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Fernández JJ, Marin A, Rosales R, Penrice-Randal R, Mlcochova P, Alvarez Y, Villalon-Letelier F, Yildiz S, Pérez E, Rathnasinghe R, Cupic A, Kehrer T, Uccellini MB, Alonso S, Martínez F, McGovern BL, Clark JJ, Sharma P, Bayón Y, Alonso A, Albrecht RA, White KM, Schotsaert M, Miorin L, Stewart JP, Hiscox JA, Gupta RK, Irigoyen N, García-Sastre A, Crespo MS, Fernández N. The IRE1α-XBP1 arm of the unfolded protein response is a host factor activated in SARS-CoV-2 infection. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167193. [PMID: 38648902 DOI: 10.1016/j.bbadis.2024.167193] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 03/30/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
SARS-CoV-2 infection can cause severe pneumonia, wherein exacerbated inflammation plays a major role. This is reminiscent of the process commonly termed cytokine storm, a condition dependent on a disproportionated production of cytokines. This state involves the activation of the innate immune response by viral patterns and coincides with the biosynthesis of the biomass required for viral replication, which may overwhelm the capacity of the endoplasmic reticulum and drive the unfolded protein response (UPR). The UPR is a signal transduction pathway composed of three branches that is initiated by a set of sensors: inositol-requiring protein 1 (IRE1), protein kinase RNA-like ER kinase (PERK), and activating transcription factor 6 (ATF6). These sensors control adaptive processes, including the transcriptional regulation of proinflammatory cytokines. Based on this background, the role of the UPR in SARS-CoV-2 replication and the ensuing inflammatory response was investigated using in vivo and in vitro models of infection. Mice and Syrian hamsters infected with SARS-CoV-2 showed a sole activation of the Ire1α-Xbp1 arm of the UPR associated with a robust production of proinflammatory cytokines. Human lung epithelial cells showed the dependence of viral replication on the expression of UPR-target proteins branching on the IRE1α-XBP1 arm and to a lower extent on the PERK route. Likewise, activation of the IRE1α-XBP1 branch by Spike (S) proteins from different variants of concern was a uniform finding. These results show that the IRE1α-XBP1 system enhances viral replication and cytokine expression and may represent a potential therapeutic target in SARS-CoV-2 severe pneumonia.
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Affiliation(s)
- Jose Javier Fernández
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003 Valladolid, Spain; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Arturo Marin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Romel Rosales
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rebekah Penrice-Randal
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Petra Mlcochova
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Yolanda Alvarez
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003 Valladolid, Spain; Departamento de Bioquímica, Biología Molecular y Fisiología, Universidad de Valladolid, 47003 Valladolid, Spain
| | | | - Soner Yildiz
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Enrique Pérez
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003 Valladolid, Spain
| | - Raveen Rathnasinghe
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anastasija Cupic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas Kehrer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa B Uccellini
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sara Alonso
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003 Valladolid, Spain
| | - Fernando Martínez
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003 Valladolid, Spain
| | - Briana Lynn McGovern
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jordan J Clark
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Parul Sharma
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Yolanda Bayón
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003 Valladolid, Spain; Departamento de Bioquímica, Biología Molecular y Fisiología, Universidad de Valladolid, 47003 Valladolid, Spain
| | - Andrés Alonso
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003 Valladolid, Spain
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - James P Stewart
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Department of Infectious Disease, University of Georgia, GA, USA
| | - Julian A Hiscox
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Infectious Diseases Horizontal Technology Centre (ID HTC), A*STAR, Singapore, Singapore; Department of Preventive Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nerea Irigoyen
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Mariano Sánchez Crespo
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003 Valladolid, Spain.
| | - Nieves Fernández
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003 Valladolid, Spain; Departamento de Bioquímica, Biología Molecular y Fisiología, Universidad de Valladolid, 47003 Valladolid, Spain
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Alrezaihi A, Penrice-Randal R, Dong X, Prince T, Randle N, Semple MG, Openshaw PJM, MacGill T, Myers T, Orr R, Zakotnik S, Suljič A, Avšič-Županc T, Petrovec M, Korva M, AlJabr W, Hiscox JA. Enrichment of SARS-CoV-2 sequence from nasopharyngeal swabs whilst identifying the nasal microbiome. J Clin Virol 2024; 171:105620. [PMID: 38237303 DOI: 10.1016/j.jcv.2023.105620] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 11/06/2023] [Accepted: 11/18/2023] [Indexed: 03/17/2024]
Abstract
Simultaneously characterising the genomic information of coronaviruses and the underlying nasal microbiome from a single clinical sample would help characterise infection and disease. Metatranscriptomic approaches can be used to sequence SARS-CoV-2 (and other coronaviruses) and identify mRNAs associated with active transcription in the nasal microbiome. However, given the large sequence background, unenriched metatranscriptomic approaches often do not sequence SARS-CoV-2 to sufficient read and coverage depth to obtain a consensus genome, especially with moderate and low viral loads from clinical samples. In this study, various enrichment methods were assessed to detect SARS-CoV-2, identify lineages and define the nasal microbiome. The methods were underpinned by Oxford Nanopore long-read sequencing and variations of sequence independent single primer amplification (SISPA). The utility of the method(s) was also validated on samples from patients infected seasonal coronaviruses. The feasibility of profiling the nasal microbiome using these enrichment methods was explored. The findings shed light on the performance of different enrichment strategies and their applicability in characterising the composition of the nasal microbiome.
