SARS-CoV-2 defective viral genomes from distinct genomic regions drive divergent interferon responses
5 affiliations
- 1Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
- 2Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- 3Division of Allergy, Immunology, and Rheumatology (AIR), Department of Medicine, University of Rochester Medical Center, Rochester, New York, United States of America
- 4Department of Pediatrics and Center for Children’s Health Research, University of Rochester Medical Center, Rochester, New York, United States of America
- 5Departments of Pediatrics and Environmental Medicine, University of Rochester Medical Center, Rochester, New York, United States of America
Abstract
Defective viral genomes (DVGs) are generated during the genomic replication of many RNA viruses. When produced early in infection or supplemented at the onset of infection, DVGs can attenuate viral pathogenesis by stimulating interferon responses and antagonizing wild type (WT) virus replication, highlighting their potential as antiviral therapeutics. However, during natural infection DVGs can exert both antiviral and proviral effects depending on their generation kinetics, species, and abundance, underscoring the need to better understand their roles in viral pathogenesis. Coronaviruses (CoVs) are RNA viruses that ubiquitously generate DVGs, yet the roles of DVGs during CoV infection are largely unknown. In a previous study we investigated SARS-CoV-2 DVG presence in vitro and in patient samples and discovered two major genomic hotspots (A and B) for their generation. Here, we first showed that overall DVG abundance tended to positively correlate with COVID-19 severity, with approximately 40% of DVGs originating from a specific genomic region designated hotspot B. Analysis of a publicly available single-cell RNA-seq dataset revealed that DVGs from hotspot B, but not hotspot A, were associated with elevated interferon responses, suggesting that DVGs derived from different genomic regions vary in their ability to stimulate innate immunity. To test this directly, we constructed two representative DVGs corresponding to hotspots A and B. Both DVGs suppressed the replication of co-infecting WT virus; however, only DVG-B induced robust interferon responses, exceeding those triggered by WT virus alone. This was further confirmed in human precision-cut lung slices. Mechanistically, DVG-B–derived dsRNA exhibited a distinct subcellular distribution compared to WT virus. Complementation with the nucleocapsid (N) partially restored dsRNA organization but did not alter the interferon response. Together, our findings demonstrate that DVGs arising from distinct genomic hotspots differentially regulate interferon responses, and N plays a unique role in regulating dsRNA distribution and interferon responses. Author summary: Defective viral genomes (DVGs) are produced during RNA virus infection and can suppress viral pathogenesis by stimulating innate immune responses. However, their roles in CoV infection, particularly SARS-CoV-2, remain poorly understood. This study investigated the species-specific function of DVGs generated during SARS-CoV-2 infection and their impact on disease outcomes. Cohort analysis revealed that overall DVG abundance tended to positively correlate with COVID-19 severity, with approximately 40% of DVGs originating from a specific genomic region designated hotspot B. Single-cell RNA sequencing showed that DVGs from hotspot B, but not hotspot A, were associated with elevated interferon responses, suggesting that DVGs from different genomic regions vary in their immunostimulatory capacities. To directly test this, we constructed representative DVGs from both hotspots. While both suppressed WT virus replication, only DVG-B induced robust interferon responses in both in vitro and ex vivo models. Mechanistically, DVG-B produced dsRNA with a distinct subcellular distribution compared to that of WT virus. Interestingly, complementation with the viral N protein partially restored dsRNA organization but did not alter interferon responses. These findings demonstrate that SARS-CoV-2 DVGs arising from different genomic hotspots differentially regulate innate immunity, and that N plays a unique role in regulating dsRNA distribution and interferon responses.
