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Beythien G, de le Roi M, Stanelle-Bertram S, Armando F, Heydemann L, Rosiak M, Becker S, Lamers MM, Kaiser FK, Haagmans BL, Ciurkiewicz M, Gabriel G, Osterhaus ADME, Baumgärtner W. Detection of Double-Stranded RNA Intermediates During SARS-CoV-2 Infections of Syrian Golden Hamsters with Monoclonal Antibodies and Its Implications for Histopathological Evaluation of In Vivo Studies. Int J Mol Sci 2024; 25:11425. [PMID: 39518980 PMCID: PMC11546166 DOI: 10.3390/ijms252111425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Revised: 10/18/2024] [Accepted: 10/21/2024] [Indexed: 11/16/2024] Open
Abstract
The SARS-CoV-2 pandemic has highlighted the challenges posed by the emergence and rapid global spread of previously unknown viruses. Early investigations on the pathogenesis of newly identified viruses are often hampered by a lack of appropriate sample material and conventional detection methods. In this study, viral replication within the lungs of SARS-CoV-2-infected Syrian golden hamsters was assessed by immunolabeling dsRNA intermediates with three different monoclonal antibodies in formalin-fixed, paraffin-embedded tissue samples. The presence of dsRNA was compared to viral antigen levels, viral titers, and genomic RNA replicates using three different variants of concern and an ancestral virus strain at a single time point and during the course of infection with an ancestral variant, and then validated using fluorescent 2-plex in situ hybridization. The results indicate that the detection of viral infection using anti-dsRNA antibodies is restricted to an early phase of infection with high viral replication activity. Additionally, the combined detection of dsRNA intermediates and viral antigens may help to bridge the interpretation gaps between viral antigen levels and viral titers at a single time point. Further testing in other viral infections or species is needed to assess the potential of dsRNA as an early marker for viral infections.
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Affiliation(s)
- Georg Beythien
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany; (G.B.); (M.d.l.R.); (F.A.); (L.H.); (M.R.); (S.B.)
- Center for Systems Neuroscience, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
| | - Madeleine de le Roi
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany; (G.B.); (M.d.l.R.); (F.A.); (L.H.); (M.R.); (S.B.)
| | | | - Federico Armando
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany; (G.B.); (M.d.l.R.); (F.A.); (L.H.); (M.R.); (S.B.)
- Pathology Unit, Department of Veterinary Science, University of Parma, 43121 Parma, Italy
| | - Laura Heydemann
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany; (G.B.); (M.d.l.R.); (F.A.); (L.H.); (M.R.); (S.B.)
- Center for Systems Neuroscience, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
| | - Malgorzata Rosiak
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany; (G.B.); (M.d.l.R.); (F.A.); (L.H.); (M.R.); (S.B.)
- Center for Systems Neuroscience, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
| | - Svenja Becker
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany; (G.B.); (M.d.l.R.); (F.A.); (L.H.); (M.R.); (S.B.)
| | - Mart M. Lamers
- Department of Viroscience, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (M.M.L.); (B.L.H.)
- Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Franziska K. Kaiser
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany; (F.K.K.); (A.D.M.E.O.)
| | - Bart L. Haagmans
- Department of Viroscience, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (M.M.L.); (B.L.H.)
| | - Malgorzata Ciurkiewicz
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany; (G.B.); (M.d.l.R.); (F.A.); (L.H.); (M.R.); (S.B.)
| | - Gülşah Gabriel
- Leibniz Institute of Virology, 20251 Hamburg, Germany; (S.S.-B.); (G.G.)
- Institute of Virology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
| | - Albert D. M. E. Osterhaus
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany; (F.K.K.); (A.D.M.E.O.)
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany; (G.B.); (M.d.l.R.); (F.A.); (L.H.); (M.R.); (S.B.)
- Center for Systems Neuroscience, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
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Shipley R, Seekings AH, Byrne AMP, Shukla S, James J, Goharriz H, Lean FZX, Núñez A, Fooks AR, McElhinney LM, Brookes SM. SARS-CoV-2 infection and transmission via the skin to oro-nasal route with the production of bioaerosols in the ferret model. J Gen Virol 2024; 105. [PMID: 39292223 PMCID: PMC11410047 DOI: 10.1099/jgv.0.002022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024] Open
Abstract
Direct and indirect transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been attributed to virus survival in droplets, bioaerosols and on fomites including skin and surfaces. Survival of SARS-CoV-2 variants of concern (Alpha, Beta, Gamma, and Delta) on the skin and virus transference following rounds of skin-to-skin contact were assessed on porcine skin as a surrogate for human skin. SARS-CoV-2 variants were detectable on skin by RT-qPCR after 72 h at biologically relevant temperatures (35.2 °C) with viral RNA (vRNA) detected after ten successive skin-to-skin contacts. Skin-to-skin virus transmission to establish infection in ferrets as a model for mild/asymptomatic SARS-CoV-2 infection in mustelids and humans was also investigated and compared to intranasal ferret inoculation. Naïve ferrets exposed to Delta variant SARS-CoV-2 in a 'wet' or 'dry' form on porcine skin resulted in robust infection with shedding detectable for up to 14 days post-exposure, at comparable viral loads to ferrets inoculated intranasally. Transmission of SARS-CoV-2 to naïve ferrets in direct contact with infected ferrets was achieved, with environmental contamination detected from ferret fur swabs and air samples. Genetic substitutions were identified in bioaerosol samples acquired following single contact passage in ferrets, including Spike, ORF1ab, and ORF3a protein sequences, suggesting a utility for monitoring host adaptation and virus evolution via air sampling. The longevity of SARS-CoV-2 variants survival directly on the skin and skin-to-skin transference, enabling subsequent infection via the skin to oro-nasal contact route, could represent a pathway for SARS-CoV-2 infection with implications to public and veterinary health.
