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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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2
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Sheng Y, Deng Y, Li X, Ji P, Sun X, Liu B, Zhu J, Zhao J, Nan Y, Zhou EM, Hiscox JA, Stewart JP, Sun Y, Zhao Q. Hepatitis E virus ORF3 protein hijacking thioredoxin domain-containing protein 5 (TXNDC5) for its stability to promote viral particle release. J Virol 2024; 98:e0164923. [PMID: 38548704 PMCID: PMC11019958 DOI: 10.1128/jvi.01649-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 03/06/2024] [Indexed: 04/17/2024] Open
Abstract
Hepatitis E virus (HEV) is the most common cause of acute viral hepatitis worldwide, responsible for approximately 20 million infections annually. Among the three open reading frames (ORFs) of the HEV genome, the ORF3 protein is involved in virus release. However, the host proteins involved in HEV release need to be clarified. In this study, a host protein, thioredoxin domain-containing protein 5 (TXNDC5), interacted with the non-palmitoylated ORF3 protein by co-immunoprecipitation analysis. We determined that the overexpression or knockdown of TXNDC5 positively regulated HEV release from the host cells. The 17FCL19 mutation of the ORF3 protein lost the ability to interact with TXNDC5. The releasing amounts of HEV with the ORF3 mutation (FCL17-19SSP) were decreased compared with wild-type HEV. The overexpression of TXNDC5 can stabilize and increase ORF3 protein amounts, but not the TXNDC5 mutant with amino acids 1-88 deletion. Meanwhile, we determined that the function of TXNDC5 on the stabilization of ORF3 protein is independent of the Trx-like domains. Knockdown of TXNDC5 could lead to the degradation of ORF3 protein by the endoplasmic reticulum (ER)-associated protein degradation-proteasome system. However, the ORF3 protein cannot be degraded in the knockout-TXNDC5 stable cells, suggesting that it may hijack other proteins for its stabilization. Subsequently, we found that the other members of protein disulfide isomerase (PDI), including PDIA1, PDIA3, PDIA4, and PDIA6, can increase ORF3 protein amounts, and PDIA3 and PDIA6 interact with ORF3 protein. Collectively, our study suggested that HEV ORF3 protein can utilize TXNDC5 for its stability in ER to facilitate viral release. IMPORTANCE Hepatitis E virus (HEV) infection is the leading cause of acute viral hepatitis worldwide. After the synthesis and modification in the cells, the mature ORF3 protein is essential for HEV release. However, the host protein involved in this process has yet to be determined. Here, we reported a novel host protein, thioredoxin domain-containing protein 5 (TXNDC5), as a chaperone, contributing to HEV release by facilitating ORF3 protein stability in the endoplasmic reticulum through interacting with non-palmitoylated ORF3 protein. However, we also found that in the knockout-TXNDC5 stable cell lines, the HEV ORF3 protein may hijack other proteins for its stabilization. For the first time, our study demonstrated the involvement of TXNDC5 in viral particle release. These findings provide some new insights into the process of the HEV life cycle, the interaction between HEV and host factors, and a new direction for antiviral design.
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Affiliation(s)
- Yamin Sheng
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Yingying Deng
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaoxuan Li
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Pinpin Ji
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Xuwen Sun
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Baoyuan Liu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Jiahong Zhu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Jiakai Zhao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuchen Nan
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - En-Min Zhou
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Julian A. Hiscox
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - James P. Stewart
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Yani Sun
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Qin Zhao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
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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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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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Deng Y, Sheng Y, Zhang G, Sun Y, Wang L, Ji P, Zhu J, Wang G, Liu B, Zhou EM, Cai X, Tu Y, Hiscox JA, Stewart JP, Mu Y, Zhao Q. A novel strategy for an anti-idiotype vaccine: nanobody mimicking neutralization epitope of porcine circovirus type 2. J Virol 2024; 98:e0165023. [PMID: 38271227 PMCID: PMC10878242 DOI: 10.1128/jvi.01650-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Vaccination is the most effective method to protect humans and animals from diseases. Anti-idiotype vaccines are safer due to their absence of pathogens. However, the commercial production of traditional anti-idiotype vaccines using monoclonal and polyclonal antibodies (mAb and pAb) is complex and has a high failure rate. The present study designed a novel, simple, low-cost strategy for developing anti-idiotype vaccines with nanobody technology. We used porcine circovirus type 2 (PCV2) as a viral model, which can result in serious economic loss in the pig industry. The neutralizing mAb-1E7 (Ab1) against PCV2 capsid protein (PCV2-Cap) was immunized in the camel. And 12 nanobodies against mAb-1E7 were screened. Among them, Nb61 (Ab2) targeted the idiotype epitope of mAb-1E7 and blocked mAb-1E7's binding to PCV2-Cap. Additionally, a high-dose Nb61 vaccination can also protect mice and pigs from PCV2 infection. Epitope mapping showed that mAb-1E7 recognized the 75NINDFL80 of PCV2-Cap and 101NYNDFLG107 of Nb61. Subsequently, the mAb-3G4 (Ab3) against Nb61 was produced and can neutralize PCV2 infection in the PK-15 cells. Structure analysis showed that the amino acids of mAb-1E7 and mAb-3G4 respective binding to PCV2-Cap and Nb61 were also similar on the amino acids sequences and spatial conformation. Collectively, our study first provided a strategy for producing nanobody-based anti-idiotype vaccines and identified that anti-idiotype nanobodies could mimic the antigen on amino acids and structures. Importantly, as more and more neutralization mAbs against different pathogens are prepared, anti-idiotype nanobody vaccines can be easily produced against the disease with our strategy, especially for dangerous pathogens.IMPORTANCEAnti-idiotype vaccines utilize idiotype-anti-idiotype network theory, eliminating the need for external antigens as vaccine candidates. Especially for dangerous pathogens, they were safer because they did not contact the live pathogenic microorganisms. However, developing anti-idiotype vaccines with traditional monoclonal and polyclonal antibodies is complex and has a high failure rate. We present a novel, universal, simple, low-cost strategy for producing anti-idiotype vaccines with nanobody technology. Using a neutralization antibody against PCV2-Cap, a nanobody (Ab2) was successfully produced and could mimic the neutralizing epitope of PCV2-Cap. The nanobody can induce protective immune responses against PCV2 infection in mice and pigs. It highlighted that the anti-idiotype vaccine using nanobody has a very good application in the future, especially for dangerous pathogens.
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Affiliation(s)
- Yingying Deng
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shannxi, China
- Engineering Research Center of Efficient New Vaccines for Animals, Universities of Shaanxi Province and Ministry of Education, Yangling, China
- Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agriculture and Rural Affairs, Yangling, China
| | - Yamin Sheng
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shannxi, China
- Engineering Research Center of Efficient New Vaccines for Animals, Universities of Shaanxi Province and Ministry of Education, Yangling, China
- Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agriculture and Rural Affairs, Yangling, China
| | - Guixi Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shannxi, China
- Engineering Research Center of Efficient New Vaccines for Animals, Universities of Shaanxi Province and Ministry of Education, Yangling, China
- Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agriculture and Rural Affairs, Yangling, China
| | - Yani Sun
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shannxi, China
- Engineering Research Center of Efficient New Vaccines for Animals, Universities of Shaanxi Province and Ministry of Education, Yangling, China
- Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agriculture and Rural Affairs, Yangling, China
| | - Lei Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shannxi, China
- Engineering Research Center of Efficient New Vaccines for Animals, Universities of Shaanxi Province and Ministry of Education, Yangling, China
- Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agriculture and Rural Affairs, Yangling, China
| | - Pinpin Ji
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shannxi, China
- Engineering Research Center of Efficient New Vaccines for Animals, Universities of Shaanxi Province and Ministry of Education, Yangling, China
- Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agriculture and Rural Affairs, Yangling, China
| | - Jiahong Zhu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shannxi, China
- Engineering Research Center of Efficient New Vaccines for Animals, Universities of Shaanxi Province and Ministry of Education, Yangling, China
- Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agriculture and Rural Affairs, Yangling, China
| | - Gang Wang
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Baoyuan Liu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shannxi, China
- Engineering Research Center of Efficient New Vaccines for Animals, Universities of Shaanxi Province and Ministry of Education, Yangling, China
- Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agriculture and Rural Affairs, Yangling, China
| | - En-Min Zhou
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shannxi, China
| | - Xuehui Cai
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yabin Tu
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Julian A. Hiscox
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - James P. Stewart
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Yang Mu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shannxi, China
- Engineering Research Center of Efficient New Vaccines for Animals, Universities of Shaanxi Province and Ministry of Education, Yangling, China
- Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agriculture and Rural Affairs, Yangling, China
| | - Qin Zhao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shannxi, China
- Engineering Research Center of Efficient New Vaccines for Animals, Universities of Shaanxi Province and Ministry of Education, Yangling, China
- Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agriculture and Rural Affairs, Yangling, China
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Alruwaili M, Armstrong S, Prince T, Erdmann M, Matthews DA, Luu L, Davidson A, Aljabr W, Hiscox JA. SARS-CoV-2 NSP12 associates with TRiC and the P323L substitution acts as a host adaption. J Virol 2023; 97:e0042423. [PMID: 37929963 PMCID: PMC10688337 DOI: 10.1128/jvi.00424-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 08/29/2023] [Indexed: 11/07/2023] Open
Abstract
IMPORTANCE SARS-CoV-2 has caused a worldwide health and economic crisis. During the course of the pandemic, genetic changes occurred in the virus, which have resulted in new properties of the virus-particularly around gains in transmission and the ability to partially evade either natural or vaccine-acquired immunity. Some of these viruses have been labeled Variants of Concern (VoCs). At the root of all VoCs are two mutations, one in the viral spike protein that has been very well characterized and the other in the virus polymerase (NSP12). This is the viral protein responsible for replicating the genome. We show that NSP12 associates with host cell proteins that act as a scaffold to facilitate the function of this protein. Furthermore, we found that different variants of NSP12 interact with host cell proteins in subtle and different ways, which affect function.
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Affiliation(s)
- Muhannad Alruwaili
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Medical Laboratory Technology Department, Northern Border University, Arar City, Saudi Arabia
| | - Stuart Armstrong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Tessa Prince
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Maximillian Erdmann
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - David A. Matthews
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Lisa Luu
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Andrew Davidson
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | | | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, 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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7
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Han X, Clark JJ, Sharma P, Bentley EG, Kipar A, Alsayer M, Ren X, Robinson A, Alaidarous S, Mu Y, Sun Y, Hiscox JA, Zhou EM, Stewart JP, Zhao Q. Amino acids 1811-1960 of myosin heavy chain 9 is involved in murine gammaherpesvirus 68 infection. Virology 2023; 587:109849. [PMID: 37515945 DOI: 10.1016/j.virol.2023.109849] [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: 06/10/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/31/2023]
Abstract
Myosin heavy chain 9 (MYH9) has been identified as a crucial factor in gammaherpesvirus infection. Murine gammaherpesvirus 68 (MHV-68) was used as an appropriate viral model for investigating gammaherpesviruses in vivo and developing antiviral treatments. However, the roles of MYH9 in MHV-68 infection have not been documented. In the study, the relationship between the expression of MYH9 and MHV-68 infection and MYH9 as the antiviral target were analyzed. The results revealed that MYH9 was enriched on the cell surface and co-localized with MHV-68 upon viral infection. Knocking down MYH9 with siRNA or using the specific inhibitor of MYH9 activity, Blebbistatin, resulted in the decreasing of MHV-68 infection. Furthermore, polyclonal antibodies against MYH9 reduced infection by approximately 74% at a dose of 100 μg/ml. The study determined that MYH9 contributes to MHV-68 infection by interacting with viral glycoprotein 150 (gp150) in the BHK-21 cell membrane. The specific region of MYH9, amino acids 1811-1960 (C-150), was identified as the key domain involved in the interaction with MHV-68 gp150 and was found to inhibit MHV-68 infection. Moreover, C-150 was also shown to decrease HSV-1 infection in Vero cells by approximately 73%. Both C-150 and Blebbistatin were found to inhibit MHV-68 replication and reduce histopathological lesions in vivo in C57BL/6J mice. Taken together, these findings suggested that MYH9 is crucial for MHV-68 infection through its interaction with viral gp150 and that C-150 may be a promising antiviral target for inhibiting MHV-68 infection in vitro and in vivo.
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Affiliation(s)
- Ximeng Han
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shannxi, 712100, China; Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, United Kingdom
| | - Jordan J Clark
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, United Kingdom
| | - Parul Sharma
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, United Kingdom
| | - Eleanor G Bentley
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, United Kingdom
| | - Anja Kipar
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, United Kingdom; Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Switzerland
| | - Mohammed Alsayer
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, United Kingdom
| | - Xiaolei Ren
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Amy Robinson
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, United Kingdom
| | - Sondus Alaidarous
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, United Kingdom
| | - Yang Mu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Yani Sun
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Julian A Hiscox
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, United Kingdom
| | - En-Min Zhou
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shannxi, 712100, China.
| | - James P Stewart
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, United Kingdom.
| | - Qin Zhao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shannxi, 712100, China.