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Affiliation(s)
| | | | | | | | | | - Malcolm G Semple
- University of Liverpool, Liverpool, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK; Alder Hey Children's Hospital, Liverpool, UK
| | | | - Tracy MacGill
- Office of Counterterrorism and Emerging Threats, U.S. Food and Drug Administration, Silver Spring, USA
| | - Todd Myers
- Office of Counterterrorism and Emerging Threats, U.S. Food and Drug Administration, Silver Spring, USA
| | - Robert Orr
- Office of Counterterrorism and Emerging Threats, U.S. Food and Drug Administration, Silver Spring, USA
| | | | - Alen Suljič
- University of Ljubljana, Ljubljana, Slovenia
| | | | | | - Miša Korva
- University of Ljubljana, Ljubljana, Slovenia
| | - Waleed AlJabr
- University of Liverpool, Liverpool, UK; King Fahad Medical City, Riyadh, Saudi Arabia
| | - Julian A Hiscox
- University of Liverpool, Liverpool, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK; Agency for Science, Technology and Research (A*STAR), Singapore.
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3
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Penrice-Randal R, Bentley EG, Sharma P, Kirby A, Donovan-Banfield I, Kipar A, Mega DF, Bramwell C, Sharp J, Owen A, Hiscox JA, Stewart JP. The effect of molnupiravir and nirmatrelvir on SARS-CoV-2 genome diversity in infected and immune suppressed mice. bioRxiv 2024:2024.02.27.582110. [PMID: 38464327 PMCID: PMC10925244 DOI: 10.1101/2024.02.27.582110] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Objectives Immunocompromised individuals are susceptible to severe COVID-19 and potentially contribute to the emergence of variants with altered pathogenicity due to persistent infection. This study investigated the impact of immunosuppression on SARS-CoV-2 infection in k18-hACE2 mice and the effectiveness of antiviral treatments in this context. Methods Mice were immunosuppressed using cyclophosphamide and infected with a B lineage of SARS-CoV-2. Molnupiravir and nirmatrelvir, alone and in combination, were administered and viral load and viral sequence diversity was assessed. Results Treatment of infected but immune compromised mice with both compounds either singly or in combination resulted in decreased viral loads and pathological changes compared to untreated animals. Treatment also abrogated infection of neuronal tissue. However, no consistent changes in the viral consensus sequence were observed, except for the emergence of the S:H655Y mutation. Molnupiravir, but not nirmatrelvir or immunosuppression alone, increased the transition/transversion (Ts/Tv) ratio, representative of A>G and C>U mutations and this increase was not altered by the co-administration of nirmatrelvir with molnupiravir.Notably, immunosuppression itself did not appear to promote the emergence of mutational characteristic of variants of concern (VOCs). Conclusions Further investigations are warranted to fully understand the role of immunocompromised individuals in VOC development and to inform optimised public health strategies. It is more likely that immunodeficiency promotes viral persistence but does not necessarily lead to substantial consensus-level changes in the absence of antiviral selection pressure. Consistent with mechanisms of action, molnupiravir showed a stronger mutagenic effect than nirmatrelvir in this model.
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Affiliation(s)
| | - Eleanor G. Bentley
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Parul Sharma
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Adam Kirby
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - I’ah Donovan-Banfield
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Anja Kipar
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Switzerland
| | - Daniele F. Mega
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Chloe Bramwell
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- Department of Pharmacology and Therapeutics, University of Liverpool, UK
| | - Joanne Sharp
- Department of Pharmacology and Therapeutics, University of Liverpool, UK
| | - Andrew Owen
- Department of Pharmacology and Therapeutics, University of Liverpool, UK
- Centre of Excellence in Long-acting Therapeutics (CELT), University of Liverpool, UK
| | - Julian A. Hiscox
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
- A*STAR Infectious Diseases Laboratories (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
| | - James P. Stewart
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- Centre of Excellence in Long-acting Therapeutics (CELT), University of Liverpool, UK
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De Neck S, Penrice-Randal R, Clark JJ, Sharma P, Bentley EG, Kirby A, Mega DF, Han X, Owen A, Hiscox JA, Stewart JP, Kipar A. The Stereotypic Response of the Pulmonary Vasculature to Respiratory Viral Infections: Findings in Mouse Models of SARS-CoV-2, Influenza A and Gammaherpesvirus Infections. Viruses 2023; 15:1637. [PMID: 37631979 PMCID: PMC10458810 DOI: 10.3390/v15081637] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 06/19/2023] [Revised: 07/14/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
The respiratory system is the main target of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 19 (COVID-19) where acute respiratory distress syndrome is considered the leading cause of death. Changes in pulmonary blood vessels, among which an endothelialitis/endotheliitis has been particularly emphasized, have been suggested to play a central role in the development of acute lung injury. Similar vascular changes are also observed in animal models of COVID-19. The present study aimed to determine whether the latter are specific for SARS-CoV-2 infection, investigating the vascular response in the lungs of mice infected with SARS-CoV-2 and other respiratory viruses (influenza A and murine gammaherpesvirus) by in situ approaches (histology, immunohistology, morphometry) combined with RNA sequencing and bioinformatic analysis. Non-selective recruitment of monocytes and T and B cells from larger muscular veins and arteries was observed with all viruses, matched by a comparable transcriptional response. There was no evidence of endothelial cell infection in any of the models. Both the morphological investigation and the transcriptomics approach support the interpretation that the lung vasculature in mice mounts a stereotypic response to alveolar and respiratory epithelial damage. This may have implications for the treatment and management of respiratory disease in humans.