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Affiliation(s)
- Rebecca Shipley
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey, KT15 3NB, UK
| | - Amanda H Seekings
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey, KT15 3NB, UK
| | - Alexander M P Byrne
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey, KT15 3NB, UK
- Present address: Worldwide Influenza Centre, The Francis Crick Institute, Midland Road, London, NW1 1AT, UK
| | - Shweta Shukla
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey, KT15 3NB, UK
| | - Joe James
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey, KT15 3NB, UK
| | - Hooman Goharriz
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey, KT15 3NB, UK
| | - Fabian Z X Lean
- Pathology and Animal Sciences Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey, KT15 3NB, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College, North Mymms, Hertfordshire, UK
| | - Alejandro Núñez
- Pathology and Animal Sciences Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey, KT15 3NB, UK
| | - Anthony R Fooks
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey, KT15 3NB, UK
| | - Lorraine M McElhinney
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey, KT15 3NB, UK
| | - Sharon M Brookes
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey, KT15 3NB, UK
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Purves K, Brown H, Haverty R, Ryan A, Griffin LL, McCormack J, O'Reilly S, Mallon PW, Gautier V, Cassidy JP, Fabre A, Carr MJ, Gonzalez G, Ciuti S, Fletcher NF. SARS-CoV-2 Seropositivity in Urban Population of Wild Fallow Deer, Dublin, Ireland, 2020-2022. Emerg Infect Dis 2024; 30:1609-1620. [PMID: 39043403 PMCID: PMC11286063 DOI: 10.3201/eid3008.231056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024] Open
Abstract
SARS-CoV-2 can infect wildlife, and SARS-CoV-2 variants of concern might expand into novel animal reservoirs, potentially by reverse zoonosis. White-tailed deer and mule deer of North America are the only deer species in which SARS-CoV-2 has been documented, raising the question of whether other reservoir species exist. We report cases of SARS-CoV-2 seropositivity in a fallow deer population located in Dublin, Ireland. Sampled deer were seronegative in 2020 when the Alpha variant was circulating in humans, 1 deer was seropositive for the Delta variant in 2021, and 12/21 (57%) sampled deer were seropositive for the Omicron variant in 2022, suggesting host tropism expansion as new variants emerged in humans. Omicron BA.1 was capable of infecting fallow deer lung type-2 pneumocytes and type-1-like pneumocytes or endothelial cells ex vivo. Ongoing surveillance to identify novel SARS-CoV-2 reservoirs is needed to prevent public health risks during human-animal interactions in periurban settings.
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Gheban-Roșca IA, Gheban BA, Pop B, Mironescu DC, Siserman VC, Jianu EM, Drugan T, Bolboacă SD. Immunohistochemical and Morphometric Analysis of Lung Tissue in Fatal COVID-19. Diagnostics (Basel) 2024; 14:914. [PMID: 38732328 PMCID: PMC11082993 DOI: 10.3390/diagnostics14090914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/15/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
The primary targets of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the lungs are type I pneumocytes, macrophages, and endothelial cells. We aimed to identify lung cells targeted by SARS-CoV-2 using viral nucleocapsid protein staining and morphometric features on patients with fatal COVID-19. We conducted a retrospective analysis of fifty-one autopsy cases of individuals who tested positive for SARS-CoV-2. Demographic and clinical information were collected from forensic reports, and lung tissue was examined for microscopic lesions and the presence of specific cell types. Half of the evaluated cohort were older than 71 years, and the majority were male (74.5%). In total, 24 patients presented diffuse alveolar damage (DAD), and 50.9% had comorbidities (56.9% obesity, 33.3% hypertension, 15.7% diabetes mellitus). Immunohistochemical analysis showed a similar pattern of infected macrophages, infected type I pneumocytes, and endothelial cells, regardless of the presence of DAD (p > 0.5). The immunohistochemical reactivity score (IRS) was predominantly moderate but without significant differences between patients with and without DAD (p = 0.633 IRS for type I pneumocytes, p = 0.773 IRS for macrophage, and p = 0.737 for IRS endothelium). The nucleus/cytoplasm ratio shows lower values in patients with DAD (median: 0.29 vs. 0.35), but the difference only reaches a tendency for statistical significance (p = 0.083). Our study confirms the presence of infected macrophages, type I pneumocytes, and endothelial cells with a similar pattern in patients with and without diffuse alveolar damage.
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Affiliation(s)
- Ioana-Andreea Gheban-Roșca
- Department of Medical Informatics and Biostatistics, Iuliu Hațieganu University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (I.-A.G.-R.); (T.D.)
- Clinical Hospital for Infectious Diseases, 400348 Cluj-Napoca, Romania
| | - Bogdan-Alexandru Gheban
- County Emergency Clinical Hospital, 400006 Cluj-Napoca, Romania
- Department of Histology, Iuliu Hațieganu University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania;
| | - Bogdan Pop
- The Oncology Institute “Prof. Dr. Ion Chiricuță”, 400015 Cluj-Napoca, Romania;
- Department of Anatomic Pathology, Iuliu Hațieganu University of Medicine and Pharmacy, 400347 Cluj-Napoca, Romania
| | - Daniela-Cristina Mironescu
- Forensic Institute, 400006 Cluj-Napoca, Romania; (D.-C.M.); (V.C.S.)
- Department of Forensic Medicine, Iuliu Hațieganu University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania
| | - Vasile Costel Siserman
- Forensic Institute, 400006 Cluj-Napoca, Romania; (D.-C.M.); (V.C.S.)
- Department of Forensic Medicine, Iuliu Hațieganu University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania
| | - Elena Mihaela Jianu
- Department of Histology, Iuliu Hațieganu University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania;
| | - Tudor Drugan
- Department of Medical Informatics and Biostatistics, Iuliu Hațieganu University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (I.-A.G.-R.); (T.D.)
| | - Sorana D. Bolboacă
- Department of Medical Informatics and Biostatistics, Iuliu Hațieganu University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (I.-A.G.-R.); (T.D.)
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5
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Seekings AH, Shipley R, Byrne AMP, Shukla S, Golding M, Amaya-Cuesta J, Goharriz H, Vitores AG, Lean FZX, James J, Núñez A, Breed A, Frost A, Balzer J, Brown IH, Brookes SM, McElhinney LM. Detection of SARS-CoV-2 Delta Variant (B.1.617.2) in Domestic Dogs and Zoo Tigers in England and Jersey during 2021. Viruses 2024; 16:617. [PMID: 38675958 PMCID: PMC11053977 DOI: 10.3390/v16040617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/02/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Reverse zoonotic transmission events of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been described since the start of the pandemic, and the World Organisation for Animal Health (WOAH) designated the detection of SARS-CoV-2 in animals a reportable disease. Eighteen domestic and zoo animals in Great Britain and Jersey were tested by APHA for SARS-CoV-2 during 2020-2023. One domestic cat (Felis catus), three domestic dogs (Canis lupus familiaris), and three Amur tigers (Panthera tigris altaica) from a zoo were confirmed positive during 2020-2021 and reported to the WOAH. All seven positive animals were linked with known SARS-CoV-2 positive human contacts. Characterisation of the SARS-CoV-2 variants by genome sequencing indicated that the cat was infected with an early SARS-CoV-2 lineage. The three dogs and three tigers were infected with the SARS-CoV-2 Delta variant of concern (B.1.617.2). The role of non-human species in the onward transmission and emergence of new variants of SARS-CoV-2 remain poorly defined. Continued surveillance of SARS-CoV-2 in relevant domestic and captive animal species with high levels of human contact is important to monitor transmission at the human-animal interface and to assess their role as potential animal reservoirs.
