Understanding the underlying mechanisms of COVID-19 progression and the impact of various pharmaceutical interventions is crucial for the clinical management of the disease. We developed a comprehensive mathematical framework based on the known mechanisms of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, incorporating the renin−angiotensin system and ACE2, which the virus exploits for cellular entry, key elements of the innate and adaptive immune responses, the role of inflammatory cytokines, and the coagulation cascade for thrombus formation. The model predicts the evolution of viral load, immune cells, cytokines, thrombosis, and oxygen saturation based on patient baseline condition and the presence of comorbidities. Model predictions were validated with clinical data from healthy people and COVID-19 patients, and the results were used to gain insight into identified risk factors of disease progression including older age; comorbidities such as obesity, diabetes, and hypertension; and dysregulated immune response. We then simulated treatment with various drug classes to identify optimal therapeutic protocols. We found that the outcome of any treatment depends on the sustained response rate of activated CD8
+ T cells and sufficient control of the innate immune response. Furthermore, the best treatment—or combination of treatments—depends on the preinfection health status of the patient. Our mathematical framework provides important insight into SARS-CoV-2 pathogenesis and could be used as the basis for personalized, optimal management of COVID-19.COVID-19 has created unprecedented challenges for the health care system, and, until an effective vaccine is developed and made widely available, treatment options are limited. A challenge to the development of optimal treatment strategies is the extreme heterogeneity of presentation. Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) results in a syndrome that ranges in severity from asymptomatic to multiorgan failure and death. In addition to local complications in the lung, the virus can cause systemic inflammation and disseminated microthrombosis, which can cause stroke, myocardial infarction, or pulmonary emboli (
1–
4). Risk factors for poor COVID-19 outcome include advanced age, obesity, diabetes, and hypertension (
5–
13).Computational analyses can provide insights into the transmission, control, progression, and underlying mechanisms of infectious diseases. Indeed, epidemiological and statistical modeling has been used for COVID-19, providing powerful insights into comorbidities, transmission dynamics, and control of the disease (
14–
17). However, to date, these analyses have been population dynamics models of SARS-CoV-2 infection and transmission or correlative analyses of COVID-19 comorbidities and treatment response. Simple viral dynamics models have been also developed and used to predict the SARS-CoV-2 response to antiviral drugs (
18,
19). These models, however, do not explicitly consider the biological or physiological mechanisms underlying disease progression or the time course of response to various therapeutic interventions, and only a few more-sophisticated models have been developed toward this direction (
20,
21).Several therapies targeting various aspects of COVID-19 pathogenesis have been proposed and have either completed—or are currently being tested in—clinical trials (
22). Despite strong biologic rationale, these treatments have generally produced conflicting results in the clinic. For example, trials of antiviral therapies (e.g., remdesivir) have been mixed: The original trial from China failed (
23), a subsequent trial in the United States led to approval of remdesivir in the United States and other countries (
24), and the recent results of the World Health Organization Solidarity trial again show no benefit (
25). Other antiviral drugs alone or in combination are also showing promise (
26).Other potential treatments include antiinflammatory drugs and antithrombotic agents. Because of the systemic inflammation seen in many patients, antiinflammatory drugs have been tested, including anti-IL6/IL6R therapy (e.g., tocilizumab, siltuximab) and anti-JAK1/2 drugs (e.g., barcitinib). It is not clear whether these drugs will be effective as stand-alone treatments, particularly after the recent failure of tocilizumab in a phase III trial (
1,
27–
29). In addition, given that a common complication of COVID-19 is the development of coagulopathies with microvascular thrombi potentially leading to the dysfunction of multiple organ systems (
2,
3), antithrombotic drugs (e.g., low molecular weight heparin) are being tested. Recognizing the interactions of COVID-19 with the immune system (
30), the corticosteroid dexamethasone has been tested, showing some promising results. Given the large range of patient comorbidities, disease severities, and variety of complications such as thrombosis, it is likely that patients will have heterogeneous responses to any given therapy, and such heterogeneity will continue to be a challenge for clinical trials of unselected COVID-19 patients (
31).Here, we developed a systems biology-based mathematical model to address this urgent need. Our model incorporates the known mechanisms of SARS-CoV-2 pathogenesis and the potential mechanisms of action of various therapeutic interventions that have been tested in COVID-19 patients. In previous work, we have exploited angiotensin receptor blockers (ARBs) and angiotensin converting enzyme inhibitors (ACEis) for the improvement of cancer therapies and developed mathematical models of the renin−angiotensin system in the context of cancer desmoplasia (
32–
35). Using a similar approach, we developed a detailed model that includes lung infection by the SARS-CoV-2 virus and a pharmacokinetic/pharmacodynamic (PK/PD) model of infection and thrombosis to simulate events that take place throughout the body during COVID-19 progression ( and
SI Appendix, Fig. S1). The model is first validated against clinical data of healthy people and COVID-19 patients and then used to simulate disease progression in patients with specific comorbidities. Subsequently, we present model predictions for various therapies currently employed for treatment of COVID-19 alone or in combination, and we identify protocols for optimal clinical management for each of the clinically observed COVID-19 phenotypes.
Open in a separate windowSchematic of the detailed lung model. The model incorporates the virus infection of epithelial and endothelial cells, the RAS, T cells activation and immune checkpoints, the known IL6 pathways, neutrophils, and macrophages, as well as the formation of NETs, and the coagulation cascade. The lung model is coupled with a PK/PD model for the virus and thrombi dissemination through the body.
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