Host–Virus Interface in Persistent SARS-CoV-2 Infections: Viral Characteristic Evolution and Gene Expression Profiling Analysis
Abstract
1. Introduction
2. Results
2.1. Clinical Patient Data and the Characteristics of SARS-CoV-2 Isolates
2.2. Dynamic Changes in Infectivity Across Persistent COVID-19 Infection
2.3. Comparison of Inflammatory Gene Expression Patterns in Host Cells
2.4. Gene Ontology (GO) Enrichment Analysis of DEGs
2.5. Gene Expression Profiling of Human Host Cell Response
2.6. Distinct Genomic Analysis Between Early-Phase and Late-Phase Infection
3. Discussion
4. Materials and Methods
4.1. Clinical Sample Collection
4.2. SARS-CoV-2 Isolates Using VERO-E6/TMPRSS2 Cells
4.3. Calu-3 Human Airway Epithelial Cell Infection
4.4. Assessment of Viral Growth Kinetics
4.5. RNA Extraction and Viral Quantification qPCR
4.6. Viral Infectivity Assessment
4.7. Gene Expression Assay Using Quantitative Real-Time PCR
4.8. Next-Generation Sequencing
4.9. Genomic Sequencing Analysis
4.10. RNA Sequencing
4.11. RNA-Sequencing Analysis
4.12. Gene Ontology (GO) Enrichment Analysis
4.13. Statistical Analysis
4.14. Generative AI Disclosure
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Patient ID | Age/Gender | Duration of Infection | Comorbidities | Symptoms | Vaccination Status | Immuno-Suppressive Medication | Complication | ICU (Yes/No) | Treatment Drug (D/R/M) * | Outcome |
---|---|---|---|---|---|---|---|---|---|---|
Patient 1 | 79/M | 57 Days | Esophageal cancer, rheumatoid arthritis, pneumonia | Fever | No | - | Pneumonia. ARDS | No | D, R (total 12 days) | Discharged (transferred to previous hospital for rehab) |
Patient 2 | 37/F | 37 Days | Pregnancy | Fever, cough, nausea | Vaccinated 2x | - | - | No | No | Discharged |
Patient 3 | 66/F | 46 Days | Lung transplant, pneumonia, CKD, Bowen’s disease | Fever, sore throat | No | Prednisolone, mycophenolate mofetil | pneumonia | No | M (total 5 days) | Discharged |
Patient 4 | 76/M | 58 Days | Lung cancer, hypertension | Fever | Unknown | - | - | No | R (total 5 days) | Discharged |
No. | Gene Region | Protein | Nucleotide | Type | Change | ||
---|---|---|---|---|---|---|---|
Start | End | Reference | Alternate | ||||
1 | ORF1ab | Nsp2 | 465 | 465 | SNP | C | T |
2 | Nsp2 | 515 | 518 | DEL | GTTA | G | |
3 | Nsp3 | 2485 | 2485 | SNP | C | T | |
4 | Nsp12 | 10,401 | 10,401 | SNP | C | T | |
5 | Nsp13 | 10,936 | 10,936 | SNP | T | G | |
6 | Nsp13 | 11,414 | 11,414 | SNP | C | T | |
7 | Nsp13 | 11,750 | 11,750 | SNP | C | T | |
8 | Nsp14 | 15,526 | 15,526 | SNP | A | G | |
9 | Nsp15 | 16,178 | 16,178 | SNP | C | T | |
10 | Nsp16 | 17,762 | 17,762 | SNP | C | T | |
11 | Nsp16 | 17,766 | 17,766 | SNP | C | T | |
12 | Nsp16 | 17,977 | 17,977 | SNP | C | T | |
13 | Nsp16 | 19,380 | 19,380 | SNP | C | T | |
14 | Nsp16 | 19,824 | 19,824 | SNP | G | A | |
