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Kitt EM, Yoon HW, Comar CE, Smith KP, Harris RM, Esona MD, Gautam R, Mijatovic-Rustempasic S, Hopkins AL, Jaimes J, Handy LK. Genotypic investigation of a rotavirus cluster at a quaternary-care pediatric hospital. Infect Control Hosp Epidemiol 2023; 44:1680-1682. [PMID: 36691772 PMCID: PMC10587370 DOI: 10.1017/ice.2022.317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/03/2022] [Accepted: 12/03/2022] [Indexed: 01/25/2023]
Abstract
Rotavirus (RV) was a common healthcare-associated infection prior to the introduction of the RV vaccine. Following widespread RV vaccination, healthcare-associated rotavirus cases are rare. We describe an investigation of a cluster of rotavirus infections in a pediatric hospital in which an uncommon genotype not typically circulating in the United States was detected.
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Affiliation(s)
- Eimear M. Kitt
- Department of Infection Prevention and Control, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Hee-won Yoon
- Department of Infection Prevention and Control, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Courtney E. Comar
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Clinical Microbiology Laboratory, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
- Infectious Diseases Diagnostics Laboratory, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Kenneth P. Smith
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Infectious Diseases Diagnostics Laboratory, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Rebecca M. Harris
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Infectious Diseases Diagnostics Laboratory, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Mathew D. Esona
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Rashi Gautam
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Slavica Mijatovic-Rustempasic
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Amy L. Hopkins
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Jose Jaimes
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Lori K. Handy
- Department of Infection Prevention and Control, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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Sanders LS, Comar CE, Srinivas KP, Lalli J, Salnikov M, Lengyel J, Southern P, Mohr I, Wilson AC, Rice SA. Herpes Simplex Virus-1 ICP27 Nuclear Export Signal Mutants Exhibit Cell Type-Dependent Deficits in Replication and ICP4 Expression. J Virol 2023; 97:e0195722. [PMID: 37310267 PMCID: PMC10373558 DOI: 10.1128/jvi.01957-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 05/23/2023] [Indexed: 06/14/2023] Open
Abstract
Herpes simplex virus type-1 (HSV-1) protein ICP27 is an essential immediate early (IE) protein that promotes the expression of viral early (E) and late (L) genes via multiple mechanisms. Our understanding of this complex regulatory protein has been greatly enhanced by the characterization of HSV-1 mutants bearing engineered alterations in the ICP27 gene. However, much of this analysis has been performed in interferon-deficient Vero monkey cells. Here, we assessed the replication of a panel of ICP27 mutants in several other cell types. Our analysis shows that mutants lacking ICP27's amino (N)-terminal nuclear export signal (NES) display a striking cell type-dependent growth phenotype, i.e., they grow semi-permissively in Vero and some other cells but are tightly blocked for replication in primary human fibroblasts and multiple human cell lines. This tight growth defect correlates with a failure of these mutants to replicate viral DNA. We also report that HSV-1 NES mutants are deficient in expressing the IE protein ICP4 at early times postinfection. Analysis of viral RNA levels suggests that this phenotype is due, at least in part, to a defect in the export of ICP4 mRNA to the cytoplasm. In combination, our results (i) show that ICP27's NES is critically important for HSV-1 replication in many human cells, and (ii) suggest that ICP27 plays a heretofore unappreciated role in the expression of ICP4. IMPORTANCE HSV-1 IE proteins drive productive HSV-1 replication. The major paradigm of IE gene induction, developed over many years, involves the parallel activation of the five IE genes by the viral tegument protein VP16, which recruits the host RNA polymerase II (RNAP II) to the IE gene promoters. Here, we provide evidence that ICP27 can enhance ICP4 expression early in infection. Because ICP4 is required for transcription of viral E and L genes, this finding may be relevant to understanding how HSV-1 enters and exits the latent state in neurons.