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8
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Dong X, Hiscox JA. Analysis of SARS-CoV-2 Population Genetics from Samples Associated with Huanan Market and Early Cases Identifies Substitutions Associated with Future Variants of Concern. Viruses 2023; 15:1728. [PMID: 37632069 PMCID: PMC10459715 DOI: 10.3390/v15081728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/04/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
SARS-CoV-2 began spreading through human-to-human transmission first within China and then worldwide, with increasing sequence diversity associated with time and the further spread of the virus. The spillover events in the Huanan market were associated with two lineages of SARS-CoV-2 (lineages A and B). Infecting virus populations and those in infected individuals consist of a dominant genomic sequence and minor genomic variants; these latter populations can indicate sites on the genome that may be subject to mutational changes-either neutral or advantageous sites and those that act as a reservoir for future dominant variants-when placed under selection pressure. The earliest deposited sequences with human infections associated with the Huanan market shared very close homology with each other and were all lineage B. However, there were minor genomic variants present in each sample that encompassed synonymous and non-synonymous changes. Fusion sequences characteristic of defective RNA were identified that could potentially link transmission chains between individuals. Although all the individuals appeared to have lineage B as the dominant sequence, nucleotides associated with lineage A could be found at very low frequencies. Several substitutions (but not deletions) associated with much later variants of concern (VoCs) were already present as minor genomic variants. This suggests that low-frequency substitutions at the start of a pandemic could be a reservoir of future dominant variants and/or provide information on potential sites within the genome associated with future plasticity.
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Affiliation(s)
- Xiaofeng Dong
- Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L3 5RF, UK;
| | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L3 5RF, UK;
- Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L69 7BE, UK
- A*STAR Infectious Diseases Laboratories (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore 138648, Singapore
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9
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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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10
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Dong X, Tree J, Banadyga L, He S, Zhu W, Tipton T, Gouriet J, Qiu X, Elmore MJ, Hall Y, Carroll M, Hiscox JA. Linked Mutations in the Ebola Virus Polymerase Are Associated with Organ Specific Phenotypes. Microbiol Spectr 2023; 11:e0415422. [PMID: 36946725 PMCID: PMC10101120 DOI: 10.1128/spectrum.04154-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/20/2023] [Indexed: 03/23/2023] Open
Abstract
Ebola virus (EBOV) causes a severe infection called Ebola virus disease (EVD). The pathogenesis of EBOV infection is complex, and outcome has been associated with a variety of immunological and cellular factors. Disease can result from several mechanisms, including direct organ and endothelial cell damage as a result of viral replication. During the2013 to 2016 Western Africa EBOV outbreak, several mutants emerged, with changes in the genes of nucleoprotein (NP), glycoprotein (GP), and the large (L) protein. Reverse genetic analysis has been used to investigate whether these mutations played any role in pathogenesis with mixed results depending on the experimental system used. Previous studies investigated the impact of three single nonsynonymous mutations (GP-A82V, NP-R111C, and L-D759G) on the fatality rate of mouse and ferret models and suggested that the L-D759G mutation decreased the virulence of EBOV. In this study, the effect of these three mutations was further evaluated by deep sequencing to determine viral population genetics and the host response in longitudinal samples of blood, liver, kidney, spleen, and lung tissues taken from the previous ferret model. The data indicated that the mutations were maintained in the different tissues, but the frequency of minor genomic mutations were different. In addition, compared to wild-type virus, the recombinant mutants had different within host effects, where the D759G (and accompanying Q986H) substitution in the L protein resulted in an upregulation of the immune response in the kidney, liver, spleen, and lungs. Together these studies provide insights into the biology of EBOV mutants both between and within hosts. IMPORTANCE Ebola virus infection can have dramatic effects on the human body which manifest in Ebola virus disease. The outcome of infection is either survival or death and in the former group with the potential of longer-term health consequences and persistent infection. Disease severity is undoubtedly associated with the host response, often with overt inflammatory responses correlated with poorer outcomes. The scale of the2013 to 2016 Western African Ebola virus outbreak revealed new aspects of viral biology. This included the emergence of mutants with potentially altered virulence. Biobanked tissue from ferret models of EBOV infected with different mutants that emerged in the Western Africa outbreak was used to investigate the effect of EBOV genomic variation in different tissues. Overall, the work provided insights into the population genetics of EBOV and showed that different organs in an animal model can respond differently to variants of EBOV.
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Affiliation(s)
- Xiaofeng Dong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Julia Tree
- UK-Health Security Agency, Salisbury, United Kingdom
| | - Logan Banadyga
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Shihua He
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Wenjun Zhu
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Tom Tipton
- UK-Health Security Agency, Salisbury, United Kingdom
| | - Jade Gouriet
- UK-Health Security Agency, Salisbury, United Kingdom
| | - Xiangguo Qiu
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | | | - Yper Hall
- UK-Health Security Agency, Salisbury, United Kingdom
| | - Miles Carroll
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
- Pandemic Sciences Institute, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Infectious Diseases Horizontal Technology Centre (ID HTC), A*STAR, Singapore, Singapore
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11
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Khoo SH, FitzGerald R, Saunders G, Middleton C, Ahmad S, Edwards CJ, Hadjiyiannakis D, Walker L, Lyon R, Shaw V, Mozgunov P, Periselneris J, Woods C, Bullock K, Hale C, Reynolds H, Downs N, Ewings S, Buadi A, Cameron D, Edwards T, Knox E, Donovan-Banfield I, Greenhalf W, Chiong J, Lavelle-Langham L, Jacobs M, Northey J, Painter W, Holman W, Lalloo DG, Tetlow M, Hiscox JA, Jaki T, Fletcher T, Griffiths G, Hayden F, Darbyshire J, Lucas A, Lorch U, Freedman A, Knight R, Julious S, Byrne R, Cubas Atienzar A, Jones J, Williams C, Song A, Dixon J, Alexandersson A, Hatchard P, Tilt E, Titman A, Doce Carracedo A, Chandran Gorner V, Davies A, Woodhouse L, Carlucci N, Okenyi E, Bula M, Dodd K, Gibney J, Dry L, Rashid Gardner Z, Sammour A, Cole C, Rowland T, Tsakiroglu M, Yip V, Osanlou R, Stewart A, Parker B, Turgut T, Ahmed A, Starkey K, Subin S, Stockdale J, Herring L, Baker J, Oliver A, Pacurar M, Owens D, Munro A, Babbage G, Faust S, Harvey M, Pratt D, Nagra D, Vyas A. Molnupiravir versus placebo in unvaccinated and vaccinated patients with early SARS-CoV-2 infection in the UK (AGILE CST-2): a randomised, placebo-controlled, double-blind, phase 2 trial. Lancet Infect Dis 2023; 23:183-195. [PMID: 36272432 PMCID: PMC9662684 DOI: 10.1016/s1473-3099(22)00644-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/06/2022] [Accepted: 09/12/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND The antiviral drug molnupiravir was licensed for treating at-risk patients with COVID-19 on the basis of data from unvaccinated adults. We aimed to evaluate the safety and virological efficacy of molnupiravir in vaccinated and unvaccinated individuals with COVID-19. METHODS This randomised, placebo-controlled, double-blind, phase 2 trial (AGILE CST-2) was done at five National Institute for Health and Care Research sites in the UK. Eligible participants were adult (aged ≥18 years) outpatients with PCR-confirmed, mild-to-moderate SARS-CoV-2 infection who were within 5 days of symptom onset. Using permuted blocks (block size 2 or 4) and stratifying by site, participants were randomly assigned (1:1) to receive either molnupiravir (orally; 800 mg twice daily for 5 days) plus standard of care or matching placebo plus standard of care. The primary outcome was the time from randomisation to SARS-CoV-2 PCR negativity on nasopharyngeal swabs and was analysed by use of a Bayesian Cox proportional hazards model for estimating the probability of a superior virological response (hazard ratio [HR]>1) for molnupiravir versus placebo. Our primary model used a two-point prior based on equal prior probabilities (50%) that the HR was 1·0 or 1·5. We defined a priori that if the probability of a HR of more than 1 was more than 80% molnupiravir would be recommended for further testing. The primary outcome was analysed in the intention-to-treat population and safety was analysed in the safety population, comprising participants who had received at least one dose of allocated treatment. This trial is registered in ClinicalTrials.gov, NCT04746183, and the ISRCTN registry, ISRCTN27106947, and is ongoing. FINDINGS Between Nov 18, 2020, and March 16, 2022, 1723 patients were assessed for eligibility, of whom 180 were randomly assigned to receive either molnupiravir (n=90) or placebo (n=90) and were included in the intention-to-treat analysis. 103 (57%) of 180 participants were female and 77 (43%) were male and 90 (50%) participants had received at least one dose of a COVID-19 vaccine. SARS-CoV-2 infections with the delta (B.1.617.2; 72 [40%] of 180), alpha (B.1.1.7; 37 [21%]), omicron (B.1.1.529; 38 [21%]), and EU1 (B.1.177; 28 [16%]) variants were represented. All 180 participants received at least one dose of treatment and four participants discontinued the study (one in the molnupiravir group and three in the placebo group). Participants in the molnupiravir group had a faster median time from randomisation to negative PCR (8 days [95% CI 8-9]) than participants in the placebo group (11 days [10-11]; HR 1·30, 95% credible interval 0·92-1·71; log-rank p=0·074). The probability of molnupiravir being superior to placebo (HR>1) was 75·4%, which was less than our threshold of 80%. 73 (81%) of 90 participants in the molnupiravir group and 68 (76%) of 90 participants in the placebo group had at least one adverse event by day 29. One participant in the molnupiravir group and three participants in the placebo group had an adverse event of a Common Terminology Criteria for Adverse Events grade 3 or higher severity. No participants died (due to any cause) during the trial. INTERPRETATION We found molnupiravir to be well tolerated and, although our predefined threshold was not reached, we observed some evidence that molnupiravir has antiviral activity in vaccinated and unvaccinated individuals infected with a broad range of SARS-CoV-2 variants, although this evidence is not conclusive. FUNDING Ridgeback Biotherapeutics, the UK National Institute for Health and Care Research, the Medical Research Council, and the Wellcome Trust.
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Affiliation(s)
- Saye H Khoo
- Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK; Tropical and Infectious Disease Unit, Liverpool University Hospital NHS Foundation Trust, Liverpool, UK.
| | - Richard FitzGerald
- Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK,NIHR Royal Liverpool and Broadgreen Clinical Research Facility, Liverpool University Hospital NHS Foundation Trust, Liverpool, UK
| | - Geoffrey Saunders
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Calley Middleton
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Shazaad Ahmad
- NIHR Manchester Clinical Research Facility, Manchester University NHS Foundation Trust, Manchester, UK
| | - Christopher J Edwards
- Human Development and Health School, University of Southampton, Southampton, UK,NIHR Southampton Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Dennis Hadjiyiannakis
- NIHR Lancashire Clinical Research Facility, Lancashire Teaching Hospitals NHS Foundation Trust, Preston, UK
| | - Lauren Walker
- Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK,NIHR Royal Liverpool and Broadgreen Clinical Research Facility, Liverpool University Hospital NHS Foundation Trust, Liverpool, UK
| | - Rebecca Lyon
- NIHR Royal Liverpool and Broadgreen Clinical Research Facility, Liverpool University Hospital NHS Foundation Trust, Liverpool, UK
| | - Victoria Shaw
- Clinical Directorate, University of Liverpool, Liverpool, UK
| | - Pavel Mozgunov
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Jimstan Periselneris
- NIHR Kings Clinical Research Facility, King's College Hospital NHS Foundation Trust, London, UK
| | - Christie Woods
- NIHR Royal Liverpool and Broadgreen Clinical Research Facility, Liverpool University Hospital NHS Foundation Trust, Liverpool, UK
| | - Katie Bullock
- Molecular & Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Colin Hale
- NIHR Royal Liverpool and Broadgreen Clinical Research Facility, Liverpool University Hospital NHS Foundation Trust, Liverpool, UK
| | - Helen Reynolds
- Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK
| | - Nichola Downs
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Sean Ewings
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Amanda Buadi
- NIHR Southampton Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - David Cameron
- NIHR Lancashire Clinical Research Facility, Lancashire Teaching Hospitals NHS Foundation Trust, Preston, UK
| | | | - Emma Knox
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - I'ah Donovan-Banfield
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK,National Institute of Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - William Greenhalf
- Molecular & Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Justin Chiong
- Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK
| | | | - Michael Jacobs
- Infectious Diseases, Royal Free London NHS Foundation Trust, London, UK
| | - Josh Northey
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | | | | | | | - Michelle Tetlow
- Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK
| | - Julian A Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK,National Institute of Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - Thomas Jaki
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK,Computational Statistics, University of Regensburg, Regensburg, Germany
| | - Thomas Fletcher
- Tropical and Infectious Disease Unit, Liverpool University Hospital NHS Foundation Trust, Liverpool, UK,Clinical Sciences, Liverpool, UK
| | - Gareth Griffiths
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
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12
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Poh XY, Tan CW, Lee IR, Chavatte JM, Fong SW, Prince T, Hartley C, Yeoh AYY, Rao S, Chia PY, Ong SWX, Lee TH, Sadarangani SP, Lin RJH, Lim C, Teo J, Lim DRX, Chia W, Hiscox JA, Ng LFP, Ren EC, Lin RTP, Renia L, Lye DC, Wang LF, Young BE. Antibody Response of Heterologous vs Homologous Messenger RNA Vaccine Boosters Against the Severe Acute Respiratory Syndrome Coronavirus 2 Omicron Variant: Interim Results from the PRIBIVAC Study, a Randomized Clinical Trial. Clin Infect Dis 2022; 75:2088-2096. [PMID: 35543372 PMCID: PMC9129205 DOI: 10.1093/cid/ciac345] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Waning antibody levels post-vaccination and the emergence of variants of concern (VOCs) capable of evading protective immunity have raised the need for booster vaccinations. However, which combination of coronavirus disease 2019 (COVID-19) vaccines offers the strongest immune response against the Omicron variant is unknown. METHODS This randomized, participant-blinded, controlled trial assessed the reactogenicity and immunogenicity of different COVID-19 vaccine booster combinations. A total of 100 BNT162b2-vaccinated individuals were enrolled and randomized 1:1 to either homologous (BNT162b2 + BNT162b2 + BNT162b2; "BBB") or heterologous messenger RNA (mRNA) (BNT162b2 + BNT162b2 + mRNA-1273; "BBM") booster vaccine. The primary end point was the level of neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) wild-type and VOCs at day 28. RESULTS A total of 51 participants were allocated to BBB and 49 to BBM; 50 and 48, respectively, were analyzed for safety and immunogenicity outcomes. At day 28 post-boost, mean SARS-CoV-2 spike antibody titers were lower with BBB (22 382 IU/mL; 95% confidence interval [CI], 18 210 to 27 517) vs BBM (29 751 IU/mL; 95% CI, 25 281 to 35 011; P = .034) as was the median level of neutralizing antibodies: BBB 99.0% (interquartile range [IQR], 97.9% to 99.3%) vs BBM 99.3% (IQR, 98.8% to 99.5%; P = .021). On subgroup analysis, significant higher mean spike antibody titer, median surrogate neutralizing antibody level against all VOCs, and live Omicron neutralization titer were observed only in older adults receiving BBM. Both vaccines were well tolerated. CONCLUSIONS Heterologous mRNA-1273 booster vaccination compared with homologous BNT123b2 induced a stronger neutralizing response against the Omicron variant in older individuals. CLINICAL TRIALS REGISTRATION NCT05142319.