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BibTeX
@article{brennan2026sarscov2,
title = {{SARS-CoV-2 defective viral genomes from distinct genomic regions drive divergent interferon responses}},
author = {Justin W. Brennan and Simone Spandau and Jiayu Xu and Xingjian Wang and Haley Aull and Gaochan Wang and Sarah Connor and Gloria S. Pryhuber and Thomas J. Mariani and Ruth Serra-Moreno and Susan R. Weiss and Yan Sun},
journal = {PLOS Pathogens},
year = {2026},
month = sep,
doi = {10.1371/journal.ppat.1014099},
url = {https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014099},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - SARS-CoV-2 defective viral genomes from distinct genomic regions drive divergent interferon responses
AU - Justin W. Brennan
AU - Simone Spandau
AU - Jiayu Xu
AU - Xingjian Wang
AU - Haley Aull
AU - Gaochan Wang
AU - Sarah Connor
AU - Gloria S. Pryhuber
AU - Thomas J. Mariani
AU - Ruth Serra-Moreno
AU - Susan R. Weiss
AU - Yan Sun
PY - 2026
DA - 2026/09/23
JO - PLOS Pathogens
DO - 10.1371/journal.ppat.1014099
UR - https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014099
AB - Defective viral genomes (DVGs) are generated during the genomic replication of many RNA viruses. When produced early in infection or supplemented at the onset of infection, DVGs can attenuate viral pathogenesis by stimulating interferon responses and antagonizing wild type (WT) virus replication, highlighting their potential as antiviral therapeutics. However, during natural infection DVGs can exert both antiviral and proviral effects depending on their generation kinetics, species, and abundance, underscoring the need to better understand their roles in viral pathogenesis. Coronaviruses (CoVs) are RNA viruses that ubiquitously generate DVGs, yet the roles of DVGs during CoV infection are largely unknown. In a previous study we investigated SARS-CoV-2 DVG presence in vitro and in patient samples and discovered two major genomic hotspots (A and B) for their generation. Here, we first showed that overall DVG abundance tended to positively correlate with COVID-19 severity, with approximately 40% of DVGs originating from a specific genomic region designated hotspot B. Analysis of a publicly available single-cell RNA-seq dataset revealed that DVGs from hotspot B, but not hotspot A, were associated with elevated interferon responses, suggesting that DVGs derived from different genomic regions vary in their ability to stimulate innate immunity. To test this directly, we constructed two representative DVGs corresponding to hotspots A and B. Both DVGs suppressed the replication of co-infecting WT virus; however, only DVG-B induced robust interferon responses, exceeding those triggered by WT virus alone. This was further confirmed in human precision-cut lung slices. Mechanistically, DVG-B–derived dsRNA exhibited a distinct subcellular distribution compared to WT virus. Complementation with the nucleocapsid (N) partially restored dsRNA organization but did not alter the interferon response. Together, our findings demonstrate that DVGs arising from distinct genomic hotspots differentially regulate interferon responses, and N plays a unique role in regulating dsRNA distribution and interferon responses. Author summary: Defective viral genomes (DVGs) are produced during RNA virus infection and can suppress viral pathogenesis by stimulating innate immune responses. However, their roles in CoV infection, particularly SARS-CoV-2, remain poorly understood. This study investigated the species-specific function of DVGs generated during SARS-CoV-2 infection and their impact on disease outcomes. Cohort analysis revealed that overall DVG abundance tended to positively correlate with COVID-19 severity, with approximately 40% of DVGs originating from a specific genomic region designated hotspot B. Single-cell RNA sequencing showed that DVGs from hotspot B, but not hotspot A, were associated with elevated interferon responses, suggesting that DVGs from different genomic regions vary in their immunostimulatory capacities. To directly test this, we constructed representative DVGs from both hotspots. While both suppressed WT virus replication, only DVG-B induced robust interferon responses in both in vitro and ex vivo models. Mechanistically, DVG-B produced dsRNA with a distinct subcellular distribution compared to that of WT virus. Interestingly, complementation with the viral N protein partially restored dsRNA organization but did not alter interferon responses. These findings demonstrate that SARS-CoV-2 DVGs arising from different genomic hotspots differentially regulate innate immunity, and that N plays a unique role in regulating dsRNA distribution and interferon responses.
SN - 1553-7374
ER -