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Affiliation(s)
- Simon De Neck
- Laboratory for Animal Model Pathology, Vetsuisse Faculty, Institute of Veterinary Pathology, University of Zurich, 8057 Zurich, Switzerland;
| | - Rebekah Penrice-Randal
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 3RF, UK; (R.P.-R.); (J.J.C.); (P.S.); (E.G.B.); (A.K.); (D.F.M.); (X.H.); (J.A.H.); (J.P.S.)
| | - Jordan J. Clark
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 3RF, UK; (R.P.-R.); (J.J.C.); (P.S.); (E.G.B.); (A.K.); (D.F.M.); (X.H.); (J.A.H.); (J.P.S.)
| | - Parul Sharma
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 3RF, UK; (R.P.-R.); (J.J.C.); (P.S.); (E.G.B.); (A.K.); (D.F.M.); (X.H.); (J.A.H.); (J.P.S.)
| | - Eleanor G. Bentley
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 3RF, UK; (R.P.-R.); (J.J.C.); (P.S.); (E.G.B.); (A.K.); (D.F.M.); (X.H.); (J.A.H.); (J.P.S.)
| | - Adam Kirby
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 3RF, UK; (R.P.-R.); (J.J.C.); (P.S.); (E.G.B.); (A.K.); (D.F.M.); (X.H.); (J.A.H.); (J.P.S.)
| | - Daniele F. Mega
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 3RF, UK; (R.P.-R.); (J.J.C.); (P.S.); (E.G.B.); (A.K.); (D.F.M.); (X.H.); (J.A.H.); (J.P.S.)
| | - Ximeng Han
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 3RF, UK; (R.P.-R.); (J.J.C.); (P.S.); (E.G.B.); (A.K.); (D.F.M.); (X.H.); (J.A.H.); (J.P.S.)
| | - Andrew Owen
- Centre of Excellence in Long-Acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool L3 3RF, UK;
| | - Julian A. Hiscox
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 3RF, UK; (R.P.-R.); (J.J.C.); (P.S.); (E.G.B.); (A.K.); (D.F.M.); (X.H.); (J.A.H.); (J.P.S.)
| | - James P. Stewart
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 3RF, UK; (R.P.-R.); (J.J.C.); (P.S.); (E.G.B.); (A.K.); (D.F.M.); (X.H.); (J.A.H.); (J.P.S.)
| | - Anja Kipar
- Laboratory for Animal Model Pathology, Vetsuisse Faculty, Institute of Veterinary Pathology, University of Zurich, 8057 Zurich, Switzerland;
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 3RF, UK; (R.P.-R.); (J.J.C.); (P.S.); (E.G.B.); (A.K.); (D.F.M.); (X.H.); (J.A.H.); (J.P.S.)
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, University of Helsinki, 00790 Helsinki, Finland
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5
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Penrice-Randal R, Hartley C, Beliavskaia A, Dong X, Brandner-Garrod L, Whitten M, Bell-Sakyi L. New Cell Lines Derived from Laboratory Colony Triatoma infestans and Rhodnius prolixus, Vectors of Trypanosoma cruzi, Do Not Harbour Triatoma Virus. Insects 2022; 13:906. [PMID: 36292854 PMCID: PMC9603895 DOI: 10.3390/insects13100906] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/27/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Triatomine bugs of the genera Triatoma and Rhodnius are vectors of Chagas disease, a neglected tropical disease of humans in South America caused by Trypanosoma cruzi. Triatoma virus (TrV), a natural pathogen of Triatoma infestans, has been proposed as a possible tool for the bio-control of triatomine bugs, but research into this virus has been hampered by a lack of suitable host cells for in vitro propagation. Here we report establishment and partial characterisation of continuous cell lines from embryos of T. infestans (TIE/LULS54) and Rhodnius prolixus (RPE/LULS53 and RPE/LULS57). RNAseq screening by a sequence-independent, single primer amplification approach confirmed the absence of TrV and other RNA viruses known to infect R. prolixus, indicating that these new cell lines could be used for propagation of TrV.
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Affiliation(s)
- Rebekah Penrice-Randal
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, 146 Brownlow Hill, Liverpool L3 5RF, UK
| | - Catherine Hartley
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, 146 Brownlow Hill, Liverpool L3 5RF, UK
| | - Alexandra Beliavskaia
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, 146 Brownlow Hill, Liverpool L3 5RF, UK
| | - Xiaofeng Dong
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, 146 Brownlow Hill, Liverpool L3 5RF, UK
| | - Luke Brandner-Garrod
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Miranda Whitten
- Swansea University Institute of Life Science, College of Medicine, Swansea University, Singleton Park, Swansea SA2 8PP, UK
| | - Lesley Bell-Sakyi
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, 146 Brownlow Hill, Liverpool L3 5RF, UK
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6
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Penrice-Randal R, Dong X, Shapanis AG, Gardner A, Harding N, Legebeke J, Lord J, Vallejo AF, Poole S, Brendish NJ, Hartley C, Williams AP, Wheway G, Polak ME, Strazzeri F, Schofield JPR, Skipp PJ, Hiscox JA, Clark TW, Baralle D. Blood gene expression predicts intensive care unit admission in hospitalised patients with COVID-19. Front Immunol 2022; 13:988685. [PMID: 36203591 PMCID: PMC9530807 DOI: 10.3389/fimmu.2022.988685] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundThe COVID-19 pandemic has created pressure on healthcare systems worldwide. Tools that can stratify individuals according to prognosis could allow for more efficient allocation of healthcare resources and thus improved patient outcomes. It is currently unclear if blood gene expression signatures derived from patients at the point of admission to hospital could provide useful prognostic information.MethodsGene expression of whole blood obtained at the point of admission from a cohort of 78 patients hospitalised with COVID-19 during the first wave was measured by high resolution RNA sequencing. Gene signatures predictive of admission to Intensive Care Unit were identified and tested using machine learning and topological data analysis, TopMD.ResultsThe best gene expression signature predictive of ICU admission was defined using topological data analysis with an accuracy: 0.72 and ROC AUC: 0.76. The gene signature was primarily based on differentially activated pathways controlling epidermal growth factor receptor (EGFR) presentation, Peroxisome proliferator-activated receptor alpha (PPAR-α) signalling and Transforming growth factor beta (TGF-β) signalling.ConclusionsGene expression signatures from blood taken at the point of admission to hospital predicted ICU admission of treatment naïve patients with COVID-19.