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Affiliation(s)
- Xuan Ying Poh
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Chee Wah Tan
- Emerging Infectious Diseases Programme, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - I Russel Lee
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Jean-Marc Chavatte
- National Centre for Infectious Diseases, Singapore, Singapore
- National Public Health Laboratory, Singapore, Singapore
| | - Siew-Wai Fong
- A*STAR Infectious Diseases Lab, Agency for Science Technology and Research, Singapore, Singapore
| | - Tessa Prince
- Department of Infection Biology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Catherine Hartley
- Department of Infection Biology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Aileen Y Y Yeoh
- Emerging Infectious Diseases Programme, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Suma Rao
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Po Ying Chia
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Sean W X Ong
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Tau Hong Lee
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Sapna P Sadarangani
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Ray J H Lin
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Clarissa Lim
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Jefanie Teo
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Daniel R X Lim
- National Centre for Infectious Diseases, Singapore, Singapore
- National Public Health Laboratory, Singapore, Singapore
| | - Wanni Chia
- Emerging Infectious Diseases Programme, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Julian A Hiscox
- A*STAR Infectious Diseases Lab, Agency for Science Technology and Research, Singapore, Singapore
- Department of Infection Biology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Lisa F P Ng
- A*STAR Infectious Diseases Lab, Agency for Science Technology and Research, Singapore, Singapore
- Department of Infection Biology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ee Chee Ren
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Singapore Immunology Network, Agency for Science Technology and Research, Singapore, Singapore
| | - Raymond T P Lin
- National Centre for Infectious Diseases, Singapore, Singapore
- National Public Health Laboratory, Singapore, Singapore
| | - Laurent Renia
- A*STAR Infectious Diseases Lab, Agency for Science Technology and Research, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - David Chien Lye
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Lin-Fa Wang
- Emerging Infectious Diseases Programme, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Barnaby E Young
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
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13
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Clark GC, Elfsmark L, Armstrong S, Essex-Lopresti A, Gustafsson Å, Ryan Y, Moore K, Paszkiewicz K, Green AC, Hiscox JA, David J, Jonasson S. From "crisis to recovery": A complete insight into the mechanisms of chlorine injury in the lung. Life Sci 2022; 312:121252. [PMID: 36460096 DOI: 10.1016/j.lfs.2022.121252] [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: 09/05/2022] [Revised: 11/11/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022]
Abstract
Chlorine (Cl2) gas is a toxic industrial chemical (TIC) that poses a hazard to human health following accidental and/or intentional (e.g. terrorist) release. By using a murine model of sub-lethal Cl2 exposure we have examined the airway hyper responsiveness, cellular infiltrates, transcriptomic and proteomic responses of the lung. In the "crisis" phase at 2 h and 6 h there is a significant decreases in leukocytes within bronchoalveolar lavage fluid accompanied by an upregulation within the proteome of immune pathways ultimately resulting in neutrophil influx at 24 h. A flip towards "repair" in the transcriptome and proteome occurs at 24 h, neutrophil influx and an associated drop in the lung function persisting until 14 d post-exposure and subsequent "recovery" after 28 days. Collectively, this research provides new insights into the mechanisms of damage, early global responses and processes of repair induced in the lung following the inhalation of Cl2.
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Affiliation(s)
- Graeme C Clark
- Chemical, Biological and Radiological Division, DSTL Porton Down, Salisbury SP4 0JQ, UK; Institute of Infection and Global Health, University of Liverpool, ic2 Building, Liverpool L3 5RF, UK.
| | - Linda Elfsmark
- Swedish Defence Research Agency, CBRN Defence and Security, Umeå, Sweden
| | - Stuart Armstrong
- Institute of Infection and Global Health, University of Liverpool, ic2 Building, Liverpool L3 5RF, UK
| | - Angela Essex-Lopresti
- Chemical, Biological and Radiological Division, DSTL Porton Down, Salisbury SP4 0JQ, UK
| | - Åsa Gustafsson
- Swedish Defence Research Agency, CBRN Defence and Security, Umeå, Sweden
| | - Yan Ryan
- Institute of Infection and Global Health, University of Liverpool, ic2 Building, Liverpool L3 5RF, UK
| | - Karen Moore
- University of Exeter, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Konrad Paszkiewicz
- University of Exeter, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - A Christopher Green
- Chemical, Biological and Radiological Division, DSTL Porton Down, Salisbury SP4 0JQ, UK
| | - Julian A Hiscox
- Institute of Infection and Global Health, University of Liverpool, ic2 Building, Liverpool L3 5RF, UK
| | - Jonathan David
- Chemical, Biological and Radiological Division, DSTL Porton Down, Salisbury SP4 0JQ, UK
| | - Sofia Jonasson
- Swedish Defence Research Agency, CBRN Defence and Security, Umeå, Sweden.
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14
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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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15
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Ryan Y, Harrison A, Trivett H, Hartley C, David J, Clark GC, Hiscox JA. RIPpore: A Novel Host-Derived Method for the Identification of Ricin Intoxication through Oxford Nanopore Direct RNA Sequencing. Toxins (Basel) 2022; 14:toxins14070470. [PMID: 35878208 PMCID: PMC9319349 DOI: 10.3390/toxins14070470] [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: 06/17/2022] [Revised: 07/01/2022] [Accepted: 07/07/2022] [Indexed: 02/01/2023] Open
Abstract
Ricin is a toxin which enters cells and depurinates an adenine base in the sarcin-ricin loop in the large ribosomal subunit, leading to the inhibition of protein translation and cell death. We postulated that this depurination event could be detected using Oxford Nanopore Technologies (ONT) direct RNA sequencing, detecting a change in charge in the ricin loop. In this study, A549 cells were exposed to ricin for 2–24 h in order to induce depurination. In addition, a novel software tool was developed termed RIPpore that could quantify the adenine modification of ribosomal RNA induced by ricin upon respiratory epithelial cells. We provided demonstrable evidence for the first time that this base change detected is specific to RIP activity using a neutralising antibody against ricin. We believe this represents the first detection of depurination in RNA achieved using ONT sequencers. Collectively, this work highlights the potential for ONT and direct RNA sequencing to detect and quantify depurination events caused by ribosome-inactivating proteins such as ricin. RIPpore could have utility in the evaluation of new treatments and/or in the diagnosis of exposure to ricin.
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Affiliation(s)
- Yan Ryan
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 5RF, UK; (Y.R.); (A.H.); (H.T.); (C.H.)
| | - Abbie Harrison
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 5RF, UK; (Y.R.); (A.H.); (H.T.); (C.H.)
| | - Hannah Trivett
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 5RF, UK; (Y.R.); (A.H.); (H.T.); (C.H.)
| | - Catherine Hartley
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 5RF, UK; (Y.R.); (A.H.); (H.T.); (C.H.)
| | - Jonathan David
- Defence Science Technology Laboratory, Salisbury SP4 0JQ, UK;
| | - Graeme C. Clark
- Defence Science Technology Laboratory, Salisbury SP4 0JQ, UK;
- Correspondence: (G.C.C.); (J.A.H.)
| | - Julian A. Hiscox
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 5RF, UK; (Y.R.); (A.H.); (H.T.); (C.H.)
- Correspondence: (G.C.C.); (J.A.H.)
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16
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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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17
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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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18
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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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19
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Seehusen F, Clark JJ, Sharma P, Bentley EG, Kirby A, Subramaniam K, Wunderlin-Giuliani S, Hughes GL, Patterson EI, Michael BD, Owen A, Hiscox JA, Stewart JP, Kipar A. Neuroinvasion and Neurotropism by SARS-CoV-2 Variants in the K18-hACE2 Mouse. Viruses 2022; 14:1020. [PMID: 35632761 PMCID: PMC9146514 DOI: 10.3390/v14051020] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [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: 03/31/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 12/15/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) not only affects the respiratory tract but also causes neurological symptoms such as loss of smell and taste, headache, fatigue or severe cerebrovascular complications. Using transgenic mice expressing human angiotensin-converting enzyme 2 (hACE2), we investigated the spatiotemporal distribution and pathomorphological features in the CNS following intranasal infection with SARS-CoV-2 variants, as well as after prior influenza A virus infection. Apart from Omicron, we found all variants to frequently spread to and within the CNS. Infection was restricted to neurons and appeared to spread from the olfactory bulb mainly in basally oriented regions in the brain and into the spinal cord, independent of ACE2 expression and without evidence of neuronal cell death, axonal damage or demyelination. However, microglial activation, microgliosis and a mild macrophage and T cell dominated inflammatory response was consistently observed, accompanied by apoptotic death of endothelial, microglial and immune cells, without their apparent infection. Microgliosis and immune cell apoptosis indicate a potential role of microglia for pathogenesis and viral effect in COVID-19 and the possible impairment of neurological functions, especially in long COVID. These data may also be informative for the selection of therapeutic candidates and broadly support the investigation of agents with adequate penetration into relevant regions of the CNS.
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Affiliation(s)
- Frauke Seehusen
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland; (F.S.); (S.W.-G.)
| | - Jordan J. Clark
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 5RF, UK; (J.J.C.); (P.S.); (E.G.B.); (A.K.); (K.S.); (J.A.H.); (J.P.S.)
| | - Parul Sharma
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 5RF, UK; (J.J.C.); (P.S.); (E.G.B.); (A.K.); (K.S.); (J.A.H.); (J.P.S.)
| | - Eleanor G. Bentley
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 5RF, UK; (J.J.C.); (P.S.); (E.G.B.); (A.K.); (K.S.); (J.A.H.); (J.P.S.)
| | - Adam Kirby
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 5RF, UK; (J.J.C.); (P.S.); (E.G.B.); (A.K.); (K.S.); (J.A.H.); (J.P.S.)
| | - Krishanthi Subramaniam
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 5RF, UK; (J.J.C.); (P.S.); (E.G.B.); (A.K.); (K.S.); (J.A.H.); (J.P.S.)
| | - Sabina Wunderlin-Giuliani
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland; (F.S.); (S.W.-G.)
| | - Grant L. Hughes
- Departments of Vector Biology and Tropical Disease Biology, Centre for Neglected Tropical Disease, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK; (G.L.H.); (E.I.P.)
| | - Edward I. Patterson
- Departments of Vector Biology and Tropical Disease Biology, Centre for Neglected Tropical Disease, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK; (G.L.H.); (E.I.P.)
| | - Benedict D. Michael
- Department of Clinical Infection Microbiology and Immunology and NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary, and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK;
- Department of Neurology, The Walton Centre NHS Foundation Trust, Liverpool L9 7AL, UK
| | - Andrew Owen
- Department of Pharmacology and Therapeutics, Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L3 3NY, UK;
| | - Julian A. Hiscox
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 5RF, UK; (J.J.C.); (P.S.); (E.G.B.); (A.K.); (K.S.); (J.A.H.); (J.P.S.)
| | - James P. Stewart
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 5RF, UK; (J.J.C.); (P.S.); (E.G.B.); (A.K.); (K.S.); (J.A.H.); (J.P.S.)
| | - Anja Kipar
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland; (F.S.); (S.W.-G.)