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Affiliation(s)
- Amanda H. Seekings
- Department of Virology, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
- National Reference Laboratory for SARS-CoV-2 in Animals, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Rebecca Shipley
- Department of Virology, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
- National Reference Laboratory for SARS-CoV-2 in Animals, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Alexander M. P. Byrne
- Department of Virology, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
- Worldwide Influenza Centre, The Francis Crick Institute, Midland Road, London NW1 1AT, UK
| | - Shweta Shukla
- Department of Virology, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
- National Reference Laboratory for SARS-CoV-2 in Animals, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Megan Golding
- Department of Virology, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Joan Amaya-Cuesta
- Department of Virology, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Hooman Goharriz
- Department of Virology, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
- National Reference Laboratory for SARS-CoV-2 in Animals, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Ana Gómez Vitores
- Department of Pathology and Animal Sciences, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Fabian Z. X. Lean
- Department of Pathology and Animal Sciences, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Joe James
- Department of Virology, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Alejandro Núñez
- Department of Pathology and Animal Sciences, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Alistair Breed
- Government of Jersey, Infrastructure Housing and Environment, Howard Davis Farm, La Route de la Trinité, Trinity, Jersey JE3 5JP, UK
| | - Andrew Frost
- One Health, Animal Health and Welfare Advice Team, Animal and Plant Health Agency, Nobel House, 17 Smith Square, London SW1P 3JR, UK
| | - Jörg Balzer
- Vet Med Labor GmbH, Division of IDEXX Laboratories, Humboldtstraße 2, 70806 Kornwestheim, Germany
| | - Ian H. Brown
- Department of Virology, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Sharon M. Brookes
- Department of Virology, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Lorraine M. McElhinney
- Department of Virology, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
- National Reference Laboratory for SARS-CoV-2 in Animals, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
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Tedesco I, Zito Marino F, Ronchi A, Duarte Neto AN, Dolhnikoff M, Municinò M, Campobasso CP, Pannone G, Franco R. COVID-19: detection methods in post-mortem samples. Pathologica 2023; 115:263-274. [PMID: 38054901 DOI: 10.32074/1591-951x-933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 12/07/2023] Open
Abstract
COVID-19 identification is routinely performed on fresh samples, such as nasopharyngeal and oropharyngeal swabs, even if, the detection of the virus in formalin-fixed paraffin-embedded (FFPE) autopsy tissues could help to underlie mechanisms of the pathogenesis that are not well understood. The gold standard for COVID-19 detection in FFPE samples remains the qRT-PCR as in swab samples, contextually other methods have been developed, including immunohistochemistry (IHC), and in situ hybridization (ISH). In this manuscript, we summarize the main data regarding the methods of COVID-19 detection in pulmonary and extra-pulmonary post-mortem samples, and especially the sensitivity and specificity of these assays will be discussed.
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Affiliation(s)
- Ilaria Tedesco
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, Università degli Studi della Campania "L. Vanvitelli", Naples, Italy
| | - Federica Zito Marino
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, Università degli Studi della Campania "L. Vanvitelli", Naples, Italy
| | - Andrea Ronchi
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, Università degli Studi della Campania "L. Vanvitelli", Naples, Italy
| | - Amaro Nunes Duarte Neto
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Patologia, São Paulo, Brazil
| | - Marisa Dolhnikoff
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Patologia, São Paulo, Brazil
| | - Maurizio Municinò
- Forensic Medicine Unit, "S. Giuliano" Hospital, Giugliano in Campania, Italy
| | - Carlo Pietro Campobasso
- Department of Experimental Medicine, University of Campania, Luigi Vanvitelli, Naples, Italy
| | - Giuseppe Pannone
- Anatomic Pathology Unit, Department of Clinic and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Renato Franco
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, Università degli Studi della Campania "L. Vanvitelli", Naples, Italy
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7
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Piantadosi A, Shariatzadeh N, Bombin A, Arkun K, Alexandrescu S, Kleinschmidt-DeMasters BK, Solomon IH. Double-stranded RNA immunohistochemistry as a screening tool for viral encephalitis. Am J Clin Pathol 2023; 160:210-219. [PMID: 37141170 PMCID: PMC10392367 DOI: 10.1093/ajcp/aqad039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 03/17/2023] [Indexed: 05/05/2023] Open
Abstract
OBJECTIVES Viral infections of the central nervous system can be challenging to diagnose because of the wide range of causative agents and nonspecific histologic features. We sought to determine whether detection of double-stranded RNA (dsRNA), produced during active RNA and DNA viral infections, could be used to select cases for metagenomic next-generation sequencing (mNGS) from formalin-fixed, paraffin-embedded brain tissue. METHODS Eight commercially available anti-dsRNA antibodies were optimized for immunohistochemistry (IHC) and the top antibody tested in a series of cases with confirmed viral infections (n = 34) and cases with inflammatory brain lesions of unclear etiology (n = 62). RESULTS Among known positives, anti-dsRNA IHC produced a strong cytoplasmic or nuclear staining pattern for Powassan virus, West Nile virus, rabies virus, JC polyoma virus, and adenovirus while failing to detect Eastern equine encephalitis virus, Jamestown Canyon virus, or any herpesvirus. All the unknown cases were negative by anti-dsRNA IHC, while mNGS detected rare viral reads (0.3-1.3 reads per million total reads) in 2 cases (3%), with only 1 having potential clinical significance. CONCLUSIONS Anti-dsRNA IHC can effectively identify a subset of clinically relevant viral infections but not all. The absence of staining should not exclude cases from mNGS if sufficient clinical and histologic suspicion exists.
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Affiliation(s)
- Anne Piantadosi
- Department of Pathology and Laboratory Medicine and Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, US
| | - Nima Shariatzadeh
- Department of Pathology and Laboratory Medicine and Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, US
| | - Andrei Bombin
- Department of Pathology and Laboratory Medicine and Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, US
| | - Knarik Arkun
- Department of Pathology and Laboratory Medicine, Tufts University School of Medicine, Boston, MA, US
| | - Sanda Alexandrescu
- Department of Pathology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, US
| | | | - Isaac H Solomon
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, US
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8
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Thomsen C, Røge R, Fred Å, Wanders A. Immunohistochemical detection of double-stranded RNA in formalin-fixed paraffin-embedded tissue. APMIS 2023; 131:197-205. [PMID: 36776120 DOI: 10.1111/apm.13300] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/05/2023] [Indexed: 02/14/2023]
Abstract
Double-stranded RNA (dsRNA) is produced during most viral infections, and immunohistochemical detection of dsRNA has been proposed as a potential screening marker for viral replication. The anti-dsRNA monoclonal antibody clone 9D5 is more sensitive than the established clone J2 but has not been validated in formalin-fixed paraffin-embedded (FFPE) tissue. This study aimed to test and compare the performance of the anti-dsRNA monoclonal antibodies, 9D5 and J2, in FFPE tissue using an automated staining platform. Archived clinical tissue samples with viral infections (n = 34) and uninfected controls (n = 30) were examined. Immunohistochemical staining for dsRNA (9D5 and J2) and virus-specific epitopes was performed. 9D5 provided a similar staining pattern but a higher signal-to-noise ratio than J2. The following proportions of virus-infected tissue samples were dsRNA-positive: SARS-CoV-2 (5/5), HPV (6/6), MCV (5/5), CMV (5/6), HSV (4/6), and EBV (0/6). Also, 18 of 30 uninfected samples were dsRNA positive, and an association between fixation time and intensity was observed. However, signals in all samples were markedly reduced by pretreatment with dsRNA-specific RNAse-III, indicating a specific reaction. In conclusion, dsRNA can be demonstrated in most viral infections with immunohistochemistry in FFPE tissue but with low clinical specificity. The antibody clone 9D5 performs better than clone J2.
