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Masirika LM, Kumar A, Dutt M, Ostadgavahi AT, Hewins B, Nadine MB, Steeven BK, Mweshi FK, Mambo LM, Mbiribindi JB, Siangoli FB, Kelvin AA, Udahemuka JC, Kelvin P, Flores L, Kelvin DJ, Sganzerla Martinez G. Complete Genome Sequencing, Annotation, and Mutational Profiling of the Novel Clade I Human Mpox Virus, Kamituga Strain. J Infect Dev Ctries 2024; 18:600-608. [PMID: 38728644 DOI: 10.3855/jidc.20136] [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: 03/29/2024] [Accepted: 04/02/2024] [Indexed: 05/12/2024] Open
Abstract
INTRODUCTION Human Mpox (formerly monkeypox) infection is an emerging zoonotic disease caused by the Mpox virus (MPXV). We describe the complete genome annotation, phylogeny, and mutational profile of a novel, sustained Clade I Mpox outbreak in the city of Kamituga in Eastern Democratic Republic of the Congo (DRC). METHODOLOGY A cross-sectional, observational, cohort study was performed among patients of all ages admitted to the Kamituga Hospital with Mpox infection symptoms between late September 2023 and late January 2024. DNA was isolated from Mpox swabbed lesions and sequenced followed by phylogenetic analysis, genome annotation, and mutational profiling. RESULTS We describe an ongoing Clade I Mpox outbreak in the city of Kamituga, South Kivu Province, Democratic Republic of Congo. Whole-genome sequencing of the viral RNA samples revealed, on average, 201.5 snps, 28 insertions, 81 deletions, 2 indels, 312.5 total variants, 158.3 amino acid changes, 81.66 intergenic variants, 72.16 synonymous mutations, 106 missense variants, 41.16 frameshift variants, and 3.33 inframe deletions across six samples. By assigning mutations at the proteome level for Kamituga MPXV sequences, we observed that seven proteins, namely, C9L (OPG047), I4L (OPG080), L6R (OPG105), A17L (OPG143), A25R (OPG151), A28L (OPG153), and B21R (OPG210) have emerged as hot spot mutations based on the consensuses inframe deletions, frameshift variants, synonymous variants, and amino acids substitutions. Based on the outcome of the annotation, we found a deletion of the D14L (OPG032) gene in all six samples. Following phylogenetic analysis and whole genome assembly, we determined that this cluster of Mpox infections is genetically distinct from previously reported Clade I outbreaks, and thus propose that the Kamituga Mpox outbreak represents a novel subgroup (subgroup VI) of Clade I MPXV. CONCLUSIONS Here we report the complete viral genome for the ongoing Clade I Mpox Kamituga outbreak for the first time. This outbreak presents a distinct mutational profile from previously sequenced Clade I MPXV oubtreaks, suggesting that this cluster of infections is a novel subgroup (we term this subgroup VI). These findings underscore the need for ongoing vigilance and continued sequencing of novel Mpox threats in endemic regions.