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Affiliation(s)
- Rebekah Penrice-Randal
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- TopMD Precision Medicine Ltd, Southampton, United Kingdom
- *Correspondence: Rebekah Penrice-Randal,
| | - Xiaofeng Dong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Andrew George Shapanis
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Aaron Gardner
- TopMD Precision Medicine Ltd, Southampton, United Kingdom
| | | | - Jelmer Legebeke
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton National Health Service (NHS) Foundation Trust, University of Southampton, Southampton, United Kingdom
| | - Jenny Lord
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Andres F. Vallejo
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Stephen Poole
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton National Health Service (NHS) Foundation Trust, University of Southampton, Southampton, United Kingdom
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Nathan J. Brendish
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton National Health Service (NHS) Foundation Trust, University of Southampton, Southampton, United Kingdom
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Catherine Hartley
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Anthony P. Williams
- Cancer Sciences Division, Faculty of Medicine, University Hospital Southampton, Southampton, United Kingdom
| | - Gabrielle Wheway
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Marta E. Polak
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | | | | | - Paul J. Skipp
- TopMD Precision Medicine Ltd, Southampton, United Kingdom
- Centre for Proteomic Research, School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
- ASTAR Infectious Diseases Laboratories (ASTAR ID Labs), Agency for Science, Technology and Research (ASTAR) Singapore, Singapore, Singapore
| | - Tristan W. Clark
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton National Health Service (NHS) Foundation Trust, University of Southampton, Southampton, United Kingdom
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Diana Baralle
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton National Health Service (NHS) Foundation Trust, University of Southampton, Southampton, United Kingdom
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7
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Prince T, Dong X, Penrice-Randal R, Randle N, Hartley C, Goldswain H, Jones B, Semple MG, Baillie JK, Openshaw PJM, Turtle L, Hughes GL, Anderson ER, Patterson EI, Druce J, Screaton G, Carroll MW, Stewart JP, Hiscox JA. Analysis of SARS-CoV-2 in Nasopharyngeal Samples from Patients with COVID-19 Illustrates Population Variation and Diverse Phenotypes, Placing the Growth Properties of Variants of Concern in Context with Other Lineages. mSphere 2022; 7:e0091321. [PMID: 35491827 PMCID: PMC9241508 DOI: 10.1128/msphere.00913-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/18/2022] [Indexed: 01/02/2023] Open
Abstract
New variants of SARS-CoV-2 are continuing to emerge and dominate the global sequence landscapes. Several variants have been labeled variants of concern (VOCs) because they may have a transmission advantage, increased risk of morbidity and/or mortality, or immune evasion upon a background of prior infection or vaccination. Placing the VOCs in context with the underlying variability of SARS-CoV-2 is essential in understanding virus evolution and selection pressures. Dominant genome sequences and the population genetics of SARS-CoV-2 in nasopharyngeal swabs from hospitalized patients were characterized. Nonsynonymous changes at a minor variant level were identified. These populations were generally preserved when isolates were amplified in cell culture. To place the Alpha, Beta, Delta, and Omicron VOCs in context, their growth was compared to clinical isolates of different lineages from earlier in the pandemic. The data indicated that the growth in cell culture of the Beta variant was more than that of the other variants in Vero E6 cells but not in hACE2-A549 cells. Looking at each time point, Beta grew more than the other VOCs in hACE2-A549 cells at 24 to 48 h postinfection. At 72 h postinfection there was no difference in the growth of any of the variants in either cell line. Overall, this work suggested that exploring the biology of SARS-CoV-2 is complicated by population dynamics and that these need to be considered with new variants. In the context of variation seen in other coronaviruses, the variants currently observed for SARS-CoV-2 are very similar in terms of their clinical spectrum of disease. IMPORTANCE SARS-CoV-2 is the causative agent of COVID-19. The virus has spread across the planet, causing a global pandemic. In common with other coronaviruses, SARS-CoV-2 genomes can become quite diverse as a consequence of replicating inside cells. This has given rise to multiple variants from the original virus that infected humans. These variants may have different properties and in the context of a widespread vaccination program may render vaccines less effective. Our research confirms the degree of genetic diversity of SARS-CoV-2 in patients. By comparing the growth of previous variants to the pattern seen with four variants of concern (VOCs) (Alpha, Beta, Delta, and Omicron), we show that, at least in cells, Beta variant growth exceeds that of Alpha, Delta, and Omicron VOCs at 24 to 48 h in both Vero E6 and hACE2-A549 cells, but by 72 h postinfection, the amount of virus is not different from that of the other VOCs.