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Affiliation(s)
- Christian Thomsen
- Department of Pathology, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Rasmus Røge
- Department of Pathology, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Åsa Fred
- Department of Pathology, Halmstad Hospital, Halmstad, Sweden.,Department of Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Alkwin Wanders
- Department of Pathology, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
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9
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Lean FZX, Leblond AL, Byrne AMP, Mollett B, James J, Watson S, Hurley S, Brookes SM, Weber A, Núñez A. Subclinical hepatitis E virus infection in laboratory ferrets in the UK. J Gen Virol 2022; 103. [DOI: 10.1099/jgv.0.001803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ferrets are widely used for experimental modelling of viral infections. However, background disease in ferrets could potentially confound intended experimental interpretation. Here we report the detection of a subclinical infection of ferret hepatitis E virus (FRHEV) within a colony sub-group of female laboratory ferrets that had been enrolled on an experimental viral infection study (non-hepatitis). Lymphoplasmacytic cuffing of periportal spaces was identified on histopathology but was negative for the RNA and antigens of the administered virus. Follow-up viral metagenomic analysis conducted on liver specimens revealed sequences attributed to FRHEV and these were confirmed by reverse-transcriptase polymerase chain reaction. Further genomic analysis revealed contiguous sequences spanning 79–95 % of the FRHEV genome and that the sequences were closely related to those reported previously in Europe. Using in situ hybridization by RNAScope, we confirmed the presence of HEV-specific RNA in hepatocytes. The HEV open reading frame 2 (ORF2) protein was also detected by immunohistochemistry in the hepatocytes and the biliary canaliculi. In conclusion, the results of our study provide evidence of background infection with FRHEV in laboratory ferrets. As this infection can be subclinical, we recommend routine monitoring of ferret populations using virological and liver function tests to avoid incorrect causal attribution of any liver disease detected in in vivo studies.
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Affiliation(s)
- Fabian Z. X. Lean
- Animal and Plant Health Agency (APHA), Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, UK
- Present address: Department of Pathobiology & Population Sciences, The Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, AL9 7TA, UK
| | - Anne-Laure Leblond
- Department of Pathology and Molecular Pathology, University Zurich and University Hospital Zurich, Zurich, Switzerland
| | - Alexander M. P. Byrne
- Animal and Plant Health Agency (APHA), Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, UK
| | - Benjamin Mollett
- Animal and Plant Health Agency (APHA), Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, UK
| | - Joe James
- Animal and Plant Health Agency (APHA), Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, UK
| | - Samantha Watson
- Animal and Plant Health Agency (APHA), Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, UK
| | - Shellene Hurley
- Animal and Plant Health Agency (APHA), Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, UK
| | - Sharon M. Brookes
- Animal and Plant Health Agency (APHA), Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, UK
| | - Achim Weber
- Department of Pathology and Molecular Pathology, University Zurich and University Hospital Zurich, Zurich, Switzerland
| | - Alejandro Núñez
- Animal and Plant Health Agency (APHA), Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, UK
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10
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Deroubaix A, Kramvis A. Imaging Techniques: Essential Tools for the Study of SARS-CoV-2 Infection. Front Cell Infect Microbiol 2022; 12:794264. [PMID: 35937687 PMCID: PMC9355083 DOI: 10.3389/fcimb.2022.794264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 06/21/2022] [Indexed: 01/08/2023] Open
Abstract
The world has seen the emergence of a new virus in 2019, SARS-CoV-2, causing the COVID-19 pandemic and millions of deaths worldwide. Microscopy can be much more informative than conventional detection methods such as RT-PCR. This review aims to present the up-to-date microscopy observations in patients, the in vitro studies of the virus and viral proteins and their interaction with their host, discuss the microscopy techniques for detection and study of SARS-CoV-2, and summarize the reagents used for SARS-CoV-2 detection. From basic fluorescence microscopy to high resolution techniques and combined technologies, this article shows the power and the potential of microscopy techniques, especially in the field of virology.
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Affiliation(s)
- Aurélie Deroubaix
- Hepatitis Virus Diversity Research Unit, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Life Sciences Imaging Facility, University of the Witwatersrand, Johannesburg, South Africa
| | - Anna Kramvis
- Hepatitis Virus Diversity Research Unit, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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11
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Lean FZX, Núñez A, Spiro S, Priestnall SL, Vreman S, Bailey D, James J, Wrigglesworth E, Suarez-Bonnet A, Conceicao C, Thakur N, Byrne AMP, Ackroyd S, Delahay RJ, van der Poel WHM, Brown IH, Fooks AR, Brookes SM. Differential susceptibility of SARS-CoV-2 in animals: Evidence of ACE2 host receptor distribution in companion animals, livestock and wildlife by immunohistochemical characterisation. Transbound Emerg Dis 2022; 69:2275-2286. [PMID: 34245662 PMCID: PMC8447087 DOI: 10.1111/tbed.14232] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 12/11/2022]
Abstract
Angiotensin converting enzyme 2 (ACE2) is a host cell membrane protein (receptor) that mediates the binding of coronavirus, most notably SARS coronaviruses in the respiratory and gastrointestinal tracts. Although SARS-CoV-2 infection is mainly confined to humans, there have been numerous incidents of spillback (reverse zoonoses) to domestic and captive animals. An absence of information on the spatial distribution of ACE2 in animal tissues limits our understanding of host species susceptibility. Here, we describe the distribution of ACE2 using immunohistochemistry (IHC) on histological sections derived from carnivores, ungulates, primates and chiroptera. Comparison of mink (Neovison vison) and ferret (Mustela putorius furo) respiratory tracts showed substantial differences, demonstrating that ACE2 is present in the lower respiratory tract of mink but not ferrets. The presence of ACE2 in the respiratory tract in some species was much more restricted as indicated by limited immunolabelling in the nasal turbinate, trachea and lungs of cats (Felis catus) and only the nasal turbinate in the golden Syrian hamster (Mesocricetus auratus). In the lungs of other species, ACE2 could be detected on the bronchiolar epithelium of the sheep (Ovis aries), cattle (Bos taurus), European badger (Meles meles), cheetah (Acinonyx jubatus), tiger and lion (Panthera spp.). In addition, ACE2 was present in the nasal mucosa epithelium of the serotine bat (Eptesicus serotinus) but not in pig (Sus scrofa domestica), cattle or sheep. In the intestine, ACE2 immunolabelling was seen on the microvillus of enterocytes (surface of intestine) across various taxa. These results provide anatomical evidence of ACE2 expression in a number of species which will enable further understanding of host susceptibility and tissue tropism of ACE2 receptor-mediated viral infection.