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Affiliation(s)
- Leandre Murhula Masirika
- Centre de Recherche en Sciences Naturelles de Lwiro, South Kivu, DS Bukavu, Democratic Republic of the Congo
| | - Anuj Kumar
- Department of Microbiology and Immunology, Canadian Center for Vaccinology (CCfV), Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - Mansi Dutt
- Department of Microbiology and Immunology, Canadian Center for Vaccinology (CCfV), Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - Ali Toloue Ostadgavahi
- Department of Microbiology and Immunology, Canadian Center for Vaccinology (CCfV), Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - Benjamin Hewins
- Department of Microbiology and Immunology, Canadian Center for Vaccinology (CCfV), Faculty of Medicine, Dalhousie University, Halifax, Canada
| | | | | | | | | | | | | | - Alyson A Kelvin
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Canada
| | | | - Patricia Kelvin
- Department of Microbiology and Immunology, Canadian Center for Vaccinology (CCfV), Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - Luis Flores
- Centre de Recherche en Sciences Naturelles de Lwiro, South Kivu, DS Bukavu, Democratic Republic of the Congo
| | - David J Kelvin
- Department of Microbiology and Immunology, Canadian Center for Vaccinology (CCfV), Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - Gustavo Sganzerla Martinez
- Department of Microbiology and Immunology, Canadian Center for Vaccinology (CCfV), Faculty of Medicine, Dalhousie University, Halifax, Canada
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Jansen EB, Ostadgavahi AT, Hewins B, Buchanan R, Thivierge BM, Sganzerla Martinez G, Goncin U, Francis ME, Swan CL, Scruten E, Bell J, Darbellay J, Facciuolo A, Falzarano D, Gerdts V, Fenton ME, Hedlin P, Kelvin DJ, Kelvin AA. PASC (Post Acute Sequelae of COVID-19) is associated with decreased neutralizing antibody titers in both biological sexes and increased ANG-2 and GM-CSF in females. Sci Rep 2024; 14:9854. [PMID: 38684819 PMCID: PMC11058778 DOI: 10.1038/s41598-024-60089-4] [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: 09/29/2023] [Accepted: 04/18/2024] [Indexed: 05/02/2024] Open
Abstract
Post-acute sequelae of COVID-19 (PASC) or the continuation of COVID-19 (Coronavirus disease 2019) symptoms past 12 weeks may affect as many as 30% of people recovering from a SARS-CoV-2 (severe acute respiratory coronavirus 2) infection. The mechanisms regulating the development of PASC are currently not known; however, hypotheses include virus reservoirs, pre-existing conditions, microblood clots, immune dysregulation, as well as poor antibody responses. Importantly, virus neutralizing antibodies are essential for COVID-19 recovery and protection from reinfection but there is currently limited information on these immune regulators and associated cytokines in PASC patients. Understanding the key drivers of general and specific symptoms associated with Long COVID and the presence of virus neutralizing antibodies in PASC will aid in the development of therapeutics, diagnostics, and vaccines which currently do not exist. We designed a cross-sectional study to investigate systemic antibody and cytokine responses during COVID-19 recovery and PASC. In total, 195 participants were recruited in one of four groups: (1) Those who never had COVID-19 (No COVID); (2) Those in acute COVID-19 recovery (Acute Recovery) (4-12 weeks post infection); (3) Those who recovered from COVID-19 (Recovered) (+ 12 weeks from infection); and (4) those who had PASC (PASC) (+ 12 weeks from infection). Participants completed a questionnaire on health history, sex, gender, demographics, experiences with COVID-19 acute and COVID-19 recovery/continuing symptoms. Serum samples collected were evaluated for antibody binding to viral proteins, virus neutralizing antibody titers, and serum cytokine levels using Ella SimplePlex Immunoassay™ panels. We found participants with PASC reported more pre-existing conditions (e.g. such as hypertension, asthma, and obesity), and PASC symptoms (e.g. fatigue, brain fog, headaches, and shortness of breath) following COVID-19 than COVID-19 Recovered individuals. Importantly, we found PASC individuals to have significantly decreased levels of neutralizing antibodies toward both SARS-CoV-2 and the Omicron BA.1 variant. Sex analysis indicated that female PASC study participants had sustained antibody levels as well as levels of the inflammatory cytokines GM-CSF and ANG-2 over time following COVID-19. Our study reports people experiencing PASC had lower levels of virus neutralizing antibodies; however, the results are limited by the collection time post-COVID-19 and post-vaccination. Moreover, we found females experiencing PASC had sustained levels of GM-CSF and ANG-2. With lower levels of virus neutralizing antibodies, this data suggests that PASC individuals not only have had a suboptimal antibody response during acute SARS-CoV-2 infection but may also have increased susceptibility to subsequent infections which may exacerbate or prolong current PASC illnesses. We also provide evidence suggesting GM-CSF and ANG-2 to play a role in the sex-bias of PASC. Taken together, our findings maybe important for understanding immune molecular drivers of PASC and PASC subgroups.