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Affiliation(s)
- Tessa Prince
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
| | - Xiaofeng Dong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Rebekah Penrice-Randal
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Nadine Randle
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Catherine Hartley
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Hannah Goldswain
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Benjamin Jones
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Malcolm G. Semple
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
- Department of Respiratory Medicine, Alder Hey Children’s Hospital, Liverpool, United Kingdom
| | - J. Kenneth Baillie
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter J. M. Openshaw
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Lance Turtle
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
| | - Grant L. Hughes
- Departments of Vector Biology and Tropical Disease Biology, Center for Neglected Tropical Diseases, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Enyia R. Anderson
- Departments of Vector Biology and Tropical Disease Biology, Center for Neglected Tropical Diseases, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Edward I. Patterson
- Departments of Vector Biology and Tropical Disease Biology, Center for Neglected Tropical Diseases, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Julian Druce
- Virus Identification Laboratory, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Gavin Screaton
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Miles W. Carroll
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Public Health England, Salisbury, United Kingdom
| | - James P. Stewart
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Department of Infectious Disease, University of Georgia, Georgia, USA
| | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
- A*STAR Infectious Diseases Laboratories (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
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8
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Legebeke J, Lord J, Penrice-Randal R, Vallejo AF, Poole S, Brendish NJ, Dong X, Hartley C, Holloway JW, Lucas JS, Williams AP, Wheway G, Strazzeri F, Gardner A, Schofield JPR, Skipp PJ, Hiscox JA, Polak ME, Clark TW, Baralle D. Evaluating the Immune Response in Treatment-Naive Hospitalised Patients With Influenza and COVID-19. Front Immunol 2022; 13:853265. [PMID: 35663963 PMCID: PMC9160963 DOI: 10.3389/fimmu.2022.853265] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/13/2022] [Indexed: 12/13/2022] Open
Abstract
The worldwide COVID-19 pandemic has claimed millions of lives and has had a profound effect on global life. Understanding the body’s immune response to SARS-CoV-2 infection is crucial in improving patient management and prognosis. In this study we compared influenza and SARS-CoV-2 infected patient cohorts to identify distinct blood transcript abundances and cellular composition to better understand the natural immune response associated with COVID-19, compared to another viral infection being influenza, and identify a prognostic signature of COVID-19 patient outcome. Clinical characteristics and peripheral blood were acquired upon hospital admission from two well characterised cohorts, a cohort of 88 patients infected with influenza and a cohort of 80 patients infected with SARS-CoV-2 during the first wave of the pandemic and prior to availability of COVID-19 treatments and vaccines. Gene transcript abundances, enriched pathways and cellular composition were compared between cohorts using RNA-seq. A genetic signature between COVID-19 survivors and non-survivors was assessed as a prognostic predictor of COVID-19 outcome. Contrasting immune responses were detected with an innate response elevated in influenza and an adaptive response elevated in COVID-19. Additionally ribosomal, mitochondrial oxidative stress and interferon signalling pathways differentiated the cohorts. An adaptive immune response was associated with COVID-19 survival, while an inflammatory response predicted death. A prognostic transcript signature, associated with circulating immunoglobulins, nucleosome assembly, cytokine production and T cell activation, was able to stratify COVID-19 patients likely to survive or die. This study provides a unique insight into the immune responses of treatment naïve patients with influenza or COVID-19. The comparison of immune response between COVID-19 survivors and non-survivors enables prognostication of COVID-19 patients and may suggest potential therapeutic strategies to improve survival.
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Affiliation(s)
- Jelmer Legebeke
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton National Health Service (NHS) Foundation Trust, Southampton, United Kingdom
| | - Jenny Lord
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Rebekah Penrice-Randal
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Andres F Vallejo
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Stephen Poole
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton National Health Service (NHS) Foundation Trust, Southampton, United Kingdom.,School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Nathan J Brendish
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton National Health Service (NHS) Foundation Trust, Southampton, United Kingdom.,School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Xiaofeng Dong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Catherine Hartley
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - John W Holloway
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton National Health Service (NHS) Foundation Trust, Southampton, United Kingdom
| | - Jane S Lucas
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton National Health Service (NHS) Foundation Trust, Southampton, United Kingdom.,School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Anthony P Williams
- Cancer Sciences Division, Faculty of Medicine, University Hospital Southampton, Southampton, United Kingdom
| | - Gabrielle Wheway
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | | | - Aaron Gardner
- TopMD Precision Medicine Ltd, Southampton, United Kingdom
| | | | - Paul J Skipp
- TopMD Precision Medicine Ltd, Southampton, United Kingdom.,Centre for Proteomic Research, School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Julian A Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom.,ASTAR Infectious Diseases Laboratories (ASTAR ID Labs), Agency for Science, Technology and Research (ASTAR) Singapore, Singapore, Singapore
| | - Marta E Polak
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Tristan W Clark
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton National Health Service (NHS) Foundation Trust, Southampton, United Kingdom.,School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Diana Baralle
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton National Health Service (NHS) Foundation Trust, Southampton, United Kingdom
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9