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Affiliation(s)
- Leon Sylvester Sanders
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Courtney E. Comar
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | | | - Joseph Lalli
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Mark Salnikov
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Joy Lengyel
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Peter Southern
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Ian Mohr
- Department of Microbiology, New York University School of Medicine, New York University, New York, New York, USA
| | - Angus C. Wilson
- Department of Microbiology, New York University School of Medicine, New York University, New York, New York, USA
| | - Stephen A. Rice
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
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Yoon HW, Kitt E, Smith K, Comar CE, Harris R, Hopkins A, Jaimes J, Rustempasic SM, Gautam R, Esona MD, Handy L. 1218. Genotypic Investigation of a Rotavirus Cluster at a Pediatric Hospital in 2022. Open Forum Infect Dis 2022. [DOI: 10.1093/ofid/ofac492.1050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Abstract
Background
Rotavirus group A (RVA) was the most common cause of infectious gastroenteritis among young children before introduction of rotavirus vaccine in the United States in 2006. Following widespread vaccination, U.S. hospital acquired (HA) rotavirus cases are rare. We describe a cluster of rotavirus infections in a pediatric hospital with a genotype uncommon among U.S. children.
Methods
Patient cases of HA gastrointestinal (GI) illness were detected through hospital-wide microbiology surveillance, performed by Infection Prevention and Control (IPC) practitioners per state requirements. Cluster procedures were implemented on a unit when 3 cases were identified by symptoms and/or laboratory tests within 48 hours. Due to the current rarity of rotavirus clusters, the hospital partnered with Centers for Disease Control and Prevention (CDC) laboratories to sequence strains in addition to instituting local control measures. RVA strains were genotyped by using the genotype specific qRT-PCR assays for VP7 and VP4 genes. Next Generation Sequencing (NGS) was performed for RVA strain characterization on Illumina MiSeq. Genotypes for all 10 RVA were determined by NCBI’s BLASTN program.
Results
Epidemiologic surveillance identified a rotavirus cluster of 10 patients aged 10 months to 10 years old, of whom 50% had received rotavirus vaccine. Symptoms included emesis and diarrhea. Cases could not be attributed to vaccine related shedding. All patients had epidemiologic links by contiguous bed spaces or shared care teams. Sequencing was conclusive for 9 of the 10 stool samples to be a G9P[4] genotype, which is rarely detected amongst U.S. children. Local control measures of increased education and cleaning, isolation of positive patients in single rooms, use of soap and water instead of alcohol-based hand sanitizer on room exit, and furlough of symptomatic healthcare workers halted transmission.
Conclusion
Routine surveillance of HA GI illness identified a cluster; RVA strain genotyping and characterization identified unusual rotavirus genotype G9P[4] as the cause. Partnership between IPC practitioners and laboratorians with CDC demonstrated the need to enhance infection prevention measures to halt transmission and identified a rare rotavirus strain as the likely cause of the cluster.
Disclosures
Courtney E. Comar, PhD, Pfizer: Stocks/Bonds|Viatris: Stocks/Bonds.
