Human Nasal Epithelial Cells Sustain Persistent SARS-CoV-2 Infection In Vitro, despite Eliciting a Prolonged Antiviral Response
ABSTRACT The dynamics of SARS-CoV-2 infection in COVID-19 patients are highly variable, with a subset of patients demonstrating prolonged virus shedding, which poses a significant challenge for disease management and transmission control. In this study, the long-term dynamics of SARS-CoV-2 infection...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2022-02-01
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| Series: | mBio |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/mbio.03436-21 |
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| author | Akshamal M. Gamage Kai Sen Tan Wharton O. Y. Chan Zhe Zhang Ryan Lew Jing Liu Chee Wah Tan Deepa Rajagopalan Quy Xiao Xuan Lin Le Min Tan Prasanna Nori Venkatesh Yew Kwang Ong Mark Thong Raymond Tzer Pin Lin Shyam Prabhakar De Yun Wang Lin-Fa Wang |
| author_facet | Akshamal M. Gamage Kai Sen Tan Wharton O. Y. Chan Zhe Zhang Ryan Lew Jing Liu Chee Wah Tan Deepa Rajagopalan Quy Xiao Xuan Lin Le Min Tan Prasanna Nori Venkatesh Yew Kwang Ong Mark Thong Raymond Tzer Pin Lin Shyam Prabhakar De Yun Wang Lin-Fa Wang |
| author_sort | Akshamal M. Gamage |
| collection | DOAJ |
| description | ABSTRACT The dynamics of SARS-CoV-2 infection in COVID-19 patients are highly variable, with a subset of patients demonstrating prolonged virus shedding, which poses a significant challenge for disease management and transmission control. In this study, the long-term dynamics of SARS-CoV-2 infection were investigated using a human well-differentiated nasal epithelial cell (NEC) model of infection. NECs were observed to release SARS-CoV-2 virus onto the apical surface for up to 28 days postinfection (dpi), further corroborated by viral antigen staining. Single-cell transcriptome sequencing (sc-seq) was utilized to explore the host response from infected NECs after short-term (3-dpi) and long-term (28-dpi) infection. We identified a unique population of cells harboring high viral loads present at both 3 and 28 dpi, characterized by expression of cell stress-related genes DDIT3 and ATF3 and enriched for genes involved in tumor necrosis factor alpha (TNF-α) signaling and apoptosis. Remarkably, this sc-seq analysis revealed an antiviral gene signature within all NEC cell types even at 28 dpi. We demonstrate increased replication of basal cells, absence of widespread cell death within the epithelial monolayer, and the ability of SARS-CoV-2 to replicate despite a continuous interferon response as factors likely contributing to SARS-CoV-2 persistence. This study provides a model system for development of therapeutics aimed at improving viral clearance in immunocompromised patients and implies a crucial role for immune cells in mediating viral clearance from infected epithelia. IMPORTANCE Increasing medical attention has been drawn to the persistence of symptoms (long-COVID syndrome) or live virus shedding from subsets of COVID-19 patients weeks to months after the initial onset of symptoms. In vitro approaches to model viral or symptom persistence are needed to fully dissect the complex and likely varied mechanisms underlying these clinical observations. We show that in vitro differentiated human NECs are persistently infected with SARS-CoV-2 for up to 28 dpi. This viral replication occurred despite the presence of an antiviral gene signature across all NEC cell types even at 28 dpi. This indicates that epithelial cell intrinsic antiviral responses are insufficient for the clearance of SARS-CoV-2, implying an essential role for tissue-resident and infiltrating immune cells for eventual viral clearance from infected airway tissue in COVID-19 patients. |
| first_indexed | 2024-12-24T00:45:43Z |
| format | Article |
| id | doaj.art-90f0bab02d34444a9ecc6db6b4004829 |
| institution | Directory Open Access Journal |
| issn | 2150-7511 |
| language | English |
| last_indexed | 2024-12-24T00:45:43Z |
| publishDate | 2022-02-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mBio |
| spelling | doaj.art-90f0bab02d34444a9ecc6db6b40048292022-12-21T17:23:49ZengAmerican Society for MicrobiologymBio2150-75112022-02-0113110.1128/mbio.03436-21Human Nasal Epithelial Cells Sustain Persistent SARS-CoV-2 Infection In Vitro, despite Eliciting a Prolonged Antiviral ResponseAkshamal M. Gamage0Kai Sen Tan1Wharton O. Y. Chan2Zhe Zhang Ryan Lew3Jing Liu4Chee Wah Tan5Deepa Rajagopalan6Quy Xiao Xuan Lin7Le Min Tan8Prasanna Nori Venkatesh9Yew Kwang Ong10Mark Thong11Raymond Tzer Pin Lin12Shyam Prabhakar13De Yun Wang14Lin-Fa Wang15Programme in Emerging Infectious Diseases, Duke-NUS Medical School, SingaporeDepartment of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, SingaporeProgramme in Emerging Infectious Diseases, Duke-NUS Medical School, SingaporeDepartment of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, SingaporeDepartment of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, SingaporeProgramme