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Dong X, Penrice-Randal R, Goldswain H, Prince T, Randle N, Donovan-Banfield I, Salguero FJ, Tree J, Vamos E, Nelson C, Clark J, Ryan Y, Stewart JP, Semple MG, Baillie JK, Openshaw PJM, Turtle L, Matthews DA, Carroll MW, Darby AC, Hiscox JA. Analysis of SARS-CoV-2 known and novel subgenomic mRNAs in cell culture, animal model, and clinical samples using LeTRS, a bioinformatic tool to identify unique sequence identifiers. Gigascience 2022; 11:6593429. [PMID: 35639883 PMCID: PMC9154083 DOI: 10.1093/gigascience/giac045] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 12/08/2021] [Accepted: 04/07/2022] [Indexed: 12/30/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a complex strategy for the transcription of viral subgenomic mRNAs (sgmRNAs), which are targets for nucleic acid diagnostics. Each of these sgmRNAs has a unique 5' sequence, the leader-transcriptional regulatory sequence gene junction (leader-TRS junction), that can be identified using sequencing. High-resolution sequencing has been used to investigate the biology of SARS-CoV-2 and the host response in cell culture and animal models and from clinical samples. LeTRS, a bioinformatics tool, was developed to identify leader-TRS junctions and can be used as a proxy to quantify sgmRNAs for understanding virus biology. LeTRS is readily adaptable for other coronaviruses such as Middle East respiratory syndrome coronavirus or a future newly discovered coronavirus. LeTRS was tested on published data sets and novel clinical samples from patients and longitudinal samples from animal models with coronavirus disease 2019. LeTRS identified known leader-TRS junctions and identified putative novel sgmRNAs that were common across different mammalian species. This may be indicative of an evolutionary mechanism where plasticity in transcription generates novel open reading frames, which can then subject to selection pressure. The data indicated multiphasic abundance of sgmRNAs in two different animal models. This recapitulates the relative sgmRNA abundance observed in cells at early points in infection but not at late points. This pattern is reflected in some human nasopharyngeal samples and therefore has implications for transmission models and nucleic acid-based diagnostics. LeTRS provides a quantitative measure of sgmRNA abundance from sequencing data. This can be used to assess the biology of SARS-CoV-2 (or other coronaviruses) in clinical and nonclinical samples, especially to evaluate different variants and medical countermeasures that may influence viral RNA synthesis.
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Affiliation(s)
- Xiaofeng Dong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Rebekah Penrice-Randal
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Hannah Goldswain
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Tessa Prince
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Nadine Randle
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - I'ah Donovan-Banfield
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, Liverpool, L69 7BE, UK
| | | | - Julia Tree
- UK-Health Security Agency, Salisbury, SP4 0JG, UK
| | - Ecaterina Vamos
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Charlotte Nelson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Jordan Clark
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Yan Ryan
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - James P Stewart
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Malcolm G Semple
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, Liverpool, L69 7BE, UK
| | - J Kenneth Baillie
- The Roslin Institute, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London, SW3 6LY, UK
| | - Lance Turtle
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, Liverpool, L69 7BE, UK
| | | | - Miles W Carroll
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, Liverpool, L69 7BE, UK
- UK-Health Security Agency, Salisbury, SP4 0JG, UK
| | - Alistair C Darby
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Julian A Hiscox
- Correspondence address.Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, ic2 Building, Liverpool, L3 5RF, UK. E-mail:
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10
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Zhou J, Peacock TP, Brown JC, Goldhill DH, Elrefaey AME, Penrice-Randal R, Cowton VM, De Lorenzo G, Furnon W, Harvey WT, Kugathasan R, Frise R, Baillon L, Lassaunière R, Thakur N, Gallo G, Goldswain H, Donovan-Banfield I, Dong X, Randle NP, Sweeney F, Glynn MC, Quantrill JL, McKay PF, Patel AH, Palmarini M, Hiscox JA, Bailey D, Barclay WS. Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Cell Rep 2022; 38:110344. [PMID: 35093235 PMCID: PMC8768428 DOI: 10.1016/j.celrep.2022.110344] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/11/2021] [Accepted: 01/14/2022] [Indexed: 12/18/2022] Open
Abstract
SARS-CoV-2 has a broad mammalian species tropism infecting humans, cats, dogs, and farmed mink. Since the start of the 2019 pandemic, several reverse zoonotic outbreaks of SARS-CoV-2 have occurred in mink, one of which reinfected humans and caused a cluster of infections in Denmark. Here we investigate the molecular basis of mink and ferret adaptation and demonstrate the spike mutations Y453F, F486L, and N501T all specifically adapt SARS-CoV-2 to use mustelid ACE2. Furthermore, we risk assess these mutations and conclude mink-adapted viruses are unlikely to pose an increased threat to humans, as Y453F attenuates the virus replication in human cells and all three mink adaptations have minimal antigenic impact. Finally, we show that certain SARS-CoV-2 variants emerging from circulation in humans may naturally have a greater propensity to infect mustelid hosts and therefore these species should continue to be surveyed for reverse zoonotic infections.
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Affiliation(s)
- Jie Zhou
- Department of Infectious Disease, Imperial College London, London, UK
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
| | - Jonathan C Brown
- Department of Infectious Disease, Imperial College London, London, UK
| | - Daniel H Goldhill
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Rebekah Penrice-Randal
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, Liverpool, UK
| | - Vanessa M Cowton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - William T Harvey
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Rebecca Frise
- Department of Infectious Disease, Imperial College London, London, UK
| | - Laury Baillon
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ria Lassaunière
- Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Nazia Thakur
- The Pirbright Institute, Woking, Surrey, UK; The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Hannah Goldswain
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, Liverpool, UK
| | - I'ah Donovan-Banfield
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, Liverpool, UK
| | - Xiaofeng Dong
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, Liverpool, UK
| | - Nadine P Randle
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, Liverpool, UK
| | - Fiachra Sweeney
- Department of Infectious Disease, Imperial College London, London, UK
| | - Martha C Glynn
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Paul F McKay
- Department of Infectious Disease, Imperial College London, London, UK
| | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Julian A Hiscox
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, Liverpool, UK; Infectious Diseases Horizontal Technology Centre (ID HTC), A(∗)STAR, Singapore, Singapore
| | | | - Wendy S Barclay
- Department of Infectious Disease, Imperial College London, London, UK.