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 5RF, UK; (J.J.C.); (P.S.); (E.G.B.); (A.K.); (K.S.); (J.A.H.); (J.P.S.)
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20
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Zhang B, Fan M, Fan J, Luo Y, Wang J, Wang Y, Liu B, Sun Y, Zhao Q, Hiscox JA, Nan Y, Zhou EM. Avian Hepatitis E Virus ORF2 Protein Interacts with Rap1b to Induce Cytoskeleton Rearrangement That Facilitates Virus Internalization. Microbiol Spectr 2022; 10:e0226521. [PMID: 35138149 PMCID: PMC8826821 DOI: 10.1128/spectrum.02265-21] [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: 12/13/2021] [Accepted: 01/05/2022] [Indexed: 12/31/2022] Open
Abstract
Avian hepatitis E virus (HEV) causes liver diseases and multiple extrahepatic disorders in chickens. However, the mechanisms involved in avian HEV entry remain elusive. Herein, we identified the RAS-related protein 1b (Rap1b) as a potential HEV-ORF2 protein interacting candidate. Experimental infection of chickens and cells with an avian HEV isolate from China (CaHEV) led to upregulated expression and activation of Rap1b both in vivo and in vitro. By using CaHEV capsid as mimic of virion to treat cell in vitro, it appears that the interaction between the viral capsid and Rap1b promoted cell membrane recruitment of the downstream effector Rap1-interacting molecule (RIAM). In turn, RIAM further enhanced Talin-1 membrane recruitment and retention, which led to the activation of integrin α5/β1, as well as integrin-associated membrane protein kinases, including focal adhesion kinase (FAK). Meanwhile, FAK activation triggered activation of downstream signaling molecules, such as Ras-related C3 botulinum toxin substrate 1 RAC1 cell division cycle 42 (CDC42), p21-activated kinase 1 (PAK1), and LIM domain kinase 1 (LIMK1). Finally, F-actin rearrangement induced by Cofilin led to the formation of lamellipodia, filopodia, and stress fibers, contributes to plasma membrane remodeling, and might enhance CaHEV virion internalization. In conclusion, our data suggested that Rap1b activation was triggered during CaHEV infection and appeared to require interaction between CaHEV-ORF2 and Rap1b, thereby further inducing membrane recruitment of Talin-1. Membrane-bound Talin-1 then activates key Integrin-FAK-Cofilin cascades involved in modulation of actin kinetics, and finally leads to F-actin rearrangement and membrane remodeling to potentially facilitate internalization of CaHEV virions into permissive cells. IMPORTANCE Rap1b is a multifunctional protein that is responsible for cell adhesion, growth, and differentiation. The inactive form of Rap1b is phosphorylated and distributed in the cytoplasm, while active Rap1b is prenylated and loaded with GTP to the cell membrane. In this study, the activation of Rap1b was induced during the early stage of avian HEV infection under the regulation of PKA and SmgGDS. Continuously activated Rap1b recruited its effector RIAM to the membrane, thereby inducing the membrane recruitment of Talin-1 that led to the activation of membrane α5/β1 integrins. The triggering of the signaling pathway-associated Integrin α5/β1-FAK-CDC42&RAC1-PAK1-LIMK1-Cofilin culminated in F-actin polymerization and membrane remodeling that might promote avian HEV virion internalization. These findings suggested a novel mechanism that is potentially utilized by avian HEV to invade susceptible cells.
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Affiliation(s)
- Beibei Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Mengnan Fan
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Jie Fan
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuhang Luo
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Jie Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Yajing Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Baoyuan Liu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Yani Sun
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Qin Zhao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Yuchen Nan
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - En-Min Zhou
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
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21
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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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22
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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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23
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Fan M, Luo Y, Zhang B, Wang J, Chen T, Liu B, Sun Y, Nan Y, Hiscox JA, Zhao Q, Zhou EM. Cell Division Control Protein 42 Interacts With Hepatitis E Virus Capsid Protein and Participates in Hepatitis E Virus Infection. Front Microbiol 2021; 12:775083. [PMID: 34790187 PMCID: PMC8591454 DOI: 10.3389/fmicb.2021.775083] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/13/2021] [Indexed: 11/30/2022] Open
Abstract
Hepatitis E Virus (HEV) causes viral hepatitis in humans worldwide, while a subset of HEV species, avian HEV, causes hepatitis-splenomegaly syndrome in chickens. To date, there are few reports on the host proteins interacting with HEV and being involved in viral infection. Previous pull-down assay combining mass spectrometry indicated that cell division control protein 42 (CDC42), a member belonging to the Rho GTPase family, was pulled down by avian HEV capsid protein. We confirmed the direct interaction between CDC42 and avian and mammalian HEV capsid proteins. The interaction can increase the amount of active guanosine triphosphate binding CDC42 state (GTP-CDC42). Subsequently, we determined that the expression and activity of CDC42 were positively correlated with HEV infection in the host cells. Using the different inhibitors of CDC42 downstream signaling pathways, we found that CDC42-MRCK (a CDC42-binding kinase)-non-myosin IIA (NMIIA) pathway is involved in naked avian and mammalian HEV infection, CDC42-associated p21-activated kinase 1 (PAK1)-NMIIA/Cofilin pathway is involved in quasi-enveloped mammalian HEV infection and CDC42-neural Wiskott-Aldrich syndrome protein-actin-polymerizing protein Arp2/3 pathway (CDC42-(N-)WASP-Arp2/3) pathway participates in naked and quasi-enveloped mammalian HEV infection. Collectively, these results demonstrated for the first time that HEV capsid protein can directly bind to CDC42, and non- and quasi-enveloped HEV use different CDC42 downstream signaling pathways to participate in viral infection. The study provided some new insights to understand the life cycle of HEV in host cells and a new target of drug design for combating HEV infection.
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Affiliation(s)
- Mengnan Fan
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Yuhang Luo
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Beibei Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Jiaxi Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Tianxiang Chen
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Baoyuan Liu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Yani Sun
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Yuchen Nan
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Julian A Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Qin Zhao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - En-Min Zhou
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
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24
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Wang B, Goh YS, Prince T, Ngoh EZX, Salleh SNM, Hor PX, Loh CY, Fong SW, Hartley C, Tan SY, Young BE, Leo YS, Lye DC, Maurer-Stroh S, Ng LFP, Hiscox JA, Renia L, Wang CI. Resistance of SARS-CoV-2 variants to neutralization by convalescent plasma from early COVID-19 outbreak in Singapore. NPJ Vaccines 2021; 6:125. [PMID: 34697298 PMCID: PMC8546091 DOI: 10.1038/s41541-021-00389-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 10/01/2021] [Indexed: 12/22/2022] Open
Abstract
The rapid spreading of SARS-CoV-2 variants B.1.1.7 originated from the United Kingdom and B.1.351 from South Africa has contributed to the second wave of COVID-19 cases in the respective countries and also around the world. In this study, we employed advanced biochemical and virological methodologies to evaluate the impact of Spike mutations of these strains on the degree of protection afforded by humoral immune responses following natural infection of the ancestral SARS-CoV-2 strain during the early stages of the outbreak. We found that antibody-mediated neutralization activity was partially reduced for B.1.1.7 variant and significantly attenuated for the B.1.351 strain. We also found that mutations outside the receptor-binding domain (RBD) can strongly influence antibody binding and neutralization, cautioning the use of solely RBD mutations in evaluating vaccine efficacy. These findings highlight an urgent need to develop new SARS-CoV-2 vaccines that are not based exclusively on the ancestral SARS-CoV-2 Spike gene sequence.
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Affiliation(s)
- Bei Wang
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yun Shan Goh
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Tessa Prince
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Eve Zi Xian Ngoh
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Siti Nazihah Mohd Salleh
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Pei Xiang Hor
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chiew Yee Loh
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Siew Wai Fong
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Catherine Hartley
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Seow-Yen Tan
- Department of Infectious Diseases, Changi General Hospital, Singapore, Singapore
| | - Barnaby Edward Young
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - David C Lye
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Sebastian Maurer-Stroh
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Bioinformatics Institute, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Lisa F P Ng
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Julian A Hiscox
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Laurent Renia
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Cheng-I Wang
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
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25
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Huo J, Mikolajek H, Le Bas A, Clark JJ, Sharma P, Kipar A, Dormon J, Norman C, Weckener M, Clare DK, Harrison PJ, Tree JA, Buttigieg KR, Salguero FJ, Watson R, Knott D, Carnell O, Ngabo D, Elmore MJ, Fotheringham S, Harding A, Moynié L, Ward PN, Dumoux M, Prince T, Hall Y, Hiscox JA, Owen A, James W, Carroll MW, Stewart JP, Naismith JH, Owens RJ. A potent SARS-CoV-2 neutralising nanobody shows therapeutic efficacy in the Syrian golden hamster model of COVID-19. Nat Commun 2021; 12:5469. [PMID: 34552091 PMCID: PMC8458290 DOI: 10.1038/s41467-021-25480-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [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: 05/27/2021] [Accepted: 08/12/2021] [Indexed: 12/18/2022] Open
Abstract
SARS-CoV-2 remains a global threat to human health particularly as escape mutants emerge. There is an unmet need for effective treatments against COVID-19 for which neutralizing single domain antibodies (nanobodies) have significant potential. Their small size and stability mean that nanobodies are compatible with respiratory administration. We report four nanobodies (C5, H3, C1, F2) engineered as homotrimers with pmolar affinity for the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. Crystal structures show C5 and H3 overlap the ACE2 epitope, whilst C1 and F2 bind to a different epitope. Cryo Electron Microscopy shows C5 binding results in an all down arrangement of the Spike protein. C1, H3 and C5 all neutralize the Victoria strain, and the highly transmissible Alpha (B.1.1.7 first identified in Kent, UK) strain and C1 also neutralizes the Beta (B.1.35, first identified in South Africa). Administration of C5-trimer via the respiratory route showed potent therapeutic efficacy in the Syrian hamster model of COVID-19 and separately, effective prophylaxis. The molecule was similarly potent by intraperitoneal injection.
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MESH Headings
- Administration, Intranasal
- Animals
- Antibodies, Neutralizing/administration & dosage
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/pharmacology
- Cryoelectron Microscopy
- Crystallography, X-Ray
- Disease Models, Animal
- Dose-Response Relationship, Immunologic
- Epitopes/chemistry
- Epitopes/metabolism
- Female
- Male
- Mesocricetus
- Neutralization Tests
- SARS-CoV-2/drug effects
- Single-Domain Antibodies/administration & dosage
- Single-Domain Antibodies/immunology
- Single-Domain Antibodies/metabolism
- Single-Domain Antibodies/pharmacology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/metabolism
- COVID-19 Drug Treatment
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Affiliation(s)
- Jiandong Huo
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Science Campus, Didcot, UK
| | | | - Audrey Le Bas
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Science Campus, Didcot, UK
| | - Jordan J Clark
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Parul Sharma
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Anja Kipar
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Joshua Dormon
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Science Campus, Didcot, UK
| | - Chelsea Norman
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Science Campus, Didcot, UK
| | - Miriam Weckener
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK
| | - Daniel K Clare
- Diamond Light Source Ltd, Harwell Science Campus, Didcot, UK
| | - Peter J Harrison
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Science Campus, Didcot, UK
- Diamond Light Source Ltd, Harwell Science Campus, Didcot, UK
| | - Julia A Tree
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Karen R Buttigieg
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | | | - Robert Watson
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Daniel Knott
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Oliver Carnell
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Didier Ngabo
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Michael J Elmore
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Susan Fotheringham
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Adam Harding
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Lucile Moynié
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK
| | - Philip N Ward
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Science Campus, Didcot, UK
| | - Maud Dumoux
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK
| | - Tessa Prince
- Diamond Light Source Ltd, Harwell Science Campus, Didcot, UK
| | - Yper Hall
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Julian A Hiscox
- Diamond Light Source Ltd, Harwell Science Campus, Didcot, UK
- Department of Preventive Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
- Infectious Diseases Horizontal Technology Centre (ID HTC), A*STAR, Singapore, Singapore
| | - Andrew Owen
- Department of Pharmacology and Therapeutics, Centre of Excellence in Long-acting Therapeutics (CELT), University of Liverpool, Liverpool, UK
| | - William James
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Miles W Carroll
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - James P Stewart
- Diamond Light Source Ltd, Harwell Science Campus, Didcot, UK
- Department of Preventive Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
- Department of Infectious Disease, University of Georgia, Georgia, USA
| | - James H Naismith
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK.
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Science Campus, Didcot, UK.
| | - Raymond J Owens
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK.
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Science Campus, Didcot, UK.