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Affiliation(s)
- Fabian Z X Lean
- Department of Pathology and Animal Sciences, Animal and Plant Health Agency (APHA), Addlestone, Surrey, UK
| | - Alejandro Núñez
- Department of Pathology and Animal Sciences, Animal and Plant Health Agency (APHA), Addlestone, Surrey, UK
| | - Simon Spiro
- Wildlife Health Services, Zoological Society of London, London, UK
| | - Simon L Priestnall
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, North Mymms, UK
| | - Sandra Vreman
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | | | - Joe James
- Department of Virology, APHA, Addlestone, Surrey, UK
| | | | - Alejandro Suarez-Bonnet
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, North Mymms, UK
| | | | | | | | - Stuart Ackroyd
- Department of Pathology and Animal Sciences, Animal and Plant Health Agency (APHA), Addlestone, Surrey, UK
| | | | | | - Ian H Brown
- Department of Virology, APHA, Addlestone, Surrey, UK
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12
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McHenry A, Iyer K, Wang J, Liu C, Harigopal M. Detection of SARS-CoV-2 in tissue: the comparative roles of RT-qPCR, in situ RNA hybridization, and immunohistochemistry. Expert Rev Mol Diagn 2022; 22:559-574. [PMID: 35658709 DOI: 10.1080/14737159.2022.2085508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION The emergence of SARS-CoV-2, the causative agent the COVID-19 pandemic, has led to a rapidly expanding arsenal of molecular diagnostic assays for the detection of viral material in tissue specimens. AREAS COVERED We review the value and shortcomings of available tissue-based assays for SARS-CoV-2 detection in formalin-fixed paraffin-embedded (FFPE) tissue, including immunohistochemistry, in situ hybridization, and quantitative reverse transcription PCR (RT-qPCR). The validation, accuracy, and comparative utility of each method is discussed. Subsequently, we identify commercially available antibodies which render the greatest specificity and reproducibility of staining in FFPE specimens. EXPERT OPINION We offer expert opinion on the efficacy of such techniques and guidance for future implementation, both clinical and experimental.
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Affiliation(s)
- Austin McHenry
- Yale University School of Medicine, Department of Pathology, New Haven, CT, 06520, United States
| | - Krishna Iyer
- Yale University School of Medicine, Department of Pathology, New Haven, CT, 06520, United States
| | - Jianhi Wang
- Yale University School of Medicine, Department of Pathology, New Haven, CT, 06520, United States
| | - Chen Liu
- Yale University School of Medicine, Department of Pathology, New Haven, CT, 06520, United States
| | - Malini Harigopal
- Yale University School of Medicine, Department of Pathology, New Haven, CT, 06520, United States
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13
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Basolo A, Poma AM, Bonuccelli D, Proietti A, Macerola E, Ugolini C, Torregrossa L, Giannini R, Vignali P, Basolo F, Santini F, Toniolo A. Adipose tissue in COVID-19: detection of SARS-CoV-2 in adipocytes and activation of the interferon-alpha response. J Endocrinol Invest 2022; 45:1021-1029. [PMID: 35169984 PMCID: PMC8852916 DOI: 10.1007/s40618-022-01742-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 01/07/2022] [Indexed: 02/08/2023]
Abstract
OBJECTIVE Obesity is a recognized risk factor for the progression to severe forms of COVID-19, yet the mechanisms of the association are unclear. METHODS Subcutaneous abdominal adipose tissue specimens of subjects deceased from COVID-19 (n = 23) were compared to those of controls dying abruptly from causes other than infectious (accidental trauma, sudden cardiac death). Alterations of lung parenchyma consistent with moderate to severe disease were detected in all COVID-19 cases, not in controls. Investigations included: histopathologic features, detection of virus antigens and genome, characterization of infiltrating leukocytes, transcription levels of immune-related genes. RESULTS By RT-PCR, the SARS-CoV-2 genome was detected in the adipose tissue of 13/23 (56%) cases of the COVID-19 cohort. The virus nucleocapsid antigen was detected in the cytoplasm of 1-5% adipocytes in 12/12 COVID-19 cases that were virus-positive by PCR in the adipose tissue (one case could not be assessed due insufficient tissue). The adipose tissue of COVID-19 cases showed leukocyte infiltrates and upregulation of the interferon-alpha pathway. After adjusting for age and sex, the activation score of IFN-alpha was directly related with transcription levels of the ACE2 gene, a key entry factor of SARS-CoV-2. CONCLUSIONS In lethal COVID-19 cases, the SARS-CoV-2 nucleocapsid antigen has been detected in a sizeable proportion of adipocytes, showing that the virus may directly infect the parenchymal cells of subcutaneous fat. Infection appears to activate the IFN alpha pathway and to attract infiltrating leukocytes. Due to the huge numbers of adipocytes in adults, the adipose tissue represents a significant reservoir for SARS-CoV-2 and an important source of inflammatory mediators.
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Affiliation(s)
- A. Basolo
- Obesity and Lipodystrophy Center, Endocrinology Unit, University Hospital of Pisa, 56124 Pisa, Italy
| | - A. M. Poma
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University Hospital of Pisa, Pisa, Italy
| | - D. Bonuccelli
- Department of Forensic Medicine, Azienda USL Toscana Nordovest, Lucca, Italy
| | - A. Proietti
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University Hospital of Pisa, Pisa, Italy
| | - E. Macerola
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University Hospital of Pisa, Pisa, Italy
| | - C. Ugolini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University Hospital of Pisa, Pisa, Italy
| | - L. Torregrossa
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University Hospital of Pisa, Pisa, Italy
| | - R. Giannini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University Hospital of Pisa, Pisa, Italy
| | - P. Vignali
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University Hospital of Pisa, Pisa, Italy
| | - F. Basolo
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University Hospital of Pisa, Pisa, Italy
| | - F. Santini
- Obesity and Lipodystrophy Center, Endocrinology Unit, University Hospital of Pisa, 56124 Pisa, Italy
| | - A. Toniolo
- Global Virus Network, University of Insubria, 21100 Varese, Italy
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14
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Iwabuchi S, Miyamoto K, Hatai M, Mikasa Y, Katsuda M, Murata SI, Kondo T, Yamaue H, Hashimoto S. Immune Cells Profiles in the Different Sites of COVID-19-Affected Lung Lobes in a Single Patient. Front Med (Lausanne) 2022; 9:841170. [PMID: 35252273 PMCID: PMC8888686 DOI: 10.3389/fmed.2022.841170] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Whereas the COVID-19 disease pathophysiology is under investigation, it is important to identify the pathways of viral transmission and inflammation from the pre-illness to the disease-onset stages. We analyzed five lung lobes from a patient with COVID-19 who finally died after prolonged lung protective ventilation. Pathological examination revealed moderate inflammation in upper lung lobes and uneven yet severe inflammation and diffuse alveolar damage in lower lung lobes. SARS-CoV-2 was detected at higher levels not in severely, but rather moderately inflamed middle lung lobes, and immunohistochemistry and bulk RNA-sequencing results showed that immune cells were detected at higher levels in lower lung lobes. The mRNA expression of cytokine families varied. We found an increase in keratin 5- or aquaporin 3-expressing basal cells in the severely inflamed lower lung lobes, and the alveolar stromal tissues were filled with them. Thus, this analysis of lung samples from a patient helps to determine the COVID-19 pathophysiology at a specific time point, and the virus localization and inflammatory responses at each site of the lungs provide various important indications.