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11
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Russell CD, Valanciute A, Gachanja NN, Stephen J, Penrice-Randal R, Armstrong SD, Clohisey S, Wang B, Al Qsous W, Wallace WA, Oniscu GC, Stevens J, Harrison DJ, Dhaliwal K, Hiscox JA, Baillie JK, Akram AR, Dorward DA, Lucas CD. Tissue Proteomic Analysis Identifies Mechanisms and Stages of Immunopathology in Fatal COVID-19. Am J Respir Cell Mol Biol 2022; 66:196-205. [PMID: 34710339 PMCID: PMC8845132 DOI: 10.1165/rcmb.2021-0358oc] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/26/2021] [Indexed: 12/15/2022] Open
Abstract
Immunopathology occurs in the lung and spleen in fatal coronavirus disease (COVID-19), involving monocytes/macrophages and plasma cells. Antiinflammatory therapy reduces mortality, but additional therapeutic targets are required. We aimed to gain mechanistic insight into COVID-19 immunopathology by targeted proteomic analysis of pulmonary and splenic tissues. Lung parenchymal and splenic tissue was obtained from 13 postmortem examinations of patients with fatal COVID-19. Control tissue was obtained from cancer resection samples (lung) and deceased organ donors (spleen). Protein was extracted from tissue by phenol extraction. Olink multiplex immunoassay panels were used for protein detection and quantification. Proteins with increased abundance in the lung included MCP-3, antiviral TRIM21, and prothrombotic TYMP. OSM and EN-RAGE/S100A12 abundance was correlated and associated with inflammation severity. Unsupervised clustering identified "early viral" and "late inflammatory" clusters with distinct protein abundance profiles, and differences in illness duration before death and presence of viral RNA. In the spleen, lymphocyte chemotactic factors and CD8A were decreased in abundance, and proapoptotic factors were increased. B-cell receptor signaling pathway components and macrophage colony stimulating factor (CSF-1) were also increased. Additional evidence for a subset of host factors (including DDX58, OSM, TYMP, IL-18, MCP-3, and CSF-1) was provided by overlap between 1) differential abundance in spleen and lung tissue; 2) meta-analysis of existing datasets; and 3) plasma proteomic data. This proteomic analysis of lung parenchymal and splenic tissue from fatal COVID-19 provides mechanistic insight into tissue antiviral responses, inflammation and disease stages, macrophage involvement, pulmonary thrombosis, splenic B-cell activation, and lymphocyte depletion.
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Affiliation(s)
- Clark D. Russell
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, Edinburgh BioQuarter, Edinburgh, United Kingdom
- Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Asta Valanciute
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, Edinburgh BioQuarter, Edinburgh, United Kingdom
| | - Naomi N. Gachanja
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, Edinburgh BioQuarter, Edinburgh, United Kingdom
| | - Jillian Stephen
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, Edinburgh BioQuarter, Edinburgh, United Kingdom
| | - Rebekah Penrice-Randal
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Stuart D. Armstrong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Sara Clohisey
- Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Bo Wang
- Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Wael Al Qsous
- Department of Pathology, Western General Hospital, Edinburgh, United Kingdom
| | | | | | - Jo Stevens
- Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - David J. Harrison
- School of Medicine, University of St. Andrews, North Haugh, St. Andrews, United Kingdom
| | - Kevin Dhaliwal
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, Edinburgh BioQuarter, Edinburgh, United Kingdom
- Department of Respiratory Medicine, and
| | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
- Infectious Diseases Horizontal Technology Centre, Agency for Science, Technology, and Research, Singapore; and
| | - J. Kenneth Baillie
- Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Ahsan R. Akram
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, Edinburgh BioQuarter, Edinburgh, United Kingdom
- Department of Respiratory Medicine, and
| | - David A. Dorward
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, Edinburgh BioQuarter, Edinburgh, United Kingdom
- Department of Pathology
| | - Christopher D. Lucas
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, Edinburgh BioQuarter, Edinburgh, United Kingdom
- Department of Respiratory Medicine, and
- Institute for Regeneration and Repair, University of Edinburgh, Edinburgh BioQuarter, Edinburgh, United Kingdom
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12
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Abstract
SARS-CoV-2 is thought to have originated in the human population from a zoonotic spillover event. Infection in humans results in a variety of outcomes ranging from asymptomatic cases to the disease COVID-19, which can have significant morbidity and mortality, with over two million confirmed deaths worldwide as of January 2021. Over a year into the pandemic, sequencing analysis has shown that variants of SARS-CoV-2 are being selected as the virus continues to circulate widely within the human population. The predominant drivers of genetic variation within SARS-CoV-2 are single nucleotide polymorphisms (SNPs) caused by polymerase error, potential host factor driven RNA modification, and insertion/deletions (indels) resulting from the discontinuous nature of viral RNA synthesis. While many mutations represent neutral 'genetic drift' or have quickly died out, a subset may be affecting viral traits such as transmissibility, pathogenicity, host range, and antigenicity of the virus. In this review, we summarise the current extent of genetic change in SARS-CoV-2, particularly recently emerging variants of concern, and consider the phenotypic consequences of this viral evolution that may impact the future trajectory of the pandemic.