15 | S | Spike | 21,986 | 21,995 | DEL | GGTGTTTATT | G |
16 | Spike | 21,987 | 21,987 | SNP | G | A | |
17 | Spike | 22,498 | 22,498 | SNP | C | T | |
18 | Spike | 23,804 | 23,804 | SNP | G | A | |
19 | Spike | 24,062 | 24,062 | SNP | A | T | |
20 | Spike | 24,452 | 24,452 | SNP | A | G | |
21 | ORF3a | Ap3a | 25,677 | 25,677 | SNP | G | T |
22 | Ap3a | 25,998 | 25,998 | SNP | A | G | |
23 | ORF7a | Ap7a | 27,505 | 27,510 | DEL | GGAACA | G |
24 | Ap7a | 27,524 | 27,524 | SNP | C | T | |
25 | ORF7b | Ap7b | 27,794 | 27,797 | DEL | TTTA | T |
26 | ORF8 | Ap8 | 28,077 | 28,077 | SNP | G | T |
27 | N | Nucleoprotein | 28,539 | 28,539 | SNP | G | T |
Name | Sequence (5′-3′) |
---|---|
2019 nCoV N F2 primer | AAATTTTGGGGACCAGGAAC |
2019 nCoV N R2 primer | TGGCAGCTGTGTAGGTCAAC |
2019 nCoV N P2 probe | FAM-ATGTCGCGCATTGGCATGGA-QSY |
Gene Expression | Primer Sequence Number | Base Pairs |
---|---|---|
ATF4 | Hs00909569_g1 | 68 |
TMPRSS2 | Hs01122322_m1 | 62 |
ACE2 | Hs01085333_m1 | 141 |
DDX58 | Hs01061436_m1 | 65 |
IFNB1 | Hs01077958_s1 | 73 |
IFNAR2 | Hs01022059_m1 | 88 |
IL6 | Hs00174131_m1 | 95 |
IL1B | Hs01555410_m1 | 91 |
TNF | Hs00174128_m1 | 80 |
ULBP2 | Hs01127964_m1 | 93 |
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Maarif, A.S.; Nishikawa, Y.; Takata, M.; Kanai, K.; Riyandani, E.; Mukuda, K.; Mimura, M.; Yamaguchi, K.; Kato, H.; Okamoto, R.; et al. Host–Virus Interface in Persistent SARS-CoV-2 Infections: Viral Characteristic Evolution and Gene Expression Profiling Analysis. Int. J. Mol. Sci. 2025, 26, 6221. https://doi.org/10.3390/ijms26136221
Maarif AS, Nishikawa Y, Takata M, Kanai K, Riyandani E, Mukuda K, Mimura M, Yamaguchi K, Kato H, Okamoto R, et al. Host–Virus Interface in Persistent SARS-CoV-2 Infections: Viral Characteristic Evolution and Gene Expression Profiling Analysis. International Journal of Molecular Sciences. 2025; 26(13):6221. https://doi.org/10.3390/ijms26136221
Chicago/Turabian StyleMaarif, Athok Shofiudin, Yukari Nishikawa, Miyako Takata, Kyosuke Kanai, Edo Riyandani, Kengo Mukuda, Momone Mimura, Kosuke Yamaguchi, Hiroyuki Kato, Ryo Okamoto, and et al. 2025. "Host–Virus Interface in Persistent SARS-CoV-2 Infections: Viral Characteristic Evolution and Gene Expression Profiling Analysis" International Journal of Molecular Sciences 26, no. 13: 6221. https://doi.org/10.3390/ijms26136221
APA StyleMaarif, A. S., Nishikawa, Y., Takata, M., Kanai, K., Riyandani, E., Mukuda, K., Mimura, M., Yamaguchi, K., Kato, H., Okamoto, R., Okada, K., Kitaura, T., Nakamoto, M., Yamasaki, A., Kageyama, S., & Chikumi, H. (2025). Host–Virus Interface in Persistent SARS-CoV-2 Infections: Viral Characteristic Evolution and Gene Expression Profiling Analysis. International Journal of Molecular Sciences, 26(13), 6221. https://doi.org/10.3390/ijms26136221