|
Total
(N = 194)
|
BA.5
(N = 54)
|
BF.7
(N = 39)
|
XBB
(N = 101)
|
BA.5 vs BF.7
|
BA.5 vs XBB
|
BF.7 vs XBB
|
Male (%, n/N)
|
57.2 (111/194)
|
53.7 (29/54)
|
51.3 (20/39)
|
61.4 (62/101)
|
0.8364
|
0.3942
|
0.3393
|
Female (%, n/N)
|
42.8 (83/194)
|
46.3 (25/54)
|
48.7 (19/39)
|
38.6 (39/101)
|
/
|
/
|
/
|
Median age (IQR)
|
42 (32–63)
|
40 (29.75-47)
|
30 (26–40)
|
57 (38-74.5)
|
0.0055
|
< 0.0001
|
< 0.0001
|
Age subgroup (%, n/N)
|
|
|
|
|
|
|
|
18–64 yr
|
75.3 (146/194)
|
90.7 (49/54)
|
94.9 (37/39)
|
59.4 (60/101)
|
0.6949
|
< 0.0001
|
< 0.0001
|
≥ 65 yr
|
24.7 (48/194)
|
9.3 (5/54)
|
5.1 (2/39)
|
40.6 (41/101)
|
/
|
/
|
/
|
Underlying health conditions (%, n/N)
|
38.1 (74/194)
|
18.5 (10/54)
|
7.7 (3/39)
|
60.4 (61/101)
|
0.2250
|
< 0.0001
|
< 0.0001
|
Disease severity (%, n/N)
|
|
|
|
|
|
|
|
Asymptomatic
|
18.6 (36/194)
|
38.9 (21/54)
|
38.5 (15/39)
|
0 (0/101)
|
0.9667
|
< 0.0001
|
< 0.0001
|
Mild
|
42.8 (83/194)
|
61.1 (33/54)
|
61.5 (24/39)
|
25.7 (26/101)
|
> 0.9999
|
< 0.0001
|
< 0.0001
|
Moderate
|
32 (62/194)
|
0 (0/54)
|
0 (0/39)
|
61.4 (62/101)
|
/
|
< 0.0001
|
< 0.0001
|
Severe
|
6.7 (13/194)
|
0 (0/54)
|
0 (0/39)
|
12.9 (13/101)
|
/
|
< 0.0001
|
< 0.0001
|
Vaccination (%, n/N)
|
|
|
|
|
|
|
|
Unvaccinated
|
22.2 (43/194)
|
24.1 (13/54)
|
0 (0/39)
|
29.7 (30/101)
|
< 0.0001
|
0.4558
|
< 0.0001
|
Regular vaccination
|
10.3 (20/194)
|
0 (0/54)
|
25.6 (10/39)
|
9.9 (10/101)
|
< 0.0001
|
< 0.0001
|
0.0170
|
Booster vaccination
|
67.5 (131/194)
|
75.9 (41/54)
|
74.4 (29/39)
|
60.4 (61/101)
|
0.8628
|
0.0521
|
0.1222
|
First infection
|
146
|
100 (54/54)
|
100 (39/39)
|
52.5 (53/101)
|
/
|
/
|
/
|
Re-infection
|
48
|
0 (0/54)
|
0 (0/39)
|
47.5 (48/101)
|
/
|
/
|
/
|
Median days between last vaccination and first infection (IQR)
|
291 (158.5-465.5)
|
225 (138–266)
|
274 (188–333)
|
466 (345.5–540)
|
0.0041
|
< 0.0001
|
< 0.0001
|
Median days between last vaccination and re-infection (IQR)
|
/
|
/
|
/
|
523 (449–617)
|
/
|
/
|
/
|
Median days between first infection and re-infection (IQR)
|
/
|
/
|
/
|
146 (140.3–151)
|
/
|
/
|
/
|
Median days between illness onset/laboratory confirmation and sample collection (IQR)
|
10 (8–14)
|
10 (8.75-12)
|
8 (8–9)
|
13 (9.5–17)
|
< 0.0001
|
< 0.0002
|
< 0.0001
|
IQR: Inter-quartile range. |
Repeated Omicron infections reduces the humoral immune imprinting from previous vaccination
Firstly, we evaluated plasma neutralization from first infections with Omicron BA.5, BF.7 and XBB variants against WT SARS-CoV-2 and the corresponding infected variants (XBB.1.16 was used as the representative variant for XBB variants). For the naive infection with BA.5 and XBB variants, significantly higher geometric mean titers (GMTs) were found for the corresponding infected variants than the WT (Fig. 2A and Fig. 2C). For the breakthrough infections, both the GMTs against the WT and the corresponding infected variants were significantly higher than the those in the naive infections (Fig. 2A-2C). However, the GMTs against the corresponding infected variants were lower than those for the WT, with greater differences in the booster vaccinees (Fig. 2A-2C). As to the cohort of re-infections, the GMTs against WT, BA.5, BF.7 and XBB.1.16 variants were analyzed (Fig. 2D). For the vaccinated participants, about 93%, 93%, 100%, and 100% of the samples showed detectable 50% inhibitory dose (ID50 ≥ 20) against these four variants with GMTs of 53.86, 275.01, 343.56 and 331.13, respectively. The GMTs against BA.5, BF.7 and XBB.1.16 variants were significantly higher than the WT, with increase folds of 5.11, 6.38, and 6.15, respectively. For the breakthrough infections, about 100%, 100%, 97%, and 100% of the samples showed detectable ID50 against these four variants with GMTs of 275.21, 438.04, 372.05 and 176.02, respectively. The GMTs against BA.5 and BF.7 showed 1.59 and 1.35 increase folds when compared with WT, while the GMT for the XBB.1.16 was 0.64 of the WT. Meanwhile, the GMTs for XBB.1.16 variant in the unvaccinated participants were significantly higher than the booster vaccinees (Fig. 2D).