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Affiliation(s)
- Sadahiro Iwabuchi
- Department of Molecular Pathophysiology, Institute of Advanced Medicine, Wakayama Medical University, Wakayama, Japan
| | - Kyohei Miyamoto
- Department of Emergency and Critical Care Medicine, Wakayama Medical University, Wakayama, Japan
| | - Mayuko Hatai
- Department of Molecular Pathophysiology, Institute of Advanced Medicine, Wakayama Medical University, Wakayama, Japan
| | - Yurina Mikasa
- Departments of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Masahiro Katsuda
- Second Department of Surgery, Wakayama Medical University, Wakayama, Japan
| | - Shin-Ichi Murata
- Departments of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Toshikazu Kondo
- Department of Forensic Medicine, Wakayama Medical University, Wakayama, Japan
| | - Hiroki Yamaue
- Second Department of Surgery, Wakayama Medical University, Wakayama, Japan
| | - Shinichi Hashimoto
- Department of Molecular Pathophysiology, Institute of Advanced Medicine, Wakayama Medical University, Wakayama, Japan
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15
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Lee JY, Wing PAC, Gala DS, Noerenberg M, Järvelin AI, Titlow J, Zhuang X, Palmalux N, Iselin L, Thompson MK, Parton RM, Prange-Barczynska M, Wainman A, Salguero FJ, Bishop T, Agranoff D, James W, Castello A, McKeating JA, Davis I. Absolute quantitation of individual SARS-CoV-2 RNA molecules provides a new paradigm for infection dynamics and variant differences. eLife 2022; 11:74153. [PMID: 35049501 PMCID: PMC8776252 DOI: 10.7554/elife.74153] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/21/2021] [Indexed: 12/11/2022] Open
Abstract
Despite an unprecedented global research effort on SARS-CoV-2, early replication events remain poorly understood. Given the clinical importance of emergent viral variants with increased transmission, there is an urgent need to understand the early stages of viral replication and transcription. We used single-molecule fluorescence in situ hybridisation (smFISH) to quantify positive sense RNA genomes with 95% detection efficiency, while simultaneously visualising negative sense genomes, subgenomic RNAs, and viral proteins. Our absolute quantification of viral RNAs and replication factories revealed that SARS-CoV-2 genomic RNA is long-lived after entry, suggesting that it avoids degradation by cellular nucleases. Moreover, we observed that SARS-CoV-2 replication is highly variable between cells, with only a small cell population displaying high burden of viral RNA. Unexpectedly, the B.1.1.7 variant, first identified in the UK, exhibits significantly slower replication kinetics than the Victoria strain, suggesting a novel mechanism contributing to its higher transmissibility with important clinical implications.
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Affiliation(s)
- Jeffrey Y Lee
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom
| | - Peter AC Wing
- Nuffield Department of Medicine, The University of OxfordOxfordUnited Kingdom,Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), The University of OxfordOxfordUnited Kingdom
| | - Dalia S Gala
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom
| | - Marko Noerenberg
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom,MRC-University of Glasgow Centre for Virus Research, The University of GlasgowGlasgowUnited Kingdom
| | - Aino I Järvelin
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom
| | - Joshua Titlow
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom
| | - Xiaodong Zhuang
- Nuffield Department of Medicine, The University of OxfordOxfordUnited Kingdom
| | - Natasha Palmalux
- MRC-University of Glasgow Centre for Virus Research, The University of GlasgowGlasgowUnited Kingdom
| | - Louisa Iselin
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom
| | - Mary Kay Thompson
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom
| | - Richard M Parton
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom
| | - Maria Prange-Barczynska
- Nuffield Department of Medicine, The University of OxfordOxfordUnited Kingdom,Ludwig Institute for Cancer Research, The University of OxfordOxfordUnited Kingdom
| | - Alan Wainman
- Sir William Dunn School of Pathology, The University of OxfordOxfordUnited Kingdom
| | | | - Tammie Bishop
- Nuffield Department of Medicine, The University of OxfordOxfordUnited Kingdom,Ludwig Institute for Cancer Research, The University of OxfordOxfordUnited Kingdom
| | - Daniel Agranoff
- Department of Infectious Diseases, University Hospitals Sussex NHS Foundation TrustBrightonUnited Kingdom
| | - William James
- Sir William Dunn School of Pathology, The University of OxfordOxfordUnited Kingdom,James & Lillian Martin Centre, Sir William Dunn School of Pathology, The University of OxfordOxfordUnited Kingdom
| | - Alfredo Castello
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom,MRC-University of Glasgow Centre for Virus Research, The University of GlasgowGlasgowUnited Kingdom
| | - Jane A McKeating
- Nuffield Department of Medicine, The University of OxfordOxfordUnited Kingdom,Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), The University of OxfordOxfordUnited Kingdom
| | - Ilan Davis
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom
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16
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Keep S, Carr BV, Lean FZX, Fones A, Newman J, Dowgier G, Freimanis G, Vatzia E, Polo N, Everest H, Webb I, Mcnee A, Paudyal B, Thakur N, Nunez A, MacLoughlin R, Maier H, Hammond J, Bailey D, Waters R, Charleston B, Tuthill T, Britton P, Bickerton E, Tchilian E. Porcine Respiratory Coronavirus as a Model for Acute Respiratory Coronavirus Disease. Front Immunol 2022; 13:867707. [PMID: 35418984 PMCID: PMC8995773 DOI: 10.3389/fimmu.2022.867707] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/02/2022] [Indexed: 12/11/2022] Open
Abstract
In the light of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, we have developed a porcine respiratory coronavirus (PRCV) model for in depth mechanistic evaluation of the pathogenesis, virology and immune responses of this important family of viruses. Pigs are a large animal with similar physiology and immunology to humans and are a natural host for PRCV. Four PRCV strains were investigated and shown to induce different degrees of lung pathology. Importantly, although all four strains replicated equally well in porcine cell lines in vitro and in the upper respiratory tract in vivo, PRCV strains causing more severe lung pathology were also able to replicate in ex vivo tracheal organ cultures as well as in vivo in the trachea and lung. The time course of infection of PRCV 135, which caused the most severe pulmonary pathology, was investigated. Virus was shed from the upper respiratory tract until day 10 post infection, with infection of the respiratory mucosa, as well as olfactory and sustentacular cells, providing an excellent model to study upper respiratory tract disease in addition to the commonly known lower respiratory tract disease from PRCV. Infected animals made antibody and T cell responses that cross reacted with the four PRCV strains and Transmissible Gastroenteritis Virus. The antibody response was reproduced in vitro in organ cultures. Comparison of mechanisms of infection and immune control in pigs infected with PRCVs of differing pathogenicity with human data from SARS-CoV-2 infection and from our in vitro organ cultures, will enable key events in coronavirus infection and disease pathogenesis to be identified.
