51
|
Knabl L, Lee HK, Wieser M, Mur A, Zabernigg A, Knabl L, Rauch S, Bock M, Schumacher J, Kaiser N, Furth PA, Hennighausen L. Impact of BNT162b first vaccination on the immune transcriptome of elderly patients infected with the B.1.351 SARS-CoV-2 variant. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.05.11.21256862. [PMID: 34013280 PMCID: PMC8132253 DOI: 10.1101/2021.05.11.21256862] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Fast-spreading variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) energize the COVID-19 pandemic. The B.1.351 variant carrying the escape mutation E484K in the receptor binding domain is of particular concern due to reduced immunological protection following vaccination. Protection can manifest as early as 10 days following immunization with full protection two weeks following the second dose, but the course is not well-characterized for variants. Here, we investigated the immune transcriptome of six elderly individuals (average age 82 yr.) from an old people's home, who contracted B.1.351, with four having received the first dose of BNT162b eight to 11 days prior to the onset of COVID-19 symptoms. The patients were hospitalized and received dexamethasone treatment. Immune transcriptomes were established from PBMCs approximately 10 and 35 days after the onset of COVID-19 symptomology. RNA-seq revealed a more intensive immune response in vaccinated patients as compared to unvaccinated ones. Specifically, transcription factors linked to the JAK/STAT pathway, interferon stimulated genes, and genes associated with innate antiviral immunity and COVID-19-SARS-CoV-2 infection were highly enriched in vaccinated patients. This rendered the transcriptomes of the older vaccinated group significantly different than older unvaccinated individuals infected at the same institution and more similar to the immune response of younger unvaccinated individuals (age range 48-62) following B.1.351 infection. All individuals in this study whether vaccinated or not were hospitalized due to B.1.351 infection and one vaccinated patient died illustrating that although an enhanced immune response was documented infection it was insufficient to protect from disease. This highlights the need for maintaining physical distancing and prevention measures throughout the time course of vaccination in older adults.
Collapse
Affiliation(s)
| | - Hye Kyung Lee
- National Institute of Diabetes, Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | | | - Anna Mur
- Division of Internal Medicine, Krankenhaus Kufstein, Kufstein, Austria
| | - August Zabernigg
- Division of Internal Medicine, Krankenhaus Kufstein, Kufstein, Austria
| | | | - Simon Rauch
- Division of Anesthesia and Intensive Care Medicine, Krankenhaus Meran, Meran, Italy
| | - Matthias Bock
- Division of Anesthesia and Intensive Care Medicine, Krankenhaus Meran, Meran, Italy
- Department of Anesthesiology, perioperative Medicine and Intensive Care Medicine, Paracelsus Medical University, Salzburg, Austria
| | - Jana Schumacher
- Division of Internal Medicine, Krankenhaus St. Johann, St. Johann, Austria
| | - Norbert Kaiser
- Division of Internal Medicine, Krankenhaus St. Johann, St. Johann, Austria
| | - Priscilla A. Furth
- Departments of Oncology & Medicine, Georgetown University, Washington, DC, USA
| | - Lothar Hennighausen
- National Institute of Diabetes, Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| |
Collapse
|
52
|
Winstone H, Lista MJ, Reid AC, Bouton C, Pickering S, Galao RP, Kerridge C, Doores KJ, Swanson CM, Neil SJD. The Polybasic Cleavage Site in SARS-CoV-2 Spike Modulates Viral Sensitivity to Type I Interferon and IFITM2. J Virol 2021; 95:e02422-20. [PMID: 33563656 PMCID: PMC8104117 DOI: 10.1128/jvi.02422-20] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 02/03/2021] [Indexed: 12/31/2022] Open
Abstract
The cellular entry of severe acute respiratory syndrome-associated coronaviruses types 1 and 2 (SARS-CoV-1 and -2) requires sequential protease processing of the viral spike glycoprotein. The presence of a polybasic cleavage site in SARS-CoV-2 spike at the S1/S2 boundary has been suggested to be a factor in the increased transmissibility of SARS-CoV-2 compared to SARS-CoV-1 by facilitating maturation of the spike precursor by furin-like proteases in the producer cells rather than endosomal cathepsins in the target. We investigate the relevance of the polybasic cleavage site in the route of entry of SARS-CoV-2 and the consequences this has for sensitivity to interferons (IFNs) and, more specifically, the IFN-induced transmembrane (IFITM) protein family that inhibit entry of diverse enveloped viruses. We found that SARS-CoV-2 is restricted predominantly by IFITM2, rather than IFITM3, and the degree of this restriction is governed by route of viral entry. Importantly, removal of the cleavage site in the spike protein renders SARS-CoV-2 entry highly pH and cathepsin dependent in late endosomes, where, like SARS-CoV-1 spike, it is more sensitive to IFITM2 restriction. Furthermore, we found that potent inhibition of SARS-CoV-2 replication by type I but not type II IFNs is alleviated by targeted depletion of IFITM2 expression. We propose that the polybasic cleavage site allows SARS-CoV-2 to mediate viral entry in a pH-independent manner, in part to mitigate against