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26
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Salzer R, Clark JJ, Vaysburd M, Chang VT, Albecka A, Kiss L, Sharma P, Gonzalez Llamazares A, Kipar A, Hiscox JA, Owen A, Aricescu AR, Stewart JP, James LC, Löwe J. Single-dose immunisation with a multimerised SARS-CoV-2 receptor binding domain (RBD) induces an enhanced and protective response in mice. FEBS Lett 2021; 595:2323-2340. [PMID: 34331769 PMCID: PMC8426897 DOI: 10.1002/1873-3468.14171] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 06/10/2021] [Revised: 07/02/2021] [Accepted: 07/13/2021] [Indexed: 11/23/2022]
Abstract
The COVID-19 pandemic, caused by the SARS-CoV-2 coronavirus, has triggered a worldwide health emergency. Here, we show that ferritin-like Dps from hyperthermophilic Sulfolobus islandicus, covalently coupled with SARS-CoV-2 antigens via the SpyCatcher system, forms stable multivalent dodecameric vaccine nanoparticles that remain intact even after lyophilisation. Immunisation experiments in mice demonstrated that the SARS-CoV-2 receptor binding domain (RBD) coupled to Dps (RBD-S-Dps) elicited a higher antibody titre and an enhanced neutralising antibody response compared to monomeric RBD. A single immunisation with RBD-S-Dps completely protected hACE2-expressing mice from serious illness and led to viral clearance from the lungs upon SARS-CoV-2 infection. Our data highlight that multimerised SARS-CoV-2 subunit vaccines are a highly efficacious modality, particularly when combined with an ultra-stable scaffold.
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Affiliation(s)
- Ralf Salzer
- MRC Laboratory of Molecular BiologyCambridgeUK
| | - Jordan J. Clark
- Institute of Infection, Veterinary and Ecological SciencesUniversity of LiverpoolUK
| | | | | | | | - Leo Kiss
- MRC Laboratory of Molecular BiologyCambridgeUK
| | - Parul Sharma
- Institute of Infection, Veterinary and Ecological SciencesUniversity of LiverpoolUK
| | | | - Anja Kipar
- Institute of Infection, Veterinary and Ecological SciencesUniversity of LiverpoolUK
- Laboratory for Animal Model PathologyInstitute of Veterinary PathologyVetsuisse FacultyUniversity of ZurichSwitzerland
| | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecological SciencesUniversity of LiverpoolUK
| | - Andrew Owen
- Department of Pharmacology and TherapeuticsCentre of Excellence in Long‐acting Therapeutics (CELT)University of LiverpoolUK
| | | | - James P. Stewart
- Institute of Infection, Veterinary and Ecological SciencesUniversity of LiverpoolUK
| | | | - Jan Löwe
- MRC Laboratory of Molecular BiologyCambridgeUK
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27
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Hiscox JA, Khoo SH, Stewart JP, Owen A. Shutting the gate before the horse has bolted: is it time for a conversation about SARS-CoV-2 and antiviral drug resistance? J Antimicrob Chemother 2021; 76:2230-2233. [PMID: 34142123 PMCID: PMC8361339 DOI: 10.1093/jac/dkab189] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
This article provides a brief overview of drug resistance to antiviral therapy as well as known and emergent variability in key SARS-CoV-2 viral sequences. The purpose is to stimulate deliberation about the need to consider drug resistance prior to widespread roll-out of antivirals for SARS-CoV-2. Many existing candidate agents have mechanisms of action involving drug targets likely to be critical for future drug development. Resistance emerged quickly with monotherapies deployed for other pulmonary viruses such as influenza virus, and in HIV mutations in key drug targets compromised efficacy of multiple drugs within a class. The potential for drug resistance in SARS-CoV-2 has not yet been rigorously debated or assessed, and we call for more academic and industry research on this potentially important future threat prior to widespread roll-out of monotherapies for COVID-19 treatment and prevention.
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Affiliation(s)
- 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
| | - Saye H. Khoo
- Department of Pharmacology and Therapeutics, Materials Innovation Factory, University of Liverpool, Liverpool, L7 3NY, UK
| | - James P. Stewart
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Andrew Owen
- Department of Pharmacology and Therapeutics, Materials Innovation Factory, University of Liverpool, Liverpool, L7 3NY, UK
- Centre of Excellence in Long acting Therapeutics (CELT), University of Liverpool, Liverpool, L69 3BX, UK
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28
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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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29
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Affiliation(s)
- Alistair C Darby
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- The COVID-19 Genomics UK (COG-UK) Consortium, University of Cambridge, Cambridge, UK
| | - Julian A Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- A*STAR Infectious Diseases Laboratories, Agency for Science, Technology and Research, Singapore
- Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
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30
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Salguero FJ, White AD, Slack GS, Fotheringham SA, Bewley KR, Gooch KE, Longet S, Humphries HE, Watson RJ, Hunter L, Ryan KA, Hall Y, Sibley L, Sarfas C, Allen L, Aram M, Brunt E, Brown P, Buttigieg KR, Cavell BE, Cobb R, Coombes NS, Darby A, Daykin-Pont O, Elmore MJ, Garcia-Dorival I, Gkolfinos K, Godwin KJ, Gouriet J, Halkerston R, Harris DJ, Hender T, Ho CMK, Kennard CL, Knott D, Leung S, Lucas V, Mabbutt A, Morrison AL, Nelson C, Ngabo D, Paterson J, Penn EJ, Pullan S, Taylor I, Tipton T, Thomas S, Tree JA, Turner C, Vamos E, Wand N, Wiblin NR, Charlton S, Dong X, Hallis B, Pearson G, Rayner EL, Nicholson AG, Funnell SG, Hiscox JA, Dennis MJ, Gleeson FV, Sharpe S, Carroll MW. Comparison of rhesus and cynomolgus macaques as an infection model for COVID-19. Nat Commun 2021; 12:1260. [PMID: 33627662 PMCID: PMC7904795 DOI: 10.1038/s41467-021-21389-9] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [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: 09/06/2020] [Accepted: 01/26/2021] [Indexed: 02/06/2023] Open
Abstract
A novel coronavirus, SARS-CoV-2, has been identified as the causative agent of the current COVID-19 pandemic. Animal models, and in particular non-human primates, are essential to understand the pathogenesis of emerging diseases and to assess the safety and efficacy of novel vaccines and therapeutics. Here, we show that SARS-CoV-2 replicates in the upper and lower respiratory tract and causes pulmonary lesions in both rhesus and cynomolgus macaques. Immune responses against SARS-CoV-2 are also similar in both species and equivalent to those reported in milder infections and convalescent human patients. This finding is reiterated by our transcriptional analysis of respiratory samples revealing the global response to infection. We describe a new method for lung histopathology scoring that will provide a metric to enable clearer decision making for this key endpoint. In contrast to prior publications, in which rhesus are accepted to be the preferred study species, we provide convincing evidence that both macaque species authentically represent mild to moderate forms of COVID-19 observed in the majority of the human population and both species should be used to evaluate the safety and efficacy of interventions against SARS-CoV-2. Importantly, accessing cynomolgus macaques will greatly alleviate the pressures on current rhesus stocks.
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Affiliation(s)
- Francisco J Salguero
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Andrew D White
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Gillian S Slack
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Susan A Fotheringham
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Kevin R Bewley
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Karen E Gooch
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Stephanie Longet
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Holly E Humphries
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Robert J Watson
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Laura Hunter
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Kathryn A Ryan
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Yper Hall
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Laura Sibley
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Charlotte Sarfas
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Lauren Allen
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Marilyn Aram
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Emily Brunt
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Phillip Brown
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Karen R Buttigieg
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Breeze E Cavell
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Rebecca Cobb
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Naomi S Coombes
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Alistair Darby
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Owen Daykin-Pont
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Michael J Elmore
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Isabel Garcia-Dorival
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Konstantinos Gkolfinos
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Kerry J Godwin
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Jade Gouriet
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Rachel Halkerston
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Debbie J Harris
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Thomas Hender
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Catherine M K Ho
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Chelsea L Kennard
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Daniel Knott
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Stephanie Leung
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Vanessa Lucas
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Adam Mabbutt
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Alexandra L Morrison
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Charlotte Nelson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Didier Ngabo
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Jemma Paterson
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Elizabeth J Penn
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Steve Pullan
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Irene Taylor
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Tom Tipton
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Stephen Thomas
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Julia A Tree
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Carrie Turner
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Edith Vamos
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Nadina Wand
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Nathan R Wiblin
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Sue Charlton
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Xiaofeng Dong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Bassam Hallis
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Geoffrey Pearson
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Emma L Rayner
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Andrew G Nicholson
- Royal Brompton and Harefield NHS Foundation Trust, and National Heart and Lung Institute, Imperial College, London, UK
| | - Simon G Funnell
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Julian A Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Infectious Diseases Horizontal Technology Centre (ID HTC), A*STAR, Singapore, Singapore
| | - Mike J Dennis
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | | | - Sally Sharpe
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Miles W Carroll
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK.
- Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, OX3 7BN, UK.
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31
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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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32
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Bosworth A, Rickett NY, Dong X, Ng LFP, García-Dorival I, Matthews DA, Fletcher T, Jacobs M, Thomson EC, Carroll MW, Hiscox JA. Analysis of an Ebola virus disease survivor whose host and viral markers were predictive of death indicates the effectiveness of medical countermeasures and supportive care. Genome Med 2021; 13:5. [PMID: 33430949 PMCID: PMC7798020 DOI: 10.1186/s13073-020-00811-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 11/27/2019] [Accepted: 11/12/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Ebola virus disease (EVD) is an often-fatal infection where the effectiveness of medical countermeasures is uncertain. During the West African outbreak (2013-2016), several patients were treated with different types of anti-viral therapies including monoclonal antibody-based cocktails that had the potential to neutralise Ebola virus (EBOV). However, at the time, the efficacy of these therapies was uncertain. Given the scale of the outbreak, several clinical phenotypes came to the forefront including the ability of the same virus to cause recrudescence in the same patient-perhaps through persisting in immune privileged sites. Several key questions remained including establishing if monoclonal antibody therapy was effective in humans with severe EVD, whether virus escape mutants were selected during treatment, and what is the potential mechanism(s) of persistence. This was made possible through longitudinal samples taken from a UK patient with EVD. METHODS Several different sample types, plasma and cerebrospinal fluid, were collected and sequenced using Illumina-based RNAseq. Sequence reads were mapped both to EBOV and the human genome and differential gene expression analysis used to identify changes in the abundance of gene transcripts as infection progressed. Digital Cell Quantitation analysis was used to predict the immune phenotype in samples derived from blood. RESULTS The findings were compared to equivalent data from West African patients. The study found that both virus and host markers were predictive of a fatal outcome. This suggested that the extensive supportive care, and most likely the application of the medical countermeasure ZMab (a monoclonal antibody cocktail), contributed to survival of the UK patient. The switch from progression to a 'fatal' outcome to a 'survival' outcome could be seen in both the viral and host markers. The UK patient also suffered a recrudescence infection 10 months after the initial infection. Analysis of the sequencing data indicated that the virus entered a period of reduced or minimal replication, rather than other potential mechanisms of persistence-such as defective interfering genomes. CONCLUSIONS The data showed that comprehensive supportive care and the application of medical countermeasures are worth pursuing despite an initial unfavourable prognosis.
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Affiliation(s)
- Andrew Bosworth
- Public Health England, Manor Farm Road, Porton Down, Salisbury, UK
- Clinical Virology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
- Health Protection Research Unit in Emerging and Zoonotic Infections, National Institute for Health Research, Liverpool, UK
| | - Natasha Y Rickett
- Health Protection Research Unit in Emerging and Zoonotic Infections, National Institute for Health Research, Liverpool, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Xiaofeng Dong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Lisa F P Ng
- Health Protection Research Unit in Emerging and Zoonotic Infections, National Institute for Health Research, Liverpool, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Infectious Disease Horizontal Technology Centre (ID HTC), A*STAR, Singapore, Singapore
| | - Isabel García-Dorival
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - David A Matthews
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Tom Fletcher
- Health Protection Research Unit in Emerging and Zoonotic Infections, National Institute for Health Research, Liverpool, UK
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - Michael Jacobs
- Department of Infection, Royal Free London NHS Foundation Trust, London, UK
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.
| | - Miles W Carroll
- Public Health England, Manor Farm Road, Porton Down, Salisbury, UK.
- Health Protection Research Unit in Emerging and Zoonotic Infections, National Institute for Health Research, Liverpool, UK.
- Nufield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Julian A Hiscox
- Health Protection Research Unit in Emerging and Zoonotic Infections, National Institute for Health Research, Liverpool, UK.
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
- Infectious Disease Horizontal Technology Centre (ID HTC), A*STAR, Singapore, Singapore.