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Affiliation(s)
- Thomas P. Peacock
- Department of Infectious Diseases, St Marys Medical School, Imperial College London, UK
| | | | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, UK
- A*STAR Infectious Diseases Laboratories (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Wendy S. Barclay
- Department of Infectious Diseases, St Marys Medical School, Imperial College London, UK
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Dorward DA, Russell CD, Um IH, Elshani M, Armstrong SD, Penrice-Randal R, Millar T, Lerpiniere CEB, Tagliavini G, Hartley CS, Randle NP, Gachanja NN, Potey PMD, Dong X, Anderson AM, Campbell VL, Duguid AJ, Al Qsous W, BouHaidar R, Baillie JK, Dhaliwal K, Wallace WA, Bellamy COC, Prost S, Smith C, Hiscox JA, Harrison DJ, Lucas CD. Tissue-Specific Immunopathology in Fatal COVID-19. Am J Respir Crit Care Med 2021; 203:192-201. [PMID: 33217246 PMCID: PMC7874430 DOI: 10.1164/rccm.202008-3265oc] [Citation(s) in RCA: 196] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Rationale: In life-threatening coronavirus disease (COVID-19), corticosteroids reduce mortality, suggesting that immune responses have a causal role in death. Whether this deleterious inflammation is primarily a direct reaction to the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or an independent immunopathologic process is unknown. Objectives: To determine SARS-CoV-2 organotropism and organ-specific inflammatory responses and the relationships among viral presence, inflammation, and organ injury. Methods: Tissue was acquired from 11 detailed postmortem examinations. SARS-CoV-2 organotropism was mapped by using multiplex PCR and sequencing, with cellular resolution achieved by in situ viral S (spike) protein detection. Histologic evidence of inflammation was quantified from 37 anatomic sites, and the pulmonary immune response was characterized by using multiplex immunofluorescence. Measurements and Main Results: Multiple aberrant immune responses in fatal COVID-19 were found, principally involving the lung and reticuloendothelial system, and these were not clearly topologically associated with the virus. Inflammation and organ dysfunction did not map to the tissue and cellular distribution of SARS-CoV-2 RNA and protein between or within tissues. An arteritis was identified in the lung, which was further characterized as a monocyte/myeloid-rich vasculitis, and occurred together with an influx of macrophage/monocyte-lineage cells into the pulmonary parenchyma. In addition, stereotyped abnormal reticuloendothelial responses, including excessive reactive plasmacytosis and iron-laden macrophages, were present and dissociated from viral presence in lymphoid tissues. Conclusions: Tissue-specific immunopathology occurs in COVID-19, implicating a significant component of the immune-mediated, virus-independent immunopathologic process as a primary mechanism in severe disease. Our data highlight novel immunopathologic mechanisms and validate ongoing and future efforts to therapeutically target aberrant macrophage and plasma-cell responses as well as promote pathogen tolerance in COVID-19.
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Affiliation(s)
- David A Dorward
- Centre for Inflammation Research, Queen's Medical Research Institute, and.,Department of Pathology
| | - Clark D Russell
- Centre for Inflammation Research, Queen's Medical Research Institute, and.,Regional Infectious Diseases Unit
| | - In Hwa Um
- School of Medicine, University of St. Andrews, St. Andrews, United Kingdom
| | - Mustafa Elshani
- School of Medicine, University of St. Andrews, St. Andrews, United Kingdom
| | - Stuart D Armstrong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Rebekah Penrice-Randal
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Tracey Millar
- Centre for Clinical Brain Sciences, Chancellor's Building, University of Edinburgh, Edinburgh BioQuarter, Edinburgh, United Kingdom
| | - Chris E B Lerpiniere
- Centre for Clinical Brain Sciences, Chancellor's Building, University of Edinburgh, Edinburgh BioQuarter, Edinburgh, United Kingdom
| | - Giulia Tagliavini
- Centre for Inflammation Research, Queen's Medical Research Institute, and
| | - Catherine S Hartley
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Nadine P Randle
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Naomi N Gachanja
- Centre for Inflammation Research, Queen's Medical Research Institute, and
| | - Philippe M D Potey
- Centre for Inflammation Research, Queen's Medical Research Institute, and
| | - Xiaofeng Dong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | | | | | | | - Wael Al Qsous
- Department of Pathology, Western General Hospital, Edinburgh, United Kingdom
| | | | - J Kenneth Baillie
- Intensive Care Unit, and.,Roslin Institute, Easter Bush Campus, University of Edinburgh, Midlothian, United Kingdom
| | - Kevin Dhaliwal
- Centre for Inflammation Research, Queen's Medical Research Institute, and.,Department of Respiratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | | | - Christopher O C Bellamy
- Centre for Inflammation Research, Queen's Medical Research Institute, and.,Department of Pathology
| | - Sandrine Prost
- Centre for Inflammation Research, Queen's Medical Research Institute, and
| | - Colin Smith
- Centre for Clinical Brain Sciences, Chancellor's Building, University of Edinburgh, Edinburgh BioQuarter, Edinburgh, United Kingdom.,Department of Pathology
| | - Julian A Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.,Singapore Immunology Network, Agency for Science, Technology and Research, Singapore; and.,Health Protection Research Unit in Emerging and Zoonotic Infections, National Institute for Health Research, United Kingdom
| | - David J Harrison
- Department of Pathology.,School of Medicine, University of St. Andrews, St. Andrews, United Kingdom
| | - Christopher D Lucas
- Centre for Inflammation Research, Queen's Medical Research Institute, and.,Department of Respiratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
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