IFITM-mediated restriction and promote replication and transmission. This suggests that therapeutic strategies that target furin-mediated cleavage of SARS-CoV-2 spike may reduce viral replication through the activity of type I IFNs.IMPORTANCE The furin cleavage site in the spike protein is a distinguishing feature of SARS-CoV-2 and has been proposed to be a determinant for the higher transmissibility between individuals, compared to SARS-CoV-1. One explanation for this is that it permits more efficient activation of fusion at or near the cell surface rather than requiring processing in the endosome of the target cell. Here, we show that SARS-CoV-2 is inhibited by antiviral membrane protein IFITM2 and that the sensitivity is exacerbated by deletion of the furin cleavage site, which restricts viral entry to low pH compartments. Furthermore, we find that IFITM2 is a significant effector of the antiviral activity of type I interferons against SARS-CoV-2 replication. We suggest that one role of the furin cleavage site is to reduce SARS-CoV-2 sensitivity to innate immune restriction, and thus, it may represent a potential therapeutic target for COVID-19 treatment development.
Collapse
Affiliation(s)
- Helena Winstone
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Maria Jose Lista
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Alisha C Reid
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Clement Bouton
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Suzanne Pickering
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Rui Pedro Galao
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Claire Kerridge
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Chad M Swanson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Stuart J D Neil
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| |
Collapse
|
53
|
The influence of IFITM3 polymorphisms on susceptibility to SARS-CoV-2 infection and severity of COVID-19. Cytokine 2021; 142:155492. [PMID: 33711707 PMCID: PMC7936555 DOI: 10.1016/j.cyto.2021.155492] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 12/20/2022]
Abstract
Background and aims The interferon-induced transmembrane protein 3 (IFITM3) plays an important role in the adaptive and innate immune response by inhibiting viral membrane hemifusion between the host and viral cell cytoplasm. Single nucleotide polymorphisms (SNPs) in the gene IFITM3 have been associated with susceptibility and severity of influenza or other viral infections. We aimed to analyze the role of SNPs in the gene IFITM3 in SARS-CoV-2 infection. Methods We performed genotyping of the SNPs rs12252 and rs34481144 in the gene IFITM3 in 239 SARS-CoV-2-positive and 253 SARS-CoV-2-negative patients. We analyzed the association of the SNPs with susceptibility to SARS-CoV-2 infection and severity of COVID-19. Results SARS-CoV-2-positive and SARS-CoV-2-negative patients did not differ regarding demographics. Neither IFITM3 rs12252 nor rs34481144 polymorphisms were related to SARS-CoV-2 infection risk or severity of COVID-19. Interestingly, we observed the putative deleterious rs12252 CC genotype only in SARS-CoV-2-positive patients (N = 2). Also, we found a non-significant higher frequency of rs34481144 A-allele carriers in the patients with 'serious' COVID-19. Conclusions In summary, we could not confirm the recently reported influence of polymorphisms in the gene IFITM3 on SARS-CoV-2 infection risk or severity of COVID-19 in a German cohort. Additional studies are needed to clarify the influence of the rs12252 CC genotype on SARS-CoV-2 infection risk and the rs34481144 A-allele on course of COVID-19.
Collapse
|
54
|
Pojero F, Candore G, Caruso C, Di Bona D, Groneberg DA, Ligotti ME, Accardi G, Aiello A. The Role of Immunogenetics in COVID-19. Int J Mol Sci 2021; 22:2636. [PMID: 33807915 PMCID: PMC7961811 DOI: 10.3390/ijms22052636] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 12/14/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is induced by SARS-CoV-2 and may arise as a variety of clinical manifestations, ranging from an asymptomatic condition to a life-threatening disease associated with cytokine storm, multiorgan and respiratory failure. The molecular mechanism behind such variability is still under investigation. Several pieces of experimental evidence suggest that genetic variants influencing the onset, maintenance and resolution of the immune response may be fundamental in predicting the evolution of the disease. The identification of genetic variants behind immune system reactivity and function in COVID-19 may help in the elaboration of personalized therapeutic strategies. In the frenetic look for universally shared treatment plans, those genetic variants that are common to other diseases/models may also help in addressing future research in terms of drug repurposing. In this paper, we discuss the most recent updates about the role of immunogenetics in determining the susceptibility to and the history of SARS-CoV-2 infection. We propose a narrative review of available data, speculating about lessons that we have learnt from other viral infections and immunosenescence, and discussing what kind of aspects of research should be deepened in order to improve our knowledge of how host genetic variability impacts the outcome for COVID-19 patients.