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Affiliation(s)
- Ethan B Jansen
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Benjamin Hewins
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - Rachelle Buchanan
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
| | - Brittany M Thivierge
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Una Goncin
- Department of Anesthesiology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Magen E Francis
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Cynthia L Swan
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
| | - Erin Scruten
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
| | - Jack Bell
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Joseph Darbellay
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
| | - Antonio Facciuolo
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Darryl Falzarano
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Volker Gerdts
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Mark E Fenton
- Division of Respirology, Critical Care, and Sleep Medicine, Department of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Peter Hedlin
- Department of Anesthesiology, University of Saskatchewan, Saskatoon, SK, Canada
| | - David J Kelvin
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - Alyson A Kelvin
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada.
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Martinez GS, Perez-Rueda E, Kumar A, Dutt M, Maya CR, Ledesma-Dominguez L, Casa PL, Kumar A, de Avila e Silva S, Kelvin DJ. CDBProm: the Comprehensive Directory of Bacterial Promoters. NAR Genom Bioinform 2024; 6:lqae018. [PMID: 38385146 PMCID: PMC10880602 DOI: 10.1093/nargab/lqae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/12/2024] [Accepted: 01/29/2024] [Indexed: 02/23/2024] Open
Abstract
The decreasing cost of whole genome sequencing has produced high volumes of genomic information that require annotation. The experimental identification of promoter sequences, pivotal for regulating gene expression, is a laborious and cost-prohibitive task. To expedite this, we introduce the Comprehensive Directory of Bacterial Promoters (CDBProm), a directory of in-silico predicted bacterial promoter sequences. We first identified that an Extreme Gradient Boosting (XGBoost) algorithm would distinguish promoters from random downstream regions with an accuracy of 87%. To capture distinctive promoter signals, we generated a second XGBoost classifier trained on the instances misclassified in our first classifier. The predictor of CDBProm is then fed with over 55 million upstream regions from more than 6000 bacterial genomes. Upon finding potential promoter sequences in upstream regions, each promoter is mapped to the genomic data of the organism, linking the predicted promoter with its coding DNA sequence, and identifying the function of the gene regulated by the promoter. The collection of bacterial promoters available in CDBProm enables the quantitative analysis of a plethora of bacterial promoters. Our collection with over 24 million promoters is publicly available at https://aw.iimas.unam.mx/cdbprom/.
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Affiliation(s)
- Gustavo Sganzerla Martinez
- Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
- Pediatrics, Izaak Walton Killam (IWK) Health Center. Canadian Center for Vaccinology (CCfV), Halifax, Nova Scotia B3H 4H7, Canada
- BioForge Canada Limited, Halifax, Nova Scotia B3N 3B9, Canada
| | - Ernesto Perez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autonóma de México, Unidad Académica del Estado de Yucatán, Mérida 97302, Yucatán, Mexico
| | - Anuj Kumar
- Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
- Pediatrics, Izaak Walton Killam (IWK) Health Center. Canadian Center for Vaccinology (CCfV), Halifax, Nova Scotia B3H 4H7, Canada
- BioForge Canada Limited, Halifax, Nova Scotia B3N 3B9, Canada
| | - Mansi Dutt
- Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
- Pediatrics, Izaak Walton Killam (IWK) Health Center. Canadian Center for Vaccinology (CCfV), Halifax, Nova Scotia B3H 4H7, Canada
- BioForge Canada Limited, Halifax, Nova Scotia B3N 3B9, Canada
