| Literature DB >> 35811681 |
Tianbin Chen1,2, Yongbin Zeng1,2, Di Yang3, Wenjing Ye4, Jiawei Zhang1,2, Caorui Lin1,2, Yihao Huang3, Yucheng Ye1,2, Jianwen Li3, Qishui Ou1,2, Jinming Li5, Can Liu1,2.
Abstract
SARS-CoV-2 breakthrough infections have been reported because of the reduced efficacy of vaccines against the emerging variants globally. However, an accurate model to predict SARS-CoV-2 breakthrough infection is still lacking. In this retrospective study, 6,189 vaccinated individuals, consisting of SARS-CoV-2 test-positive cases (n = 219) and test-negative controls (n = 5970) during the outbreak of the Delta variant in September 2021 in Xiamen and Putian cities, Fujian province of China, were included. The vaccinated individuals were randomly split into a training (70%) cohort and a validation (30%) cohort. In the training cohort, a visualized nomogram was built based on the stepwise multivariate logistic regression. The area under the curve (AUC) of the nomogram in the training and validation cohorts was 0.819 (95% CI, 0.780-0.858) and 0.838 (95% CI, 0.778-0.897). The calibration curves for the probability of SARS-CoV-2 breakthrough infection showed optimal agreement between prediction by nomogram and actual observation. Decision curves indicated that nomogram conferred high clinical net benefit. In conclusion, a nomogram model for predicting SARS-CoV-2 breakthrough infection based on the real-world setting was successfully constructed, which will be helpful in the management of SARS-CoV-2 breakthrough infection.Entities:
Keywords: SARS-CoV-2 breakthrough infection; model; nomogram; prediction; vaccinated individuals
Mesh:
Year: 2022 PMID: 35811681 PMCID: PMC9259977 DOI: 10.3389/fcimb.2022.932204
Source DB: PubMed Journal: Front Cell Infect Microbiol ISSN: 2235-2988 Impact factor: 6.073
Figure 1Flowchart of selection of study participants.
Characteristics of vaccinated individuals with or without SARS-CoV-2 breakthrough infection.
| Non-breakthrough infection | Breakthrough infection |
| |
|---|---|---|---|
| n = 5,970 | n = 219 | ||
| Age (years, %) | <0.001 | ||
| <20 | 839 (14.1) | 15 (6.8) | |
| 20–30 | 1,124 (18.8) | 18 (8.2) | |
| 30–40 | 1,743 (29.2) | 71 (32.4) | |
| 40–50 | 1,204 (20.2) | 68 (31.1) | |
| 50–60 | 770 (12.9) | 33 (15.1) | |
| >60 | 290 (4.9) | 14 (6.4) | |
| Sex (%) | 0.017 | ||
| Female | 3,039 (50.9) | 130 (59.4) | |
| Male | 2,931 (49.1) | 89 (40.6) | |
| Vaccine situation (%) | 0.458 | ||
| Partially vaccinated | 705 (11.8) | 30 (13.7) | |
| Fully vaccinated | 5,265 (88.2) | 189 (86.3) | |
| First dose brand (%) | 0.014 | ||
| Sinovac | 3,082 (51.6) | 132 (60.3) | |
| Sinopharm | 2,888 (48.4) | 87 (39.7) | |
| Second dose brand (%) | 0.009 | ||
| Sinopharm | 2,494 (41.8) | 71 (32.4) | |
| Sinovac | 3,137 (52.5) | 129 (58.9) | |
| Unvaccinated | 339 (5.7) | 19 (8.7) | |
| First dose time (days, %) | <0.001 | ||
| <60 | 1,854 (31.1) | 62 (28.3) | |
| 60–120 | 2,586 (43.3) | 122 (55.7) | |
| >120 | 1,530 (25.6) | 35 (16.0) | |