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Affiliation(s)
- Hee-won Yoon
- Children's Hospital of Philadelphia , Philadelphia, Pennsylvania
| | - Eimear Kitt
- Children's Hospital of Philadelphia , Philadelphia, Pennsylvania
| | - Kenneth Smith
- Children's Hospital of Philadelphia , Philadelphia, Pennsylvania
| | - Courtney E Comar
- Children's Hospital of Philadelphia , Philadelphia, Pennsylvania
| | - Rebecca Harris
- Children's Hospital of Philadelphia , Philadelphia, Pennsylvania
| | - Amy Hopkins
- Centers for Disease Control and Prevention , Atlanta , Georgia
| | - Jose Jaimes
- Centers for Disease Control and Prevention , Atlanta , Georgia
| | | | - Rashi Gautam
- Centers for Disease Control and Prevention , Atlanta , Georgia
| | - Mathew D Esona
- Centers for Disease Control and Prevention , Atlanta , Georgia
| | - Lori Handy
- Children's Hospital of Philadelphia , Philadelphia, Pennsylvania
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Comar CE, Otter CJ, Pfannenstiel J, Doerger E, Renner DM, Tan LH, Perlman S, Cohen NA, Fehr AR, Weiss SR. MERS-CoV endoribonuclease and accessory proteins jointly evade host innate immunity during infection of lung and nasal epithelial cells. Proc Natl Acad Sci U S A 2022; 119:e2123208119. [PMID: 35594398 PMCID: PMC9173776 DOI: 10.1073/pnas.2123208119] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 04/13/2022] [Indexed: 12/25/2022] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) emerged into humans in 2012, causing highly lethal respiratory disease. The severity of disease may be, in part, because MERS-CoV is adept at antagonizing early innate immune pathways—interferon (IFN) production and signaling, protein kinase R (PKR), and oligoadenylate synthetase/ribonuclease L (OAS/RNase L)—activated in response to viral double-stranded RNA (dsRNA) generated during genome replication. This is in contrast to severe acute respiratory syndrome CoV-2 (SARS-CoV-2), which we recently reported to activate PKR and RNase L and, to some extent, IFN signaling. We previously found that MERS-CoV accessory proteins NS4a (dsRNA binding protein) and NS4b (phosphodiesterase) could weakly suppress these pathways, but ablation of each had minimal effect on virus replication. Here we investigated the antagonist effects of the conserved coronavirus endoribonuclease (EndoU), in combination with NS4a or NS4b. Inactivation of EndoU catalytic activity alone in a recombinant MERS-CoV caused little if any effect on activation of the innate immune pathways during infection. However, infection with recombinant viruses containing combined mutations with inactivation of EndoU and deletion of NS4a or inactivation of the NS4b phosphodiesterase promoted robust activation of dsRNA-induced innate immune pathways. This resulted in at least tenfold attenuation of replication in human lung–derived A549 and primary nasal cells. Furthermore, replication of these recombinant viruses could be rescued to the level of wild-type MERS-CoV by knockout of host immune mediators MAVS, PKR, or RNase L. Thus, EndoU and accessory proteins NS4a and NS4b together suppress dsRNA-induced innate immunity during MERS-CoV infection in order to optimize viral replication.
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Affiliation(s)
- Courtney E. Comar
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Clayton J. Otter
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | | | - Ethan Doerger
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045
| | - David M. Renner
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Li Hui Tan
- Otorhinolaryngology-Head and Neck Surgery, University of Pennsylvania, Philadelphia, PA 19104
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242
| | - Noam A. Cohen
- Otorhinolaryngology-Head and Neck Surgery, University of Pennsylvania, Philadelphia, PA 19104
- Department of Surgery, Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA 19104
| | - Anthony R. Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242
| | - Susan R. Weiss
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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Comar CE, Otter CJ, Pfannenstiel J, Doerger E, Renner DM, Tan LH, Perlman S, Cohen NA, Fehr AR, Weiss SR. MERS-CoV endoribonuclease and accessory proteins jointly evade host innate immunity during infection of lung and nasal epithelial cells. bioRxiv 2021. [PMID: 34981054 DOI: 10.1101/2021.12.20.473564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) emerged into humans in 2012, causing highly lethal respiratory disease. The severity of disease may be in part because MERS-CoV is adept at antagonizing early innate immune pathways - interferon (IFN) production and signaling, protein kinase R (PKR), and oligoadenylate synthetase ribonuclease L (OAS/RNase L) - generated