| | - Cinthia Rodríguez Maya
- Facultad de Ciencias e Ingeniería, Universidad Nacional Autonoma de Mexico, Mexico City 04510, Mexico
| | - Leonardo Ledesma-Dominguez
- Instituto de Investigaciones en Matematicas Aplicadas y en Sistemas, Universidad Nacional Autonoma de Mexico, Mexico City 04510, Mexico
| | - Pedro Lenz Casa
- Biotechnology Institute, Universidade de Caxias do Sul, Caxias do Sul, Rio Grande do Sul 95070-560, Brazil
| | - Aditya Kumar
- Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam 784028, India
| | - Scheila de Avila e Silva
- Biotechnology Institute, Universidade de Caxias do Sul, Caxias do Sul, Rio Grande do Sul 95070-560, Brazil
| | - David J Kelvin
- Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
- Pediatrics, Izaak Walton Killam (IWK) Health Center. Canadian Center for Vaccinology (CCfV), Halifax, Nova Scotia B3H 4H7, Canada
- BioForge Canada Limited, Halifax, Nova Scotia B3N 3B9, Canada
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Umutoni B, Tumushime JC, Hewins B, Udahemuka JC, Ndishimye P, Kelvin DJ, Sganzerla Martinez G. The impact of public transportation on the transmission of COVID-19 in Rwanda. Front Public Health 2024; 12:1345433. [PMID: 38476489 PMCID: PMC10927834 DOI: 10.3389/fpubh.2024.1345433] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/06/2024] [Indexed: 03/14/2024] Open
Abstract
Introduction The onset of the COVID-19 pandemic has placed a significant burden on healthcare systems worldwide, particularly in sub-Saharan regions where healthcare resources are limited. The transmission of SARS-CoV-2 is facilitated by the movement of people from place to place. Therefore, implementing measures that restrict movement of people and contacts is crucial in controlling the spread of the disease. Following the identification of the first COVID-19 case in Rwanda, the government implemented stringent measures, including a complete nationwide lockdown, border closures, curfews, reduced capacity in public transportation and businesses, and mandatory testing. This study aims to assess epidemiological trends in COVID-19 cases in relation to changes in population mobility within the public transportation system. Methods A descriptive analysis using publicly available data on COVID-19 epidemiological indicators (cases, deaths, vaccinations, and stringency index) and mobility data was conducted. Results The results reveal a strong correlation between mobility in public transportation and other activities, underscoring Rwanda's reliance on its public transportation system. The study also identifies a pattern where increases in transit station mobility preceded spikes in COVID-19 cases, suggesting that the subsequent rise in public transportation usage may contribute to higher infection rates. Discussion Therefore, this study emphasizes the importance of ongoing vigilance and regulatory measures regarding public transportation during infectious disease outbreaks.
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Affiliation(s)
- Brigitte Umutoni
- College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
- Center for Research and Innovation, African Institute for Mathematical Sciences (AIMS), Kigali, Rwanda
| | - Jean Claude Tumushime
- College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
- Center for Research and Innovation, African Institute for Mathematical Sciences (AIMS), Kigali, Rwanda
| | - Benjamin Hewins
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
- Department of Pediatrics, Izaak Walton Killam (IWK) Health Center, Canadian Center for Vaccinology (CCfV), Halifax, NS, Canada
| | | | - Pacifique Ndishimye
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
- Department of Pediatrics, Izaak Walton Killam (IWK) Health Center, Canadian Center for Vaccinology (CCfV), Halifax, NS, Canada
| | - David J. Kelvin
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
- Department of Pediatrics, Izaak Walton Killam (IWK) Health Center, Canadian Center for Vaccinology (CCfV), Halifax, NS, Canada
| | - Gustavo Sganzerla Martinez
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
- Department of Pediatrics, Izaak Walton Killam (IWK) Health Center, Canadian Center for Vaccinology (CCfV), Halifax, NS, Canada
