# Ordinary differential equation models of SARS-CoV-2 replication dynamics and antiviral drug efficacies

**Authors:** Timon Kapischke, Simon T. Herrmann, Luca D. Bertzbach, Stephanie Pfaender, Lars Kaderali

PMC · DOI: 10.1038/s44298-026-00183-8 · npj Viruses · 2026-03-13

## TL;DR

This paper reviews mathematical models of SARS-CoV-2 replication and antiviral effects to better understand virus-host interactions and improve treatment strategies.

## Contribution

The paper provides a systematic review of ODE models for SARS-CoV-2, highlighting model limitations and data gaps.

## Key findings

- TCL ODE models offer insights into SARS-CoV-2 replication dynamics.
- Incorporating antiviral treatments into models reveals drug efficacy patterns.
- Structural identifiability issues and limited datasets hinder model accuracy.

## Abstract

There is a critical need for precise analysis of virus–host interactions to improve our understanding of infection processes. The integration of quantitative measurements with dynamic mathematical modeling has changed how we perceive cellular infection processes, offering profound insights into how viruses function at the cellular level. Here, we systematically review target cell-limited (TCL) ordinary differential equation (ODE) models related to SARS-CoV-2. We examine the spectrum of available models from basic TCL frameworks to more complex models incorporating antiviral treatments—and highlight key findings, discuss strengths and limitations, and identify a shortage of comprehensive datasets, emphasizing structural identifiability issues.

## Linked entities

- **Diseases:** SARS-CoV-2 (MONDO:0100096)

## Full-text entities

- **Genes:** RHOJ (ras homolog family member J) [NCBI Gene 57381] {aka ARHJ, RASL7B, TC10B, TCL}, IFNA1 (interferon alpha 1) [NCBI Gene 3439] {aka IFL, IFN, IFN-ALPHA, IFN-alphaD, IFNA13, IFNA@}, S (surface glycoprotein) [NCBI Gene 43740568] {aka spike glycoprotein}, GZMB (granzyme B) [NCBI Gene 3002] {aka C11, CCPI, CGL-1, CGL1, CSP-B, CSPB}, ACE2 (angiotensin converting enzyme 2) [NCBI Gene 59272] {aka ACEH}, IFI27 (interferon alpha inducible protein 27) [NCBI Gene 3429] {aka FAM14D, ISG12, ISG12A, P27}, CD8A (CD8 subunit alpha) [NCBI Gene 925] {aka CD8, CD8alpha, IMD116, Leu2, p32}, IL6 (interleukin 6) [NCBI Gene 3569] {aka BSF-2, BSF2, CDF, HGF, HSF, IFN-beta-2}, CD4 (CD4 molecule) [NCBI Gene 920] {aka CD4mut, IMD79, Leu-3, OKT4D, T4}, IL2 (interleukin 2) [NCBI Gene 3558] {aka IL-2, TCGF, lymphokine}, TMPRSS2 (transmembrane serine protease 2) [NCBI Gene 7113] {aka PRSS10}
- **Diseases:** tissue damage (MESH:D017695), immune dysregulation (OMIM:614878), long COVID (MESH:D000094024), influenza (MESH:D007251), COVID-19 (MESH:D000086382), Coinfection (MESH:D060085), inflammatory (MESH:D007249), delta infections (MESH:D003699), infected (MESH:D007239), disease (MESH:D004194), death (MESH:D003643), ODE (MESH:D012734), lung disease (MESH:D008171), CRS (MESH:D000080424)
- **Chemicals:** remdesivir (MESH:C000606551), selinexor (MESH:C585161), BAM (MESH:C000711749)
- **Species:** Candidatus Accumulibacter adiacens (species) [taxon 2954378], Influenza A virus (no rank) [taxon 11320], Cricetinae (hamsters, subfamily) [taxon 10026], Human immunodeficiency virus (species) [taxon 12721], Mus musculus (house mouse, species) [taxon 10090], Human immunodeficiency virus 1 (no rank) [taxon 11676], Severe acute respiratory syndrome coronavirus 2 (no rank) [taxon 2697049], Homo sapiens (human, species) [taxon 9606], Mustela putorius furo (black ferret, subspecies) [taxon 9669], Severe acute respiratory syndrome-related coronavirus (no rank) [taxon 694009], Macaca mulatta (rhesus macaque, species) [taxon 9544], Human coronavirus 229E (no rank) [taxon 11137], Middle East respiratory syndrome-related coronavirus (no rank) [taxon 1335626]
- **Cell lines:** BHK-21 — Mesocricetus auratus (Golden hamster), Spontaneously immortalized cell line (CVCL_RQ70), Caco-2 — Homo sapiens (Human), Colon adenocarcinoma, Cancer cell line (CVCL_0025), A549-ACE2 — Homo sapiens (Human), Lung adenocarcinoma, Cancer cell line (CVCL_C0Q5), Calu-3 — Homo sapiens (Human), Lung adenocarcinoma, Cancer cell line (CVCL_0609), Vero E6 — Chlorocebus sabaeus (Green monkey), Spontaneously immortalized cell line (CVCL_0574), Caco-3 — Homo sapiens (Human), Colon carcinoma, Cancer cell line (CVCL_QW78), 293T — Homo sapiens (Human), Transformed cell line (CVCL_0063)

## Full text

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## Figures

2 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12988066/full.md

## References

25 references — full list in the complete paper: https://tomesphere.com/paper/PMC12988066/full.md

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Source: https://tomesphere.com/paper/PMC12988066