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33
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Daly JL, Simonetti B, Klein K, Chen KE, Williamson MK, Antón-Plágaro C, Shoemark DK, Simón-Gracia L, Bauer M, Hollandi R, Greber UF, Horvath P, Sessions RB, Helenius A, Hiscox JA, Teesalu T, Matthews DA, Davidson AD, Collins BM, Cullen PJ, Yamauchi Y. Neuropilin-1 is a host factor for SARS-CoV-2 infection. Science 2020; 370:861-865. [PMID: 33082294 DOI: 10.1101/2020.06.05.134114] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 10/12/2020] [Indexed: 05/20/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), uses the viral spike (S) protein for host cell attachment and entry. The host protease furin cleaves the full-length precursor S glycoprotein into two associated polypeptides: S1 and S2. Cleavage of S generates a polybasic Arg-Arg-Ala-Arg carboxyl-terminal sequence on S1, which conforms to a C-end rule (CendR) motif that binds to cell surface neuropilin-1 (NRP1) and NRP2 receptors. We used x-ray crystallography and biochemical approaches to show that the S1 CendR motif directly bound NRP1. Blocking this interaction by RNA interference or selective inhibitors reduced SARS-CoV-2 entry and infectivity in cell culture. NRP1 thus serves as a host factor for SARS-CoV-2 infection and may potentially provide a therapeutic target for COVID-19.
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Affiliation(s)
- James L Daly
- School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Boris Simonetti
- School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK.
| | - Katja Klein
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Kai-En Chen
- Institute for Molecular Bioscience, the University of Queensland, St. Lucia, QLD 4072, Australia
| | - Maia Kavanagh Williamson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Carlos Antón-Plágaro
- School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Deborah K Shoemark
- School of Biochemistry and BrisSynBio Centre, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Lorena Simón-Gracia
- Laboratory of Cancer Biology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Michael Bauer
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Reka Hollandi
- Synthetic and Systems Biology Unit, Biological Research Centre (BRC), Szeged, Hungary
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Peter Horvath
- Synthetic and Systems Biology Unit, Biological Research Centre (BRC), Szeged, Hungary
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Richard B Sessions
- School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Ari Helenius
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Julian A Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Singapore Immunology Network, Agency for Science, Technology, and Research, 138648, Singapore
| | - Tambet Teesalu
- Laboratory of Cancer Biology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - David A Matthews
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Andrew D Davidson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Brett M Collins
- Institute for Molecular Bioscience, the University of Queensland, St. Lucia, QLD 4072, Australia
| | - Peter J Cullen
- School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK.
| | - Yohei Yamauchi
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK.
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
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34
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Wang Y, Li R, Qiao S, Wang J, Liu H, Li Z, Ma H, Yang L, Ruan H, Weng M, Hiscox JA, Stewart JP, Nan Y, Zhang G, Zhou EM. Structural Characterization of Non-structural Protein 9 Complexed With Specific Nanobody Pinpoints Two Important Residues Involved in Porcine Reproductive and Respiratory Syndrome Virus Replication. Front Microbiol 2020; 11:581856. [PMID: 33281776 PMCID: PMC7688669 DOI: 10.3389/fmicb.2020.581856] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 07/10/2020] [Accepted: 10/26/2020] [Indexed: 12/11/2022] Open
Abstract
Porcine reproductive and respiratory syndrome (PRRS), caused by PRRS virus (PRRSV), is a widespread viral disease that has led to huge economic losses for the global swine industry. Non-structural protein 9 (Nsp9) of PRRSV possesses essential RNA-dependent RNA polymerase (RdRp) activity for viral RNA replication. Our previous report showed that Nsp9-specific nanobody, Nb6, was able to inhibit PRRSV replication. In this study, recombinant Nsp9 and Nsp9-Nb6 complex were prepared then characterized using bio-layer interferometry (BLI) and dynamic light scattering (DLS) analyses that demonstrated high-affinity binding of Nb6 to Nsp9 to form a homogeneous complex. Small-angle X-ray scattering (SAXS) characterization analyses revealed that spatial interactions differed between Nsp9 and Nsp9-Nb6 complex molecular envelopes. Enzyme-linked immunosorbent assays (ELISAs) revealed key involvement of Nsp9 residues Ile588, Asp590, and Leu643 and Nb6 residues Tyr62, Trp105, and Pro107 in the Nsp9-Nb6 interaction. After reverse genetics-based techniques were employed to generate recombinant Nsp9 mutant viruses, virus replication efficiencies were assessed in MARC-145 cells. The results revealed impaired viral replication of recombinant viruses bearing I588A and L643A mutations as compared with replication of wild type virus, as evidenced by reduced negative-strand genomic RNA [(−) gRNA] synthesis and attenuated viral infection. Moreover, the isoleucine at position 588 of Nsp9 was conserved across PRRSV genotypes. In conclusion, structural analysis of the Nsp9-Nb6 complex revealed novel amino acid interactions involved in viral RNA replication that will be useful for guiding development of structure-based anti-PRRSV agents.
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Affiliation(s)
- Yan Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Rui Li
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Songlin Qiao
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Jiaxi Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Hongliang Liu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Zhijun Li
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Hongfang Ma
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Lei Yang
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Haiyu Ruan
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Maoyang Weng
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Julian A Hiscox
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - James P Stewart
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Yuchen Nan
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Gaiping Zhang
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - En-Min Zhou
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
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35
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Daly JL, Simonetti B, Klein K, Chen KE, Williamson MK, Antón-Plágaro C, Shoemark DK, Simón-Gracia L, Bauer M, Hollandi R, Greber UF, Horvath P, Sessions RB, Helenius A, Hiscox JA, Teesalu T, Matthews DA, Davidson AD, Collins BM, Cullen PJ, Yamauchi Y. Neuropilin-1 is a host factor for SARS-CoV-2 infection. Science 2020; 370:861-865. [PMID: 33082294 DOI: 10.1126/science.abd3072] [Citation(s) in RCA: 845] [Impact Index Per Article: 211.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 10/12/2020] [Indexed: 12/12/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), uses the viral spike (S) protein for host cell attachment and entry. The host protease furin cleaves the full-length precursor S glycoprotein into two associated polypeptides: S1 and S2. Cleavage of S generates a polybasic Arg-Arg-Ala-Arg carboxyl-terminal sequence on S1, which conforms to a C-end rule (CendR) motif that binds to cell surface neuropilin-1 (NRP1) and NRP2 receptors. We used x-ray crystallography and biochemical approaches to show that the S1 CendR motif directly bound NRP1. Blocking this interaction by RNA interference or selective inhibitors reduced SARS-CoV-2 entry and infectivity in cell culture. NRP1 thus serves as a host factor for SARS-CoV-2 infection and may potentially provide a therapeutic target for COVID-19.
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Affiliation(s)
- James L Daly
- School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Boris Simonetti
- School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK.
| | - Katja Klein
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Kai-En Chen
- Institute for Molecular Bioscience, the University of Queensland, St. Lucia, QLD 4072, Australia
| | - Maia Kavanagh Williamson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Carlos Antón-Plágaro
- School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Deborah K Shoemark
- School of Biochemistry and BrisSynBio Centre, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Lorena Simón-Gracia
- Laboratory of Cancer Biology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Michael Bauer
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Reka Hollandi
- Synthetic and Systems Biology Unit, Biological Research Centre (BRC), Szeged, Hungary
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Peter Horvath
- Synthetic and Systems Biology Unit, Biological Research Centre (BRC), Szeged, Hungary.,Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Richard B Sessions
- School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Ari Helenius
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Julian A Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.,Singapore Immunology Network, Agency for Science, Technology, and Research, 138648, Singapore
| | - Tambet Teesalu
- Laboratory of Cancer Biology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - David A Matthews
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Andrew D Davidson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Brett M Collins
- Institute for Molecular Bioscience, the University of Queensland, St. Lucia, QLD 4072, Australia
| | - Peter J Cullen
- School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK.
| | - Yohei Yamauchi
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK. .,Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
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36
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Dong X, Munoz-Basagoiti J, Rickett NY, Pollakis G, Paxton WA, Günther S, Kerber R, Ng LFP, Elmore MJ, Magassouba N, Carroll MW, Matthews DA, Hiscox JA. Variation around the dominant viral genome sequence contributes to viral load and outcome in patients with Ebola virus disease. Genome Biol 2020; 21:238. [PMID: 32894206 PMCID: PMC7475720 DOI: 10.1186/s13059-020-02148-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 11/28/2019] [Accepted: 08/17/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Viral load is a major contributor to outcome in patients with Ebola virus disease (EVD), with high values leading to a fatal outcome. Evidence from the 2013-2016 Ebola virus (EBOV) outbreak indicated that different genotypes of the virus can have different phenotypes in patients. Additionally, due to the error-prone nature of viral RNA synthesis in an individual patient, the EBOV genome exists around a dominant viral genome sequence. The minor variants within a patient may contribute to the overall phenotype in terms of viral protein function. To investigate the effects of these minor variants, blood samples from patients with acute EVD were deeply sequenced. RESULTS We examine the minor variant frequency between patients with acute EVD who survived infection with those who died. Non-synonymous differences in viral proteins were identified that have implications for viral protein function. The greatest frequency of substitution was identified at three codon sites in the L gene-which encodes the viral RNA-dependent RNA polymerase (RdRp). Recapitulating this in an assay for virus replication, these substitutions result in aberrant viral RNA synthesis and correlate with patient outcome. CONCLUSIONS Together, these findings support the notion that in patients who survived EVD, in some cases, the genetic variability of the virus resulted in deleterious mutations that affected viral protein function, leading to reduced viral load. Such mutations may also lead to persistent strains of the virus and be associated with recrudescent infections.
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Affiliation(s)
- Xiaofeng Dong
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jordana Munoz-Basagoiti
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Natasha Y Rickett
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Georgios Pollakis
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - William A Paxton
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Stephan Günther
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Romy Kerber
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Lisa F P Ng
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK.,Singapore Immunology Network, A*STAR, Singapore, Singapore
| | | | - N'faly Magassouba
- Laboratoire des fièvres hémorragiques en Guinée, Université Gamal Abdel Nasser de Conakry, Conakry, Guinea
| | - Miles W Carroll
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK.,Public Health England, Salisbury, UK
| | - David A Matthews
- School of Cellular and Molecular Medicine, University of Bristol, Singapore, Singapore
| | - Julian A Hiscox
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK. .,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK. .,Singapore Immunology Network, A*STAR, Singapore, Singapore.
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Davidson AD, Williamson MK, Lewis S, Shoemark D, Carroll MW, Heesom KJ, Zambon M, Ellis J, Lewis PA, Hiscox JA, Matthews DA. Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein. Genome Med 2020; 12:68. [PMID: 32723359 PMCID: PMC7386171 DOI: 10.1186/s13073-020-00763-0] [Citation(s) in RCA: 268] [Impact Index Per Article: 67.0] [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: 03/31/2020] [Accepted: 07/10/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND SARS-CoV-2 is a recently emerged respiratory pathogen that has significantly impacted global human health. We wanted to rapidly characterise the transcriptomic, proteomic and phosphoproteomic landscape of this novel coronavirus to provide a fundamental description of the virus's genomic and proteomic potential. METHODS We used direct RNA sequencing to determine the transcriptome of SARS-CoV-2 grown in Vero E6 cells which is widely used to propagate the novel coronavirus. The viral transcriptome was analysed using a recently developed ORF-centric pipeline. Allied to this, we used tandem mass spectrometry to investigate the proteome and phosphoproteome of the same virally infected cells. RESULTS Our integrated analysis revealed that the viral transcripts (i.e. subgenomic mRNAs) generally fitted the expected transcription model for coronaviruses. Importantly, a 24 nt in-frame deletion was detected in over half of the subgenomic mRNAs encoding the spike (S) glycoprotein and was predicted to remove a proposed furin cleavage site from the S glycoprotein. Tandem mass spectrometry identified over 500 viral peptides and 44 phosphopeptides in virus-infected cells, covering almost all proteins predicted to be encoded by the SARS-CoV-2 genome, including peptides unique to the deleted variant of the S glycoprotein. CONCLUSIONS Detection of an apparently viable deletion in the furin cleavage site of the S glycoprotein, a leading vaccine target, shows that this and other regions of SARS-CoV-2 proteins may readily mutate. The furin site directs cleavage of the S glycoprotein into functional subunits during virus entry or exit and likely contributes strongly to the pathogenesis and zoonosis of this virus. Our data emphasises that the viral genome sequence should be carefully monitored during the growth of viral stocks for research, animal challenge models and, potentially, in clinical samples. Such variations may result in different levels of virulence, morbidity and mortality.
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Affiliation(s)
- Andrew D Davidson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK.
| | - Maia Kavanagh Williamson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK
| | - Sebastian Lewis
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK
| | - Deborah Shoemark
- School of Biochemistry, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK
| | - Miles W Carroll
- Research and Development Institute, National Infection Service, Public Health, England, Porton Down, Wiltshire, UK
- National Institute Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Kate J Heesom
- Proteomics Facility Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK
| | - Maria Zambon
- Virus Reference Department, Public Health England (Colindale), London, UK
| | - Joanna Ellis
- Virus Reference Department, Public Health England (Colindale), London, UK
| | - Philip A Lewis
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK
| | - Julian A Hiscox
- National Institute Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Liverpool Health Partners, Liverpool, UK
| | - David A Matthews
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK.