Then we further analyzed the ratios of the corresponding infected variants/WT ID50 titer between first infection and re-infection (Fig. 2E-2G). For the unvaccinated participants, the mean ratios were all above 1 and there were no significant differences between the first infection and re-infection (Fig. 2E and 2G). While for the booster vaccinees, the mean ratios for BA.5 and BF.7 from the first infection were all below 1, and increased to above 1 during re-infection with statistical differences (p < 0.0001) (Fig. 2E and 2F). Although the mean ratios for the XBB.1.16 variant were all below 1, the ratio for the re-infection is significantly higher than the first infection (p = 0.037). Meanwhile, the ratios for BA.5 and XBB.1.16 variants were both significantly higher in the unvaccinated participants during the first infection and the re-infection (Fig. 2E and 2G). Moreover, vaccination reduced the percentages of samples with undetectable neutralizing activities (ID50 < 20) for the first infection, while the percentages of samples with high neutralizing activities (ID50 > 500) against BA.5, BF.7 and XBB.1.16 decreased with vaccination doses (Fig. 2H). For the re-infection, high and comparable percentages of samples from both unvaccinated participants and booster vaccinees showed high percentages of samples against BA.5 and BF.7 variants (Fig. 2I). However, significantly higher percentage of samples with high neutralizing activities against XBB.1.16 was found the unvaccinated participants (Fig. 2I).
Repeated Omicron infections drives broad neutralizing antibodies against other Omicron sub-variants
Next, we evaluated the neutralizing profiles of first infection and re-infection with XBB variants against other Omicron sub-variants, and the GMTs against XBB.1.16 were used as the reference. Firstly, the participants with first infection were analyzed (Fig. 3A-3D). For the naive infections (N = 15), about 80%, 66.7%, 53.3%, 73.3%, 46.7%, 53.3%, 40%, 46.7%, 53.3%, and 46.7% of the samples showed detectable ID50 against XBB.1.16, XBB.1.5, XBB.1.9, EG.5.1, BA.1, BA.2, BA.2.75.2, BA.4/5, BF.7, and BQ.1.1, with GMTs of 64.27, 83.95, 42.37, 63.02, 23.43, 27.29, 17.57, 29.51, 25.83 and 25.35, respectively (Fig. 3B). Except for the BA.1 and BA.2.75.2, no statistical differences were found between XBB.1.16 and the other sub-variants. For the participants with regular vaccination (N = 13), about 92.3%, 92.3%, 92.3%, 92.3%, 69.2%, 84.6%, 76.9%, 100%, 92.3%, and 92.3% of samples showed detectable ID50 against these ten sub-variants with GMTs of 117.07, 103.24, 112.2, 82.92, 51.38, 79.15, 73.61, 152.7, 114 and 108.49, respectively (Fig. 3B). For the participants with booster vaccination (N = 25), about 84%, 84%, 88%, 80%, 76%, 88%, 80%, 84%, 84%, and 88% of samples showed detectable ID50 against these ten sub-variants with GMTs of 63.5, 69.09, 66.56, 42.13, 62.23, 90.21, 64.51, 92.05, 58.57 and 72.65, respectively (Fig. 3C). No statistical differences were found between XBB.1.16 and the other sub-variants both in the participants with regular and booster vaccination.
Then, the participants with re-infection were analyzed (Fig. 3D-3F). For the unvaccinated participants with re-infection (N = 15), about 100%, 86.7%, 86.7%, 86.7%, 80%, 86.7%, 80%, 93.3%, 100%, and 100% of samples showed detectable ID50 against XBB.1.16, XBB.1.5, XBB.1.9, EG.5.1, BA.1, BA.2, BA.2.75.2, BA.4/5, BF.7, and BQ.1.1 with GMTs of 331.13, 431.19, 222.84, 180.65, 61.68, 159.96, 94.64, 275, 343.56 and 259.8, respectively (Fig. 3D). Statistical differences were found between BA.1, BA.2.75.2 and the XBB.1.16 variant, with reduction folds of 5.37 and 3.5, respectively. For the participants with booster vaccination (N = 33), about 100%, 100%, 100%, 100%, 93.9%, 97%, 97%, 100%, 100%, and 100% of samples showed detectable ID50 against these ten sub-variants with GMTs of 176.02, 218.98, 187.3, 134.06, 198.06, 292.65, 182.35, 438.04, 372.05 and 304, respectively (Fig. 3E). Statistical differences were found between BA.4/5, BF.7 and the XBB.1.16 variant, with increase folds of 2.49 and 2.11, respectively. The radar graph showed that first infection in regular vaccinees induced stronger neutralizing potency and neutralizing profiles, followed by the booster vaccinees and then the unvaccinated participants (Fig. 3F). Notably, re-infection drives much stronger neutralizing potency with broader neutralizing profiles both in the unvaccinated participants and the booster vaccinees. Moreover, the neutralizing profiles of the re-infection in booster vaccinees was prone to the XBB sub-variants and the more recently emerged sub-variants (Fig. 3F).