| Second dose time (days, %) | <0.001 | ||
| <60 | 3,105 (52.0) | 97 (44.3) | |
| 60–120 | 1,883 (31.5) | 109 (49.8) | |
| >120 | 982 (16.4) | 13 (5.9) | |
| IC age (years, %) | <0.001 | ||
| <20 | 1,057 (17.7) | 36 (16.4) | |
| 20–30 | 347 (5.8) | 6 (2.7) | |
| 30–40 | 1,686 (28.2) | 123 (56.2) | |
| 40–50 | 2,301 (38.5) | 36 (16.4) | |
| 50–60 | 398 (6.7) | 8 (3.7) | |
| >60 | 181 (3.0) | 10 (4.6) | |
| IC sex (%) | 0.769 | ||
| Female | 3,318 (55.6) | 119 (54.3) | |
| Male | 2,652 (44.4) | 100 (45.7) | 0.769 |
| IC vaccine situation (%) | 0.767 | ||
| Partially vaccinated | 365 (6.1) | 16 (7.3) | |
| Fully vaccinated | 4,325 (72.4) | 156 (71.2) | |
| Unvaccinated | 1,280 (21.4) | 47 (21.5) | |
| IC first dose brand (%) | <0.001 | ||
| Sinopharm | 2,143 (35.9) | 128 (58.4) | |
| Sinovac | 2,956 (49.5) | 47 (21.5) | |
| Unvaccinated | 871 (14.6) | 44 (20.1) | |
| IC second dose brand (%) | <0.001 | ||
| Sinopharm | 2,042 (34.2) | 26 (11.9) | |
| Sinovac | 2,438 (40.8) | 139 (63.5) | |
| Unvaccinated | 1,490 (25.0) | 54 (24.7) | |
| IC first dose time (days, %) | <0.001 | ||
| <60 | 2,090 (35.0) | 71 (32.4) | |
| 60–120 | 2,063 (34.6) | 132 (60.3) | |
| >120 | 1,817 (30.4) | 16 (7.3) | |
| IC second dose time (days, %) | <0.001 | ||
| <60 | 2,850 (47.7) | 133 (60.7) | |
| 60–120 | 1,980 (33.2) | 82 (37.4) | |
| >120 | 1,140 (19.1) | 4 (1.8) | |
| IC ORF1ab gene (Ct values) | 24.24 (6.42) | 21.54 (6.02) | <0.001 |
| IC N gene (Ct values) | 23.19 (6.56) | 21.78 (5.59) | 0.002 |
IC, index cases of vaccinated individuals.
Univariate and multivariate logistic regression analyses of SARS-CoV-2 breakthrough infection in vaccinated individuals.
| Variable | Univariate analysis | Multivariate analysis | ||
|---|---|---|---|---|
| OR (95% CI) |
| OR (95% CI) |
| |
| Sex | ||||
| Male | Reference | |||
| Female | 1.709 (1.227–2.38) | 0.002 | 1.500 (1.042–2.161) | 0.029 |
| Age (years) | ||||
| <20 | Reference | |||
| 20–30 | 0.88 (0.378–2.05) | 0.767 | ||
| 30–40 | 2.499 (1.261–4.952) | 0.009 | ||
| 40–50 | 3.296 (1.654–6.567) | 0.001 | ||
| 50–60 | 2.674 (1.273–5.619) | 0.009 | ||
| 60–100 | 2.747 (1.1–6.86) | 0.03 | ||
| First dose brand | ||||
| Sinopharm | Reference | |||
| Sinovac | 1.462 (1.054–2.028) | 0.023 | ||
| First dose time (days) | ||||
| <60 | Reference | |||
| 60–120 | 1.883 (1.279–2.773) | 0.001 | ||
| >120 | 0.844 (0.505–1.412) | 0.519 | ||
| Second dose brand | ||||
| Unvaccinated | Reference | |||
| Sinopharm | 0.533 (0.286–0.994) | 0.048 | 0.403 (0.193–0.839) | 0.015 |
| Sinovac | 0.722 (0.397–1.311) | 0.284 | 0.336 (0.163–0.693) | 0.003 |
| Second dose time (days) | ||||
| <60 | Reference | |||
| 60–120 | 2.127 (1.523–2.97) | <0.001 | 1.846 (1.235–2.758) | 0.003 |
| >120 | 0.489 (0.25–0.958) | 0.037 | 0.979 (0.455–2.107) | 0.957 |
| IC sex | ||||
| Male | Reference | |||
| Female | 1.006 (0.729–1.388) | 0.972 | ||
| IC age (years) | ||||
| <20 | Reference | |||
| 20–30 | 0.749 (0.303–1.854) | 0.532 | 2.184 (0.764–6.245) | 0.145 |
| 30–40 | 2.363 (1.492–3.741) | <0.001 | 3.170 (1.653–6.078) | 0.001 |