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38
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Smither SJ, Garcia-Dorival I, Eastaugh L, Findlay JS, O'Brien LM, Carruthers J, Williamson ED, Molina-París C, Hiscox JA, Laws TR. An Investigation of the Effect of Transfected Defective, Ebola Virus Genomes on Ebola Replication. Front Cell Infect Microbiol 2020; 10:159. [PMID: 32373552 PMCID: PMC7187655 DOI: 10.3389/fcimb.2020.00159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 09/30/2019] [Accepted: 03/24/2020] [Indexed: 12/28/2022] Open
Abstract
As the ongoing outbreak in the Democratic Republic of Congo illustrates, Ebola virus disease continues to pose a significant risk to humankind and this necessitates the continued development of therapeutic options. One option that warrants evaluation is that of defective genomes; these can potentially parasitize resources from the wild-type virus and may even be packaged for repeated co-infection cycles. Deletion and copy-back defective genomes have been identified and reported in the literature. As a crude, mixed preparation these were found to have limiting effects on cytopathology. Here we have used synthetic virology to clone and manufacture two deletion defective genomes. These genomes were tested with Ebola virus using in vitro cell culture and shown to inhibit viral replication; however, and against expectations, the defective genomes were not released in biologically significant numbers. We propose that EBOV might have yet unknown mechanisms to prevent parasitisation by defective interfering particles beyond the known mechanism that prevents sequential infection of the same cell. Understanding this mechanism would be necessary in any development of a defective interfering particle-based therapy.
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Affiliation(s)
| | - Isabel Garcia-Dorival
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Lin Eastaugh
- CBR Division, Dstl Porton Down, Salisbury, United Kingdom
| | | | - Lyn M O'Brien
- CBR Division, Dstl Porton Down, Salisbury, United Kingdom
| | | | | | | | - Julian A Hiscox
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Thomas R Laws
- CBR Division, Dstl Porton Down, Salisbury, United Kingdom
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39
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Touzelet O, Broadbent L, Armstrong SD, Aljabr W, Cloutman-Green E, Power UF, Hiscox JA. The Secretome Profiling of a Pediatric Airway Epithelium Infected with hRSV Identified Aberrant Apical/Basolateral Trafficking and Novel Immune Modulating (CXCL6, CXCL16, CSF3) and Antiviral (CEACAM1) Proteins. Mol Cell Proteomics 2020; 19:793-807. [PMID: 32075873 PMCID: PMC7196588 DOI: 10.1074/mcp.ra119.001546] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 05/23/2019] [Revised: 02/13/2020] [Indexed: 11/19/2022] Open
Abstract
The respiratory epithelium comprises polarized cells at the interface between the environment and airway tissues. Polarized apical and basolateral protein secretions are a feature of airway epithelium homeostasis. Human respiratory syncytial virus (hRSV) is a major human pathogen that primarily targets the respiratory epithelium. However, the consequences of hRSV infection on epithelium secretome polarity and content remain poorly understood. To investigate the hRSV-associated apical and basolateral secretomes, a proteomics approach was combined with an ex vivo pediatric human airway epithelial (HAE) model of hRSV infection (data are available via ProteomeXchange and can be accessed at https://www.ebi.ac.uk/pride/ with identifier PXD013661). Following infection, a skewing of apical/basolateral abundance ratios was identified for several individual proteins. Novel modulators of neutrophil and lymphocyte activation (CXCL6, CSF3, SECTM1 or CXCL16), and antiviral proteins (BST2 or CEACAM1) were detected in infected, but not in uninfected cultures. Importantly, CXCL6, CXCL16, CSF3 were also detected in nasopharyngeal aspirates (NPA) from hRSV-infected infants but not healthy controls. Furthermore, the antiviral activity of CEACAM1 against RSV was confirmed in vitro using BEAS-2B cells. hRSV infection disrupted the polarity of the pediatric respiratory epithelial secretome and was associated with immune modulating proteins (CXCL6, CXCL16, CSF3) never linked with this virus before. In addition, the antiviral activity of CEACAM1 against hRSV had also never been previously characterized. This study, therefore, provides novel insights into RSV pathogenesis and endogenous antiviral responses in pediatric airway epithelium.
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Affiliation(s)
- Olivier Touzelet
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK; Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry & Biomedical Sciences, Queens University Belfast, Belfast BT9 7BL, UK
| | - Lindsay Broadbent
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry & Biomedical Sciences, Queens University Belfast, Belfast BT9 7BL, UK
| | - Stuart D Armstrong
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, L69 7BE, UK
| | - Waleed Aljabr
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK; Biomedical Research Administration, Research Centre, King Fahad Medical City, P.O. Box 59046 Riyadh 11252, Saudi Arabia
| | - Elaine Cloutman-Green
- Microbiology, Virology and Infection Control, Level 4 Camelia Botnar Laboratory, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Ultan F Power
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry & Biomedical Sciences, Queens University Belfast, Belfast BT9 7BL, UK.
| | - Julian A Hiscox
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, L69 7BE, UK; Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore 138648, Singapore.
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40
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Donovan-Banfield I, Turnell AS, Hiscox JA, Leppard KN, Matthews DA. Deep splicing plasticity of the human adenovirus type 5 transcriptome drives virus evolution. Commun Biol 2020; 3:124. [PMID: 32170151 PMCID: PMC7070027 DOI: 10.1038/s42003-020-0849-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [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: 10/17/2019] [Accepted: 02/12/2020] [Indexed: 02/06/2023] Open
Abstract
Viral genomes have high gene densities and complex transcription strategies rendering transcriptome analysis through short-read RNA-seq approaches problematic. Adenovirus transcription and splicing is especially complex. We used long-read direct RNA sequencing to study adenovirus transcription and splicing during infection. This revealed a previously unappreciated complexity of alternative splicing and potential for secondary initiating codon usage. Moreover, we find that most viral transcripts tend to shorten polyadenylation lengths as infection progresses. Development of an open reading frame centric bioinformatics analysis pipeline provided a deeper quantitative and qualitative understanding of adenovirus's genetic potential. Across the viral genome adenovirus makes multiple distinctly spliced transcripts that code for the same protein. Over 11,000 different splicing patterns were recorded across the viral genome, most occurring at low levels. This low-level use of alternative splicing patterns potentially enables the virus to maximise its coding potential over evolutionary timescales.
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Affiliation(s)
- I'ah Donovan-Banfield
- Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol, Bristol, BS8 1TD, UK
| | - Andrew S Turnell
- Institute of Cancer and Genomic Sciences College of Medical and Dental Sciences University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
| | - Julian A Hiscox
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, ic2 Building, Liverpool, L3 5RF, UK
| | - Keith N Leppard
- Life Sciences University of Warwick Coventry, Coventry, CV4 7AL, UK
| | - David A Matthews
- Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol, Bristol, BS8 1TD, UK.
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41
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Affiliation(s)
- Lisa F P Ng
- Institute for Infection and Global Health, University of Liverpool, UK
- Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
- Singapore Immunology Network, A*STAR, Singapore
| | - Julian A Hiscox
- Institute for Infection and Global Health, University of Liverpool, UK
- Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
- Singapore Immunology Network, A*STAR, Singapore
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42
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Aljabr W, Armstrong S, Rickett NY, Pollakis G, Touzelet O, Cloutman-Green E, Matthews DA, Hiscox JA. High Resolution Analysis of Respiratory Syncytial Virus Infection In Vivo. Viruses 2019; 11:v11100926. [PMID: 31658630 PMCID: PMC6832471 DOI: 10.3390/v11100926] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 12/27/2022] Open
Abstract
Human respiratory syncytial virus (HRSV) is a major cause of pediatric infection and also causes disease in the elderly and those with underlying respiratory problems. There is no vaccine for HRSV and anti-viral therapeutics are not broadly applicable. To investigate the effect of HRSV biology in children, nasopharyngeal aspirates were taken from children with different viral loads and a combined high throughput RNAseq and label free quantitative proteomics approach was used to characterize the nucleic acid and proteins in these samples. HRSV proteins were identified in the nasopharyngeal aspirates from infected children, and their abundance correlated with viral load (Ct value), confirming HRSV infection. Analysis of the HRSV genome indicated that the children were infected with sub-group A virus and that minor variants in nucleotide frequency occurred in discrete clusters along the HRSV genome, and within a patient clustered distinctly within the glycoprotein gene. Data from the samples were binned into four groups; no-HRSV infection (control), high viral load (Ct < 20), medium viral load (Ct = 20-25), and low viral load (Ct > 25). Cellular proteins associated with the anti-viral response (e.g., ISG15) were identified in the nasopharyngeal aspirates and their abundance was correlated with viral load. These combined approaches have not been used before to study HRSV biology in vivo and can be readily applied to the study the variation of virus host interactions.
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Affiliation(s)
- Waleed Aljabr
- King Fahad Medical City, Research Center, 59046 Riyadh 11525, Saudi Arabia.
| | - Stuart Armstrong
- Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK.
- National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L3 5RF, UK.
| | - Natasha Y Rickett
- Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK.
- National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L3 5RF, UK.
| | - Georgios Pollakis
- Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK.
| | - Olivier Touzelet
- School of Medicine, Dentistry & Biomedical Sciences, Queen's University Belfast, Belfast BT9 7BL, UK.
| | | | - David A Matthews
- School of Medical Sciences, University of Bristol, Bristol BS8 1TD, UK.
| | - Julian A Hiscox
- Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK.
- National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L3 5RF, UK.
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43
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Kafetzopoulou LE, Efthymiadis K, Lewandowski K, Crook A, Carter D, Osborne J, Aarons E, Hewson R, Hiscox JA, Carroll MW, Vipond R, Pullan ST. Assessment of metagenomic Nanopore and Illumina sequencing for recovering whole genome sequences of chikungunya and dengue viruses directly from clinical samples. ACTA ACUST UNITED AC 2019; 23. [PMID: 30563591 PMCID: PMC6299504 DOI: 10.2807/1560-7917.es.2018.23.50.1800228] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [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: 12/31/2022]
Abstract
Background The recent global emergence and re-emergence of arboviruses has caused significant human disease. Common vectors, symptoms and geographical distribution make differential diagnosis both important and challenging. Aim To investigate the feasibility of metagenomic sequencing for recovering whole genome sequences of chikungunya and dengue viruses from clinical samples. Methods We performed metagenomic sequencing using both the Illumina MiSeq and the portable Oxford Nanopore MinION on clinical samples which were real-time reverse transcription-PCR (qRT-PCR) positive for chikungunya (CHIKV) or dengue virus (DENV), two of the most important arboviruses. A total of 26 samples with a range of representative clinical Ct values were included in the study. Results Direct metagenomic sequencing of nucleic acid extracts from serum or plasma without viral enrichment allowed for virus identification, subtype determination and elucidated complete or near-complete genomes adequate for phylogenetic analysis. One PCR-positive CHIKV sample was also found to be coinfected with DENV. Conclusions This work demonstrates that metagenomic whole genome sequencing is feasible for the majority of CHIKV and DENV PCR-positive patient serum or plasma samples. Additionally, it explores the use of Nanopore metagenomic sequencing for DENV and CHIKV, which can likely be applied to other RNA viruses, highlighting the applicability of this approach to front-line public health and potential portable applications using the MinION.
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Affiliation(s)
- Liana E Kafetzopoulou
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom.,Public Health England, National Infections Service, Porton Down, United Kingdom
| | - Kyriakos Efthymiadis
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, Brussels, Belgium
| | - Kuiama Lewandowski
- Public Health England, National Infections Service, Porton Down, United Kingdom
| | - Ant Crook
- Public Health England, National Infections Service, Porton Down, United Kingdom
| | - Dan Carter
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom.,Public Health England, National Infections Service, Porton Down, United Kingdom
| | - Jane Osborne
- Rare and Imported Pathogens Laboratory, Public Health England, Porton Down, United Kingdom
| | - Emma Aarons
- Rare and Imported Pathogens Laboratory, Public Health England, Porton Down, United Kingdom
| | - Roger Hewson
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom.,Public Health England, National Infections Service, Porton Down, United Kingdom
| | - Julian A Hiscox
- Institute of Infection and Global Health, University of Liverpool, United Kingdom.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
| | - Miles W Carroll
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom.,Public Health England, National Infections Service, Porton Down, United Kingdom
| | - Richard Vipond
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom.,Public Health England, National Infections Service, Porton Down, United Kingdom
| | - Steven T Pullan
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom.,Public Health England, National Infections Service, Porton Down, United Kingdom
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44
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Speranza E, Ruibal P, Port JR, Feng F, Burkhardt L, Grundhoff A, Günther S, Oestereich L, Hiscox JA, Connor JH, Muñoz-Fontela C. T-Cell Receptor Diversity and the Control of T-Cell Homeostasis Mark Ebola Virus Disease Survival in Humans. J Infect Dis 2019; 218:S508-S518. [PMID: 29986035 DOI: 10.1093/infdis/jiy352] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Differences in T-cell phenotype, particularly the expression of markers of T-cell homeostasis, have been observed in fatal and nonfatal Ebola virus disease (EVD). However, the relationship between these markers with T-cell function and virus clearance during EVD is poorly understood. To gain biological insight into the role of T cells during EVD, combined transcriptomics and T-cell receptor sequencing was used to profile blood samples from fatal and nonfatal EVD patients from the recent West African EVD epidemic. Fatal EVD was characterized by strong T-cell activation and increased abundance of T-cell inhibitory molecules. However, the early T-cell response was oligoclonal and did not result in viral clearance. In contrast, survivors mounted highly diverse T-cell responses, maintained low levels of T-cell inhibitors, and cleared Ebola virus. Our findings highlight the importance of T-cell immunity in surviving EVD and strengthen the foundation for further research on targeting of the dendritic cell-T cell interface for postexposure immunotherapy.