in response to viral double-stranded (ds)RNA generated during genome replication. This is in contrast to SARS-CoV-2, which we recently reported activates PKR and RNase L and to some extent, IFN signaling. We previously found that MERS-CoV accessory proteins NS4a (dsRNA binding protein) and NS4b (phosphodiesterase) could weakly suppress these pathways, but ablation of each had minimal effect on virus replication. Here we investigated the antagonist effects of the conserved coronavirus endoribonuclease (EndoU), in combination with NS4a or NS4b. Inactivation of EndoU catalytic activity alone in a recombinant MERS-CoV caused little if any effect on activation of the innate immune pathways during infection. However, infection with recombinant viruses containing combined mutations with inactivation of EndoU and deletion of NS4a or inactivation of the NS4b phosphodiesterase promoted robust activation of the dsRNA-induced innate immune pathways. This resulted in ten-fold attenuation of replication in human lung derived A549 and primary nasal cells. Furthermore, replication of these recombinant viruses could be rescued to the level of WT MERS-CoV by knockout of host immune mediators MAVS, PKR, or RNase L. Thus, EndoU and accessory proteins NS4a and NS4b together suppress dsRNA-induced innate immunity during MERS-CoV infection in order to optimize viral replication. IMPORTANCE Middle East Respiratory Syndrome Coronavirus (MERS-CoV) causes highly lethal respiratory disease. MERS-CoV encodes several innate immune antagonists, accessory proteins NS4a and NS4b unique to the merbeco lineage and the nsp15 protein endoribonuclease (EndoU), conserved among all coronaviruses. While mutation of each antagonist protein alone has little effect on innate immunity, infections with recombinant MERS-CoVs with mutations of EndoU in combination with either NS4a or NS4b, activate innate signaling pathways and are attenuated for replication. Our data indicate that EndoU and accessory proteins NS4a and NS4b together suppress innate immunity during MERS-CoV infection, to optimize viral replication. This is in contrast to SARS-CoV-2 which activates these pathways and consistent with greater mortality observed during MERS-CoV infection compared to SARS-CoV-2.
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Acheampong KK, Schaff DL, Emert BL, Lake J, Reffsin S, Shea EK, Comar CE, Litzky LA, Khurram NA, Linn RL, Feldman M, Weiss SR, Montone KT, Cherry S, Shaffer SM. Multiplexed detection of SARS-CoV-2 genomic and subgenomic RNA using in situ hybridization. bioRxiv 2021:2021.08.11.455959. [PMID: 34401878 PMCID: PMC8366794 DOI: 10.1101/2021.08.11.455959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The widespread Coronavirus Disease 2019 (COVID-19) is caused by infection with the novel coronavirus SARS-CoV-2. Currently, we have a limited toolset available for visualizing SARS-CoV-2 in cells and tissues, particularly in tissues from patients who died from COVID-19. Generally, single-molecule RNA FISH techniques have shown mixed results in formalin fixed paraffin embedded tissues such as those preserved from human autopsies. Here, we present a platform for preparing autopsy tissue for visualizing SARS-CoV-2 RNA using RNA FISH with amplification by hybridization chain reaction (HCR). We developed probe sets that target different regions of SARS-CoV-2 (including ORF1a and N) as well as probe sets that specifically target SARS-CoV-2 subgenomic mRNAs. We validated these probe sets in cell culture and tissues (lung, lymph node, and placenta) from infected patients. Using this technology, we observe distinct subcellular localization patterns of the ORF1a and N regions, with the ORF1a concentrated around the nucleus and the N showing a diffuse distribution across the cytoplasm. In human lung tissue, we performed multiplexed RNA FISH HCR for SARS-CoV-2 and cell-type specific marker genes. We found viral RNA in cells containing the alveolar type 2 (AT2) cell marker gene (SFTPC) and the alveolar macrophage marker gene (MARCO), but did not identify viral RNA in cells containing the alveolar type 1 (AT1) cell marker gene (AGER). Moreover, we observed distinct subcellular localization patterns of viral RNA in AT2 cells and alveolar macrophages, consistent with phagocytosis of infected cells. In sum, we demonstrate the use of RNA FISH HCR for visualizing different RNA species from SARS-CoV-2 in cell lines and FFPE autopsy specimens. Furthermore, we multiplex this assay with probes for cellular genes to determine what cell-types are infected within the lung. We anticipate that this platform could be broadly useful for studying SARS-CoV-2 pathology in tissues as well as extended for other applications including investigating the viral life cycle, viral diagnostics, and drug screening.