Collapse
Affiliation(s)
- Fanny Pojero
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neuroscience and Advanced Diagnostic, University of Palermo, 90134 Palermo, Italy; (F.P.); (G.C.); (M.E.L.); (G.A.)
| | - Giuseppina Candore
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neuroscience and Advanced Diagnostic, University of Palermo, 90134 Palermo, Italy; (F.P.); (G.C.); (M.E.L.); (G.A.)
| | - Calogero Caruso
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neuroscience and Advanced Diagnostic, University of Palermo, 90134 Palermo, Italy; (F.P.); (G.C.); (M.E.L.); (G.A.)
| | - Danilo Di Bona
- Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, 70124 Bari, Italy;
| | - David A. Groneberg
- Institute of Occupational, Social and Environmental Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60596 Frankfurt, Germany;
| | - Mattia E. Ligotti
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neuroscience and Advanced Diagnostic, University of Palermo, 90134 Palermo, Italy; (F.P.); (G.C.); (M.E.L.); (G.A.)
| | - Giulia Accardi
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neuroscience and Advanced Diagnostic, University of Palermo, 90134 Palermo, Italy; (F.P.); (G.C.); (M.E.L.); (G.A.)
| | - Anna Aiello
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neuroscience and Advanced Diagnostic, University of Palermo, 90134 Palermo, Italy; (F.P.); (G.C.); (M.E.L.); (G.A.)
| |
Collapse
|
55
|
Tanaka ML, Marentes Ruiz CJ, Malhotra S, Turner L, Peralta A, Lee Y, Jumarang J, Perez SE, Navarro J, Dien Bard J, Gordon A, Allen EK, Thomas PG, Pannaraj PS. SARS-CoV-2 Transmission Dynamics in Households With Children, Los Angeles, California. Front Pediatr 2021; 9:752993. [PMID: 35071125 PMCID: PMC8767010 DOI: 10.3389/fped.2021.752993] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/30/2021] [Indexed: 12/23/2022] Open
Abstract
Objectives: Studies of household transmission of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) focused on households with children are limited. We investigated household secondary attack rate (SAR), transmission dynamics, and contributing factors in households with children. Materials and Methods: In this prospective case-ascertained study in Los Angeles County, California, all households members were enrolled if ≥1 member tested positive for SARS-CoV-2 by polymerase chain reaction (PCR). Nasopharyngeal PCRs, serology, and symptom data were obtained over multiple visits. Results: A total of 489 individuals in 105 households were enrolled from June to December 2020. The majority (77.3%) reported a household annual income of <$50,000, and most (92.9%) were of Hispanic/Latinx ethnicity. Children <18 years old accounted for 46.9% index cases, of whom 45.3% were asymptomatic. Household index cases were predominantly children during low community transmission and adults during the high community transmission period (χ2 = 7.647, p = 0.0036. The mean household SAR was 77.0% (95% CI: 69.4-84.6%). Child and adult index cases both efficiently transmitted SARS-CoV-2 within households [81.9%, (95% CI: 72.1-91.9%) vs. 72.4% (95% CI: 59.8-85.1%), p = 0.23]. Household income and pets were significantly associated with higher SAR in the multivariable analysis of household factors (p = 0.0013 and 0.004, respectively). Conclusions: The SAR in households with children in an urban setting with a large ethnic minority population is much higher than previously described. Children play important roles as index cases. SAR was disproportionately impacted by household income. Vaccination and public health efforts need special focus on children and vulnerable communities to help mitigate SARS-CoV-2 spread.
Collapse
Affiliation(s)
- Melissa Lucero Tanaka
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | | | - Sanchi Malhotra
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Lauren Turner
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Ariana Peralta
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Yesun Lee
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Jaycee Jumarang
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Stephanie E Perez
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Jocelyn Navarro
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Aubree Gordon
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Pia S Pannaraj
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States.,Department of Pediatrics and Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| |
Collapse
|