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Affiliation(s)
- Emily Speranza
- Department of Microbiology, Boston University School of Medicine, Boston MA.,Department of Bioinformatics Program, Boston University, Boston MA.,Department of National Emerging Infectious Diseases Laboratories, Boston University, Boston MA.,Department of Mathematics and Statistics, Boston University, Boston MA
| | - Paula Ruibal
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Julia R Port
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Partner SiteHamburg, Germany
| | - Feng Feng
- Department of Microbiology, Boston University School of Medicine, Boston MA.,Department of Mathematics and Statistics, Boston University, Boston MA
| | - Lia Burkhardt
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Adam Grundhoff
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Stephan Günther
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Partner SiteHamburg, Germany
| | - Lisa Oestereich
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Partner SiteHamburg, Germany
| | - Julian A Hiscox
- Institute for Infection and Global Health, University of Liverpool, United Kingdom.,Singapore Immunology Network, A*STAR, Singapore
| | - John H Connor
- Department of Microbiology, Boston University School of Medicine, Boston MA.,Department of Bioinformatics Program, Boston University, Boston MA.,Department of National Emerging Infectious Diseases Laboratories, Boston University, Boston MA.,Department of Mathematics and Statistics, Boston University, Boston MA
| | - César Muñoz-Fontela
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Partner SiteHamburg, Germany
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45
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Abstract
Control of virus infection relies on the stimulation of interferon-stimulated genes (ISGs) that inhibit viral replication. In a recent Nature paper, Gizzi et al. (2018) discovered that the ISG viperin inhibits virus replication by generating the ribonucleotide ddhCTP, which interferes with RNA synthesis, thus offering insights into drug design.
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Affiliation(s)
- Lisa F P Ng
- Singapore Immunology Network, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore; Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK; National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool L69 3GL, UK.
| | - Julian A Hiscox
- Singapore Immunology Network, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore; Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK; National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool L69 3GL, UK
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Hou G, Xue B, Li L, Nan Y, Zhang L, Li K, Zhao Q, Hiscox JA, Stewart JP, Wu C, Wang J, Zhou EM. Direct Interaction Between CD163 N-Terminal Domain and MYH9 C-Terminal Domain Contributes to Porcine Reproductive and Respiratory Syndrome Virus Internalization by Permissive Cells. Front Microbiol 2019; 10:1815. [PMID: 31447818 PMCID: PMC6691103 DOI: 10.3389/fmicb.2019.01815] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 05/12/2019] [Accepted: 07/23/2019] [Indexed: 12/16/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) has a highly restricted tropism for cells of the monocyte-macrophage lineage, including porcine alveolar macrophages (PAMs). PRRSV entry into permissive cells involves several mediators in addition to two required host cell receptors, CD163 and MYH9. It is unknown whether CD163 directly interacts and/or cooperates with MYH9 to facilitate PRRSV infection. In this study, CD163 and MYH9 were co-immunoprecipitated from PAMs regardless of PRRSV infection status. Further truncation analysis indicated that the CD163 N-terminal region, containing scavenger receptor cysteine-rich domains 1 to 4 (SRCR1-4), directly interacts with the MYH9 C-terminal domain region without involvement of other adaptor proteins. Meanwhile, non-permissive HEK293T cells that stably expressed truncated swine CD163 SRCR1-4 domain did not support virus attachment. However, virus attachment to cells stably expressing SRCR5-CT domain was demonstrated to occur without appreciable virus internalization. The involvement of the SRCR1-4 domain in virus internalization was further demonstrated by the fact that incubation of recombinant SRCR1-4 protein with PAMs abolished subsequent virus internalization by permissive cells. These results demonstrated that CD163 SRCR1-4 interacts with the MYH9 C–terminal domain to facilitate PRRSV virion internalization in permissive cells, thus expanding our understanding of PRRSV cell-invasion mechanisms.
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Affiliation(s)
- Gaopeng Hou
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Biyun Xue
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Liangliang Li
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yuchen Nan
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Lu Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Kuokuo Li
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Qin Zhao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Julian A Hiscox
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - James P Stewart
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Chunyan Wu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Jingfei Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - En-Min Zhou
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
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47
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Kafetzopoulou LE, Pullan ST, Lemey P, Suchard MA, Ehichioya DU, Pahlmann M, Thielebein A, Hinzmann J, Oestereich L, Wozniak DM, Efthymiadis K, Schachten D, Koenig F, Matjeschk J, Lorenzen S, Lumley S, Ighodalo Y, Adomeh DI, Olokor T, Omomoh E, Omiunu R, Agbukor J, Ebo B, Aiyepada J, Ebhodaghe P, Osiemi B, Ehikhametalor S, Akhilomen P, Airende M, Esumeh R, Muoebonam E, Giwa R, Ekanem A, Igenegbale G, Odigie G, Okonofua G, Enigbe R, Oyakhilome J, Yerumoh EO, Odia I, Aire C, Okonofua M, Atafo R, Tobin E, Asogun D, Akpede N, Okokhere PO, Rafiu MO, Iraoyah KO, Iruolagbe CO, Akhideno P, Erameh C, Akpede G, Isibor E, Naidoo D, Hewson R, Hiscox JA, Vipond R, Carroll MW, Ihekweazu C, Formenty P, Okogbenin S, Ogbaini-Emovon E, Günther S, Duraffour S. Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak. Science 2019; 363:74-77. [PMID: 30606844 DOI: 10.1126/science.aau9343] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/12/2018] [Indexed: 12/15/2022]
Abstract
The 2018 Nigerian Lassa fever season saw the largest ever recorded upsurge of cases, raising concerns over the emergence of a strain with increased transmission rate. To understand the molecular epidemiology of this upsurge, we performed, for the first time at the epicenter of an unfolding outbreak, metagenomic nanopore sequencing directly from patient samples, an approach dictated by the highly variable genome of the target pathogen. Genomic data and phylogenetic reconstructions were communicated immediately to Nigerian authorities and the World Health Organization to inform the public health response. Real-time analysis of 36 genomes and subsequent confirmation using all 120 samples sequenced in the country of origin revealed extensive diversity and phylogenetic intermingling with strains from previous years, suggesting independent zoonotic transmission events and thus allaying concerns of an emergent strain or extensive human-to-human transmission.
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Affiliation(s)
- L E Kafetzopoulou
- Public Health England, National Infection Service, Porton Down, UK.,National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - S T Pullan
- Public Health England, National Infection Service, Porton Down, UK.,National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - P Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
| | - M A Suchard
- Departments of Biomathematics, Biostatistics, and Human Genetics, University of California, Los Angeles, CA, USA
| | - D U Ehichioya
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - M Pahlmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - A Thielebein
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - J Hinzmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - L Oestereich
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - D M Wozniak
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - K Efthymiadis
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, Brussels, Belgium
| | - D Schachten
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - F Koenig
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - J Matjeschk
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - S Lorenzen
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - S Lumley
- Public Health England, National Infection Service, Porton Down, UK
| | - Y Ighodalo
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - D I Adomeh
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - T Olokor
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - E Omomoh
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - R Omiunu
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - J Agbukor
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - B Ebo
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - J Aiyepada
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - P Ebhodaghe
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - B Osiemi
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | | | - P Akhilomen
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - M Airende
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - R Esumeh
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - E Muoebonam
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - R Giwa
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - A Ekanem
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - G Igenegbale
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - G Odigie
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - G Okonofua
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - R Enigbe
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - J Oyakhilome
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - E O Yerumoh
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - I Odia
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - C Aire
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - M Okonofua
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - R Atafo
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - E Tobin
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - D Asogun
- Irrua Specialist Teaching Hospital, Irrua, Nigeria.,Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Nigeria
| | - N Akpede
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - P O Okokhere
- Irrua Specialist Teaching Hospital, Irrua, Nigeria.,Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Nigeria
| | - M O Rafiu
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - K O Iraoyah
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | | | - P Akhideno
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - C Erameh
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - G Akpede
- Irrua Specialist Teaching Hospital, Irrua, Nigeria.,Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Nigeria
| | - E Isibor
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - D Naidoo
- World Health Organization, Geneva, Switzerland
| | - R Hewson
- Public Health England, National Infection Service, Porton Down, UK.,National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK.,Faculty of Infectious and Tropical Diseases, Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK.,Faculty of Clinical Sciences and International Public Health, Liverpool School of Tropical Medicine, Liverpool, UK
| | - J A Hiscox
- National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK.,Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore.,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - R Vipond
- Public Health England, National Infection Service, Porton Down, UK.,National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - M W Carroll
- Public Health England, National Infection Service, Porton Down, UK.,National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - C Ihekweazu
- Nigeria Centre for Disease Control, Abuja, Nigeria
| | - P Formenty
- World Health Organization, Geneva, Switzerland
| | - S Okogbenin
- Irrua Specialist Teaching Hospital, Irrua, Nigeria.,Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Nigeria
| | | | - S Günther
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany. .,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - S Duraffour
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
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48
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Essex-Lopresti A, David J, Moore K, Armstrong S, Auton P, Rutter S, Green C, Hiscox JA, Paszkiewicz KH, Clark GC. Unbiased whole genome sequence analysis of the murine transcriptome in response to ricin exposure via the pulmonary route. Toxicon 2019. [DOI: 10.1016/j.toxicon.2018.10.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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49
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Liu B, Chen Y, Sun Y, Nan Y, Li H, Du T, Hiscox JA, Zhao Q, Zhou EM. Experimental infection of rabbit with swine-derived hepatitis E virus genotype 4. Vet Microbiol 2019; 229:168-175. [DOI: 10.1016/j.vetmic.2019.01.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 01/03/2019] [Accepted: 01/03/2019] [Indexed: 01/15/2023]
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50
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Song L, Han X, Jia C, Zhang X, Jiao Y, Du T, Xiao S, Hiscox JA, Zhou EM, Mu Y. Porcine reproductive and respiratory syndrome virus inhibits MARC-145 proliferation via inducing apoptosis and G2/M arrest by activation of Chk/Cdc25C and p53/p21 pathway. Virol J 2018; 15:169. [PMID: 30400903 PMCID: PMC6219034 DOI: 10.1186/s12985-018-1081-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 08/03/2018] [Accepted: 10/16/2018] [Indexed: 12/03/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus(PRRSV) is an important immunosuppressive virus which can suppresses infected cells proliferation. In this work, we examined PRRSV ability to manipulate cell cycle progression of MARC-145 cells and explored the potential molecular mechanisms. The results showed that PRRSV infection imposed a growth-inhibitory effect on MARC-145 cells by inducing cell cycle arrest at G2/M phase. This arrest was due to the significant decrease of Cdc2-cyclinB1 complex activity in PRRSV-infected cells and the activity reduction was a result of Cdc2 Tyr15 phosphorylation and the accumulation of Cdc2 and cyclinB1 in the nucleus. Not only elevated Wee1 and Myt1 expression and inactivated Cdc25C, but also increase of p21 and 14–3-3σ in a p53-dependent manner caused the inhibitory Tyr15 phosphorylation of Cdc2. PRRSV infection also activated Chk1. Our data suggest PRRSV infection induces G2/M arrest via various molecular regulatory mechanisms. These results provide a new insights for PRRSV pathogenesis.
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Affiliation(s)
- Linlin Song
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Scientific Observing and Experimental Station of Veterinary Pharmacology and Diagnostic Technology, Ministry of Agriculture, Yangling, Shaanxi, China
| | - Ximeng Han
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Scientific Observing and Experimental Station of Veterinary Pharmacology and Diagnostic Technology, Ministry of Agriculture, Yangling, Shaanxi, China
| | - Cunyu Jia
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Scientific Observing and Experimental Station of Veterinary Pharmacology and Diagnostic Technology, Ministry of Agriculture, Yangling, Shaanxi, China
| | - Xin Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Scientific Observing and Experimental Station of Veterinary Pharmacology and Diagnostic Technology, Ministry of Agriculture, Yangling, Shaanxi, China
| | - Yunjie Jiao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Scientific Observing and Experimental Station of Veterinary Pharmacology and Diagnostic Technology, Ministry of Agriculture, Yangling, Shaanxi, China
| | - Taofeng Du
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Scientific Observing and Experimental Station of Veterinary Pharmacology and Diagnostic Technology, Ministry of Agriculture, Yangling, Shaanxi, China
| | - Shuqi Xiao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Scientific Observing and Experimental Station of Veterinary Pharmacology and Diagnostic Technology, Ministry of Agriculture, Yangling, Shaanxi, China
| | - Julian A Hiscox
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - En-Min Zhou
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China. .,Scientific Observing and Experimental Station of Veterinary Pharmacology and Diagnostic Technology, Ministry of Agriculture, Yangling, Shaanxi, China.
| | - Yang Mu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China. .,Scientific Observing and Experimental Station of Veterinary Pharmacology and Diagnostic Technology, Ministry of Agriculture, Yangling, Shaanxi, China.
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