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Affiliation(s)
- Sarah Keep
- The Pirbright Institute, Pirbright, United Kingdom
| | | | - Fabian Z X Lean
- Department of Pathology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Albert Fones
- The Pirbright Institute, Pirbright, United Kingdom
| | | | | | | | - Eleni Vatzia
- The Pirbright Institute, Pirbright, United Kingdom
| | - Noemi Polo
- The Pirbright Institute, Pirbright, United Kingdom
| | | | - Isobel Webb
- The Pirbright Institute, Pirbright, United Kingdom
| | - Adam Mcnee
- The Pirbright Institute, Pirbright, United Kingdom
| | - Basu Paudyal
- The Pirbright Institute, Pirbright, United Kingdom
| | - Nazia Thakur
- The Pirbright Institute, Pirbright, United Kingdom
| | - Alejandro Nunez
- Department of Pathology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Ronan MacLoughlin
- Research and Development, Science and Emerging Technologies, Aerogen, Galway, Ireland
| | - Helena Maier
- The Pirbright Institute, Pirbright, United Kingdom
| | - John Hammond
- The Pirbright Institute, Pirbright, United Kingdom
| | - Dalan Bailey
- The Pirbright Institute, Pirbright, United Kingdom
| | - Ryan Waters
- The Pirbright Institute, Pirbright, United Kingdom
| | | | - Toby Tuthill
- The Pirbright Institute, Pirbright, United Kingdom
| | - Paul Britton
- The Pirbright Institute, Pirbright, United Kingdom
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17
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Kawang K, Naoudom U, Kowitdamrong E, Kerr SJ, Ruxrungtham K, Nilaratanakul V. Sensitivity and specificity of anti-double-stranded RNA immunofluorescence for universal detection of viral infection in respiratory specimens. Heliyon 2021; 7:e08471. [PMID: 34977399 PMCID: PMC8689082 DOI: 10.1016/j.heliyon.2021.e08471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/21/2021] [Accepted: 11/22/2021] [Indexed: 11/25/2022] Open
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18
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Baldwin J, Piplani S, Sakala IG, Honda-Okubo Y, Li L, Petrovsky N. Rapid development of analytical methods for evaluating pandemic vaccines: a COVID-19 perspective. Bioanalysis 2021; 13:1805-1826. [PMID: 34645288 PMCID: PMC8516068 DOI: 10.4155/bio-2021-0096] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 09/28/2021] [Indexed: 12/24/2022] Open
Abstract
Vaccines are key in charting a path out of the COVID-19 pandemic. However, development of new vaccines is highly dependent on availability of analytical methods for their design and evaluation. This paper highlights the challenges presented in having to rapidly develop vaccine analytical tools during an ongoing pandemic, including the need to address progressive virus mutation and adaptation which can render initial assays unreliable or redundant. It also discusses the potential of new computational modeling techniques to model and analyze key viral proteins and their attributes to assist vaccine production and assay design. It then reviews the current range of analytical tools available for COVID-19 vaccine application, ranging from in vitro assays for immunogen characterization to assays to measure vaccine responses in vivo. Finally, it provides a future perspective for COVID-19 vaccine analytical tools and attempts to predict how the field might evolve over the next 5-10 years.
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Affiliation(s)
- Jeremy Baldwin
- Vaxine Pty Ltd, 11 Walkley Avenue, Adelaide, 5046, Australia
| | - Sakshi Piplani
- Vaxine Pty Ltd, 11 Walkley Avenue, Adelaide, 5046, Australia
- College of Medicine & Public Health, Flinders University, Adelaide, 5042, Australia
| | - Isaac G Sakala
- Vaxine Pty Ltd, 11 Walkley Avenue, Adelaide, 5046, Australia
- College of Medicine & Public Health, Flinders University, Adelaide, 5042, Australia
| | - Yoshikazu Honda-Okubo
- Vaxine Pty Ltd, 11 Walkley Avenue, Adelaide, 5046, Australia
- College of Medicine & Public Health, Flinders University, Adelaide, 5042, Australia
| | - Lei Li
- Vaxine Pty Ltd, 11 Walkley Avenue, Adelaide, 5046, Australia
- College of Medicine & Public Health, Flinders University, Adelaide, 5042, Australia
| | - Nikolai Petrovsky
- Vaxine Pty Ltd, 11 Walkley Avenue, Adelaide, 5046, Australia
- College of Medicine & Public Health, Flinders University, Adelaide, 5042, Australia
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19
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Postmortem Cardiopulmonary Pathology in Patients with COVID-19 Infection: Single-Center Report of 12 Autopsies from Lausanne, Switzerland. Diagnostics (Basel) 2021; 11:diagnostics11081357. [PMID: 34441292 PMCID: PMC8393761 DOI: 10.3390/diagnostics11081357] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/22/2021] [Accepted: 07/22/2021] [Indexed: 12/12/2022] Open
Abstract
We report postmortem cardio-pulmonary findings including detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in formalin-fixed paraffin embedded tissue in 12 patients with COVID-19. The 5 women and 7 men (median age: 73 years; range 35–96) died 6–38 days after onset of symptoms (median: 14.5 days). Eight patients received mechanical ventilation. Ten patients showed diffuse alveolar damage (DAD), 7 as exudative and 3 as proliferative/organizing DAD. One case presented as acute fibrinous and organizing pneumonia. Seven patients (58%) had acute bronchopneumonia, 1/7 without associated DAD and 1/7 with aspergillosis and necrotic bronchitis. Microthrombi were present in 5 patients, only in exudative DAD. Reverse transcriptase quantitative PCR detected high virus amounts in 6 patients (50%) with exudative DAD and symptom-duration ≤14 days, supported by immunohistochemistry and in-situ RNA hybridization (RNAscope). The 6 patients with low viral copy levels were symptomatic for ≥15 days, comprising all cases with organizing DAD, the patient without DAD and one exudative DAD. We show the high prevalence of DAD as a reaction pattern in COVID-19, the high number of overlying acute bronchopneumonia, and high-level pulmonary virus detection limited to patients who died ≤2 weeks after onset of symptoms, correlating with exudative phase of DAD.