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Affiliation(s)
- Kofi K Acheampong
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Dylan L Schaff
- Department of Bioengineering, School of Engineering Arts and Sciences, University of Pennsylvania, Philadelphia, PA
| | - Benjamin L Emert
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Jonathan Lake
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Sam Reffsin
- Department of Bioengineering, School of Engineering Arts and Sciences, University of Pennsylvania, Philadelphia, PA
| | - Emily K Shea
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Courtney E Comar
- Department of Microbiology, University of Pennsylvania, Philadelphia PA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Philadelphia, PA
| | - Leslie A Litzky
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Nigar A Khurram
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, IL
| | - Rebecca L Linn
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Division of Anatomic Pathology, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Michael Feldman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Susan R Weiss
- Department of Microbiology, University of Pennsylvania, Philadelphia PA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Philadelphia, PA
| | - Kathleen T Montone
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Sara Cherry
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Philadelphia, PA
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA
| | - Sydney M Shaffer
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Department of Bioengineering, School of Engineering Arts and Sciences, University of Pennsylvania, Philadelphia, PA
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Li Y, Renner DM, Comar CE, Whelan JN, Reyes HM, Cardenas-Diaz FL, Truitt R, Tan LH, Dong B, Alysandratos KD, Huang J, Palmer JN, Adappa ND, Kohanski MA, Kotton DN, Silverman RH, Yang W, Morrisey E, Cohen NA, Weiss SR. SARS-CoV-2 induces double-stranded RNA-mediated innate immune responses in respiratory epithelial derived cells and cardiomyocytes. bioRxiv 2020. [PMID: 32995797 DOI: 10.1101/2020.09.24.312553] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Coronaviruses are adept at evading host antiviral pathways induced by viral double-stranded RNA, including interferon (IFN) signaling, oligoadenylate synthetase-ribonuclease L (OAS-RNase L), and protein kinase R (PKR). While dysregulated or inadequate IFN responses have been associated with severe coronavirus infection, the extent to which the recently emerged SARS-CoV-2 activates or antagonizes these pathways is relatively unknown. We found that SARS-CoV-2 infects patient-derived nasal epithelial cells, present at the initial site of infection, induced pluripotent stem cell-derived alveolar type 2 cells (iAT2), the major cell type infected in the lung, and cardiomyocytes (iCM), consistent with cardiovascular consequences of COVID-19 disease. Robust activation of IFN or OAS-RNase L is not observed in these cell types, while PKR activation is evident in iAT2 and iCM. In SARS-CoV-2 infected Calu-3 and A549 ACE2 lung-derived cell lines, IFN induction remains relatively weak; however activation of OAS-RNase L and PKR is observed. This is in contrast to MERS-CoV, which effectively inhibits IFN signaling as well as OAS-RNase L and PKR pathways, but similar to mutant MERS-CoV lacking innate immune antagonists. Remarkably, both OAS-RNase L and PKR are activated in MAVS knockout A549 ACE2 cells, demonstrating that SARS-CoV-2 can induce these host antiviral pathways despite minimal IFN production. Moreover, increased replication and cytopathic effect in RNASEL knockout A549 ACE2 cells implicates OAS-RNase L in restricting SARS-CoV-2. Finally, while SARS-CoV-2 fails to antagonize these host defense pathways, which contrasts with other coronaviruses, the IFN signaling response is generally weak. These host-virus interactions may contribute to the unique pathogenesis of SARS-CoV-2. Significance SARS-CoV-2 emergence in late 2019 led to the COVID-19 pandemic that has had devastating effects on human health and the economy. Early innate immune responses are essential for protection against virus invasion. While inadequate innate immune responses are associated with severe COVID-19 diseases, understanding of the interaction of SARS-CoV-2 with host antiviral pathways is minimal. We have characterized the innate immune response to SARS-CoV-2 infections in relevant respiratory tract derived cells and cardiomyocytes and found that SARS-CoV-2 activates two antiviral pathways, oligoadenylate synthetase-ribonuclease L (OAS-RNase L), and protein kinase R (PKR), while inducing minimal levels of interferon. This in contrast to MERS-CoV which inhibits all three pathways. Activation of these pathways may contribute to the distinctive pathogenesis of SARS-CoV-2.
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