in Emerging Infectious Diseases, Duke-NUS Medical School, SingaporeLaboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, SingaporeLaboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, SingaporeLaboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, SingaporeLaboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, SingaporeDepartment of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, SingaporeDepartment of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, SingaporeDepartment of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, SingaporeLaboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, SingaporeDepartment of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, SingaporeProgramme in Emerging Infectious Diseases, Duke-NUS Medical School, SingaporeABSTRACT The dynamics of SARS-CoV-2 infection in COVID-19 patients are highly variable, with a subset of patients demonstrating prolonged virus shedding, which poses a significant challenge for disease management and transmission control. In this study, the long-term dynamics of SARS-CoV-2 infection were investigated using a human well-differentiated nasal epithelial cell (NEC) model of infection. NECs were observed to release SARS-CoV-2 virus onto the apical surface for up to 28 days postinfection (dpi), further corroborated by viral antigen staining. Single-cell transcriptome sequencing (sc-seq) was utilized to explore the host response from infected NECs after short-term (3-dpi) and long-term (28-dpi) infection. We identified a unique population of cells harboring high viral loads present at both 3 and 28 dpi, characterized by expression of cell stress-related genes DDIT3 and ATF3 and enriched for genes involved in tumor necrosis factor alpha (TNF-α) signaling and apoptosis. Remarkably, this sc-seq analysis revealed an antiviral gene signature within all NEC cell types even at 28 dpi. We demonstrate increased replication of basal cells, absence of widespread cell death within the epithelial monolayer, and the ability of SARS-CoV-2 to replicate despite a continuous interferon response as factors likely contributing to SARS-CoV-2 persistence. This study provides a model system for development of therapeutics aimed at improving viral clearance in immunocompromised patients and implies a crucial role for immune cells in mediating viral clearance from infected epithelia. IMPORTANCE Increasing medical attention has been drawn to the persistence of symptoms (long-COVID syndrome) or live virus shedding from subsets of COVID-19 patients weeks to months after the initial onset of symptoms. In vitro approaches to model viral or symptom persistence are needed to fully dissect the complex and likely varied mechanisms underlying these clinical observations. We show that in vitro differentiated human NECs are persistently infected with SARS-CoV-2 for up to 28 dpi. This viral replication occurred despite the presence of an antiviral gene signature across all NEC cell types even at 28 dpi. This indicates that epithelial cell intrinsic antiviral responses are insufficient for the clearance of SARS-CoV-2, implying an essential role for tissue-resident and infiltrating immune cells for eventual viral clearance from infected airway tissue in COVID-19 patients.https://journals.asm.org/doi/10.1128/mbio.03436-21COVID-19nasal epithelial cellsSARS-CoV-2single-cell sequencingviral persistence |
| spellingShingle | Akshamal M. Gamage Kai Sen Tan Wharton O. Y. Chan Zhe Zhang Ryan Lew Jing Liu Chee Wah Tan Deepa Rajagopalan Quy Xiao Xuan Lin Le Min Tan Prasanna Nori Venkatesh Yew Kwang Ong Mark Thong Raymond Tzer Pin Lin Shyam Prabhakar De Yun Wang Lin-Fa Wang Human Nasal Epithelial Cells Sustain Persistent SARS-CoV-2 Infection In Vitro, despite Eliciting a Prolonged Antiviral Response mBio COVID-19 nasal epithelial cells SARS-CoV-2 single-cell sequencing viral persistence |
| title | Human Nasal Epithelial Cells Sustain Persistent SARS-CoV-2 Infection In Vitro, despite Eliciting a Prolonged Antiviral Response |
| title_full | Human Nasal Epithelial Cells Sustain Persistent SARS-CoV-2 Infection In Vitro, despite Eliciting a Prolonged Antiviral Response |
| title_fullStr | Human Nasal Epithelial Cells Sustain Persistent SARS-CoV-2 Infection In Vitro, despite Eliciting a Prolonged Antiviral Response |
| title_full_unstemmed | Human Nasal Epithelial Cells Sustain Persistent SARS-CoV-2 Infection In Vitro, despite Eliciting a Prolonged Antiviral Response |
| title_short | Human Nasal Epithelial Cells Sustain Persistent SARS-CoV-2 Infection In Vitro, despite Eliciting a Prolonged Antiviral Response |
| title_sort | human nasal epithelial cells sustain persistent sars cov 2 infection in vitro despite eliciting a prolonged antiviral response |
| topic | COVID-19 nasal epithelial cells SARS-CoV-2 single-cell sequencing viral persistence |
| url | https://journals.asm.org/doi/10.1128/mbio.03436-21 |
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