| 40–50 | 0.494 (0.282–0.867) | 0.014 | 0.899 (0.427–1.892) | 0.779 |
| 50–60 | 0.413 (0.142–1.201) | 0.105 | 0.909 (0.285–2.897) | 0.872 |
| 60–100 | 1.445 (0.579–3.605) | 0.43 | 1.732 (0.616–4.871) | 0.298 |
| IC first dose brand | ||||
| Unvaccinated | Reference | |||
| Sinopharm | 1.414 (0.913–2.19) | 0.12 | 0.645 (0.24–1.736) | 0.385 |
| Sinovac | 0.356 (0.212–0.597) | <0.001 | 0.105 (0.042–0.259) | <0.001 |
| IC first dose time (days) | ||||
| <60 | Reference | |||
| 60–120 | 1.893 (1.333–2.688) | <0.001 | 3.634 (1.809–7.301) | <0.001 |
| >120 | 0.272 (0.144–0.513) | <0.001 | 0.786 (0.275–2.245) | 0.653 |
| IC second dose brand | ||||
| Unvaccinated | Reference | |||
| Sinopharm | 0.398 (0.227–0.7) | 0.001 | 0.826 (0.292–2.341) | 0.720 |
| Sinovac | 1.763 (1.192–2.608) | 0.005 | 3.208 (1.228–8.383) | 0.017 |
| IC second dose time (days) | ||||
| <60 | Reference | |||
| 60–120 | 0.843 (0.603–1.179) | 0.319 | 0.302 (0.177–0.516) | <0.001 |
| >120 | 0.078 (0.025–0.248) | <0.001 | 0.140 (0.030–0.649) | 0.012 |
| IC ORF1ab gene (Ct values) | 0.931 (0.907–0.956) | <0.001 | 0.941 (0.911–0.972) | <0.001 |
IC, index case of vaccinated individuals; Reference, the reference group in the univariate or multivariable logistic regression models.
Figure 2A predictive nomogram model for SARS-CoV-2 breakthrough infection established by independently associated risk factors from multivariate logistic regression. IC, index case of vaccinated individuals.
The performance of the nomogram for predicting SARS-CoV-2 breakthrough infection in vaccinated individuals.
| Index | Training cohort | Validation cohort |
|---|---|---|
| (n = 4,332) | (n = 1,857) | |
| AUC (95% CI) | 0.819 (0.780–0.858) | 0.838 (0.778–0.897) |
| Sensitivity | 0.801 | 0.794 |
| Specificity | 0.712 | 0.792 |
| Positive predictive value | 0.094 | 0.118 |
| Negative predictive value | 0.989 | 0.990 |
| Recall | 0.801 | 0.794 |
| Accuracy | 0.715 | 0.792 |
AUC, area under the curve.
Figure 3ROC curves of the nomogram for predicting SARS-CoV-2 breakthrough infection among vaccinated individuals in training cohort (AUC, 0.819; 95% CI, 0.780–0.858; sensitivity, 0.712; and specificity, 0.801 at the optimal cutoff of 0.027) and validation cohort (AUC, 0.838; 95% CI, 0.778–0.897; sensitivity, 0.792; and specificity, 0.794 at the optimal cutoff of 0.041). AUC, the area under the receiver operating characteristic (ROC) curve.
Figure 4The calibration plot of the nomogram in the training (A) and validation cohorts (B). Actual rate of SARS-CoV-2 breakthrough infection is shown on the y-axis, and the nomogram-predicted probability of SARS-CoV-2 breakthrough infection is shown on the x-axis. Decision curve compared the net clinical benefits of three scenarios in predicting the SARS-CoV-2 breakthrough infection probability: a perfect prediction model (gray line), no screen (horizontal solid black line), and screen based on the nomogram (red or blue line) in training cohort (C) and validation cohort (D).