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20
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von Stillfried S, Villwock S, Bülow RD, Djudjaj S, Buhl EM, Maurer A, Ortiz‐Brüchle N, Celec P, Klinkhammer BM, Wong DW, Cacchi C, Braunschweig T, Knüchel‐Clarke R, Dahl E, Boor P. SARS-CoV-2 RNA screening in routine pathology specimens. Microb Biotechnol 2021; 14:1627-1641. [PMID: 33993637 PMCID: PMC8209898 DOI: 10.1111/1751-7915.13828] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 04/27/2021] [Indexed: 12/18/2022] Open
Abstract
Virus detection methods are important to cope with the SARS-CoV-2 pandemics. Apart from the lung, SARS-CoV-2 was detected in multiple organs in severe cases. Less is known on organ tropism in patients developing mild or no symptoms, and some of such patients might be missed in symptom-indicated swab testing. Here, we tested and validated several approaches and selected the most reliable RT-PCR protocol for the detection of SARS-CoV-2 RNA in patients' routine diagnostic formalin-fixed and paraffin-embedded (FFPE) specimens available in pathology, to assess (i) organ tropism in samples from COVID-19-positive patients, (ii) unrecognized cases in selected tissues from negative or not-tested patients during a pandemic peak, and (iii) retrospectively, pre-pandemic lung samples. We identified SARS-CoV-2 RNA in seven samples from confirmed COVID-19 patients, in two gastric biopsies, one small bowel and one colon resection, one lung biopsy, one pleural resection and one pleural effusion specimen, while all other specimens were negative. In the pandemic peak cohort, we identified one previously unrecognized COVID-19 case in tonsillectomy samples. All pre-pandemic lung samples were negative. In conclusion, SARS-CoV-2 RNA detection in FFPE pathology specimens can potentially improve surveillance of COVID-19, allow retrospective studies, and advance our understanding of SARS-CoV-2 organ tropism and effects.
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Affiliation(s)
| | - Sophia Villwock
- Institute of PathologyRWTH Aachen University HospitalAachenGermany
| | - Roman D. Bülow
- Institute of PathologyRWTH Aachen University HospitalAachenGermany
| | - Sonja Djudjaj
- Institute of PathologyRWTH Aachen University HospitalAachenGermany
| | - Eva M. Buhl
- Institute of PathologyRWTH Aachen University HospitalAachenGermany
- Electron Microscopy FacilityRWTH Aachen University HospitalAachenGermany
| | - Angela Maurer
- Institute of PathologyRWTH Aachen University HospitalAachenGermany
| | | | - Peter Celec
- Institute of VirologyBiomedical Research CenterSlovak Academy of SciencesBratislavaSlovakia
- Institute of PathophysiologyFaculty of MedicineComenius UniversityBratislavaSlovakia
- Department of Molecular BiologyFaculty of Natural SciencesComenius UniversityBratislavaSlovakia
| | | | | | - Claudio Cacchi
- Institute of PathologyRWTH Aachen University HospitalAachenGermany
| | | | | | - Edgar Dahl
- Institute of PathologyRWTH Aachen University HospitalAachenGermany
- RWTH Centralized Biomaterial Bank (RWTH cBMB)RWTH Aachen University HospitalAachenGermany
| | - Peter Boor
- Institute of PathologyRWTH Aachen University HospitalAachenGermany
- Electron Microscopy FacilityRWTH Aachen University HospitalAachenGermany
- Department of NephrologyRWTH Aachen University HospitalAachenGermany
- Department of ImmunologyRWTH Aachen University HospitalAachenGermany
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21
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Everett HE, Lean FZX, Byrne AMP, van Diemen PM, Rhodes S, James J, Mollett B, Coward VJ, Skinner P, Warren CJ, Bewley KR, Watson S, Hurley S, Ryan KA, Hall Y, Simmons H, Núñez A, Carroll MW, Brown IH, Brookes SM. Intranasal Infection of Ferrets with SARS-CoV-2 as a Model for Asymptomatic Human Infection. Viruses 2021; 13:113. [PMID: 33467732 PMCID: PMC7830262 DOI: 10.3390/v13010113] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/07/2021] [Accepted: 01/10/2021] [Indexed: 02/07/2023] Open
Abstract
Ferrets were experimentally inoculated with SARS-CoV-2 (severe acute respiratory syndrome (SARS)-related coronavirus 2) to assess infection dynamics and host response. During the resulting subclinical infection, viral RNA was monitored between 2 and 21 days post-inoculation (dpi), and reached a peak in the upper respiratory cavity between 4 and 6 dpi. Viral genomic sequence analysis in samples from three animals identified the Y453F nucleotide substitution relative to the inoculum. Viral RNA was also detected in environmental samples, specifically in swabs of ferret fur. Microscopy analysis revealed viral protein and RNA in upper respiratory tract tissues, notably in cells of the respiratory and olfactory mucosae of the nasal turbinates, including olfactory neuronal cells. Antibody responses to the spike and nucleoprotein were detected from 21 dpi, but virus-neutralizing activity was low. A second intranasal inoculation (re-exposure) of two ferrets after a 17-day interval did not produce re-initiation of viral RNA shedding, but did amplify the humoral response in one animal. Therefore, ferrets can be experimentally infected with SARS-CoV-2 to model human asymptomatic infection.
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Affiliation(s)
- Helen E. Everett
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Fabian Z. X. Lean
- Pathology and Animal Sciences Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (F.Z.X.L.); (S.W.); (S.H.); (H.S.); (A.N.)
| | - Alexander M. P. Byrne
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Pauline M. van Diemen
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Shelley Rhodes
- Bacteriology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK;
| | - Joe James
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Benjamin Mollett
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Vivien J. Coward
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Paul Skinner
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Caroline J. Warren
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Kevin R. Bewley
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, UK; (K.R.B.); (K.A.R.); (Y.H.); (M.W.C.)
| | - Samantha Watson
- Pathology and Animal Sciences Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (F.Z.X.L.); (S.W.); (S.H.); (H.S.); (A.N.)
| | - Shellene Hurley
- Pathology and Animal Sciences Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (F.Z.X.L.); (S.W.); (S.H.); (H.S.); (A.N.)
| | - Kathryn A. Ryan
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, UK; (K.R.B.); (K.A.R.); (Y.H.); (M.W.C.)
| | - Yper Hall
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, UK; (K.R.B.); (K.A.R.); (Y.H.); (M.W.C.)
| | - Hugh Simmons
- Pathology and Animal Sciences Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (F.Z.X.L.); (S.W.); (S.H.); (H.S.); (A.N.)
| | - Alejandro Núñez
- Pathology and Animal Sciences Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (F.Z.X.L.); (S.W.); (S.H.); (H.S.); (A.N.)
| | - Miles W. Carroll
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, UK; (K.R.B.); (K.A.R.); (Y.H.); (M.W.C.)
- Nuffield Department of Medicine, Oxford University, Oxford OX1 3SY, UK
| | - Ian H. Brown
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Sharon M. Brookes
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
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