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Zhou K, Sun Y, Li L, Zang Z, Wang J, Li J, Liang J, Zhang F, Zhang Q, Ge W, Chen H, Sun X, Yue L, Wu X, Shen B, Xu J, Zhu H, Chen S, Yang H, Huang S, Peng M, Lv D, Zhang C, Zhao H, Hong L, Zhou Z, Chen H, Dong X, Tu C, Li M, Zhu Y, Chen B, Li SZ, Guo T. Eleven routine clinical features predict COVID-19 severity uncovered by machine learning of longitudinal measurements. Comput Struct Biotechnol J 2021; 19:3640-3649. [PMID: 34188785 PMCID: PMC8225590 DOI: 10.1016/j.csbj.2021.06.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 01/08/2023] Open
Abstract
Severity prediction of COVID-19 remains one of the major clinical challenges for the ongoing pandemic. Here, we have recruited a 144 COVID-19 patient cohort, resulting in a data matrix containing 3,065 readings for 124 types of measurements over 52 days. A machine learning model was established to predict the disease progression based on the cohort consisting of training, validation, and internal test sets. A panel of eleven routine clinical factors constructed a classifier for COVID-19 severity prediction, achieving accuracy of over 98% in the discovery set. Validation of the model in an independent cohort containing 25 patients achieved accuracy of 80%. The overall sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were 0.70, 0.99, 0.93, and 0.93, respectively. Our model captured predictive dynamics of lactate dehydrogenase (LDH) and creatine kinase (CK) while their levels were in the normal range. This model is accessible at https://www.guomics.com/covidAI/ for research purpose.
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Key Words
- ABG, arterial blood gas
- APTT, activated partial thromboplastin time
- AST, aspartate aminotransferase
- AUC, area under the curve
- BASO#, basophil counts
- CFDA, China Food and Drug Administration
- CK, creatine kinase
- COVID-19
- CRP, C-reactive protein
- CT, computed tomography
- ESR, erythrocyte sedimentation rate
- GA, genetic algorithm
- GGT, gamma glutamyl transpeptidase
- HIS, hospital information system
- LAC, lactate
- LDH, lactate dehydrogenase
- LOESS, locally estimated scatterplot smoothing
- LOS, length of stay
- Longitudinal dynamics
- Machine learning
- Mg, magnesium
- NETs, neutrophil extracellular traps
- NPV, negative predictive value
- PCT, procalcitonin
- PPV, positive predictive value
- ROC, receiver operating characteristics
- RT-PCR, reverse transcriptase -polymerase chain reaction
- Routine clinical test
- SARS-CoV-2
- SHAP, SHapley Additive exPlanations
- SVM, support vector machine
- SaO2, oxygen saturation
- Severity prediction
- TT, thrombin time
- eGFR, estimated glomerular filtration rate
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Affiliation(s)
- Kai Zhou
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
| | - Yaoting Sun
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang Province, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China
| | - Lu Li
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang Province, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China
| | - Zelin Zang
- School of Engineering, Westlake University, Hangzhou 310024, Zhejiang Province, China
| | - Jing Wang
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
| | - Jun Li
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
| | - Junbo Liang
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
| | - Fangfei Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang Province, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China
| | - Qiushi Zhang
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., Hangzhou 310024, Zhejiang Province, China
| | - Weigang Ge
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., Hangzhou 310024, Zhejiang Province, China
| | - Hao Chen
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., Hangzhou 310024, Zhejiang Province, China
| | - Xindong Sun
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang Province, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China
| | - Liang Yue
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang Province, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China
| | - Xiaomai Wu
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
| | - Bo Shen
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
| | - Jiaqin Xu
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
| | - Hongguo Zhu
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
| | - Shiyong Chen
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
| | - Hai Yang
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
| | - Shigao Huang
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, 999078 Macau SAR, China
| | - Minfei Peng
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
| | - Dongqing Lv
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
| | - Chao Zhang
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
| | - Haihong Zhao
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
| | - Luxiao Hong
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
| | - Zhehan Zhou
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
| | - Haixiao Chen
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
| | - Xuejun Dong
- Shaoxing People's Hospital, Shaoxing Hospital, Zhejiang University School of Medicine, Shaoxing 312000, Zhejiang Province, China
| | - Chunyu Tu
- Shaoxing People's Hospital, Shaoxing Hospital, Zhejiang University School of Medicine, Shaoxing 312000, Zhejiang Province, China
| | - Minghui Li
- Shaoxing People's Hospital, Shaoxing Hospital, Zhejiang University School of Medicine, Shaoxing 312000, Zhejiang Province, China
| | - Yi Zhu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang Province, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China
| | - Baofu Chen
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
| | - Stan Z. Li
- School of Engineering, Westlake University, Hangzhou 310024, Zhejiang Province, China
| | - Tiannan Guo
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang Province, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China
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