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Martinez GS, Dutt M, Kelvin DJ, Kumar A. PoxiPred: An Artificial-Intelligence-Based Method for the Prediction of Potential Antigens and Epitopes to Accelerate Vaccine Development Efforts against Poxviruses. Biology (Basel) 2024; 13:125. [PMID: 38392343 PMCID: PMC10887159 DOI: 10.3390/biology13020125] [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] [Received: 12/22/2023] [Revised: 01/29/2024] [Accepted: 02/01/2024] [Indexed: 02/24/2024]
Abstract
Poxviridae is a family of large, complex, enveloped, and double-stranded DNA viruses. The members of this family are ubiquitous and well known to cause contagious diseases in humans and other types of animals as well. Taxonomically, the poxviridae family is classified into two subfamilies, namely Chordopoxvirinae (affecting vertebrates) and Entomopoxvirinae (affecting insects). The members of the Chordopoxvirinae subfamily are further divided into 18 genera based on the genome architecture and evolutionary relationship. Of these 18 genera, four genera, namely Molluscipoxvirus, Orthopoxvirus, Parapoxvirus, and Yatapoxvirus, are known for infecting humans. Some of the popular members of poxviridae are variola virus, vaccine virus, Mpox (formerly known as monkeypox), cowpox, etc. There is still a pressing demand for the development of effective vaccines against poxviruses. Integrated immunoinformatics and artificial-intelligence (AI)-based methods have emerged as important approaches to design multi-epitope vaccines against contagious emerging infectious diseases. Despite significant progress in immunoinformatics and AI-based techniques, limited methods are available to predict the epitopes. In this study, we have proposed a unique method to predict the potential antigens and T-cell epitopes for multiple poxviruses. With PoxiPred, we developed an AI-based tool that was trained and tested with the antigens and epitopes of poxviruses. Our tool was able to locate 3191 antigen proteins from 25 distinct poxviruses. From these antigenic proteins, PoxiPred redundantly located up to five epitopes per protein, resulting in 16,817 potential T-cell epitopes which were mostly (i.e., 92%) predicted as being reactive to CD8+ T-cells. PoxiPred is able to, on a single run, identify antigens and T-cell epitopes for poxviruses with one single input, i.e., the proteome file of any poxvirus.
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Affiliation(s)
- Gustavo Sganzerla Martinez
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS B3H 4H7, Canada
- Department of Pediatrics, Izaak Walton Killam (IWK) Health Center, Canadian Center for Vaccinology (CCfV), Halifax, NS B3H 4H7, Canada
- Laboratory of Immunity, Shantou University Medical College, Shantou 512025, China
- BioForge Canada Limited, Halifax, B3N3B9, NS, Canada
| | - Mansi Dutt
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS B3H 4H7, Canada
- Department of Pediatrics, Izaak Walton Killam (IWK) Health Center, Canadian Center for Vaccinology (CCfV), Halifax, NS B3H 4H7, Canada
- Laboratory of Immunity, Shantou University Medical College, Shantou 512025, China
- BioForge Canada Limited, Halifax, B3N3B9, NS, Canada
| | - David J Kelvin
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS B3H 4H7, Canada
- Department of Pediatrics, Izaak Walton Killam (IWK) Health Center, Canadian Center for Vaccinology (CCfV), Halifax, NS B3H 4H7, Canada
- Laboratory of Immunity, Shantou University Medical College, Shantou 512025, China
- BioForge Canada Limited, Halifax, B3N3B9, NS, Canada
| | - Anuj Kumar
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS B3H 4H7, Canada
- Department of Pediatrics, Izaak Walton Killam (IWK) Health Center, Canadian Center for Vaccinology (CCfV), Halifax, NS B3H 4H7, Canada
- Laboratory of Immunity, Shantou University Medical College, Shantou 512025, China
- BioForge Canada Limited, Halifax, B3N3B9, NS, Canada
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Kumar A, Dutt M, Dehury B, Sganzerla Martinez G, Swan CL, Kelvin AA, Richardson CD, Kelvin DJ. Inhibition potential of natural flavonoids against selected omicron (B.1.19) mutations in the spike receptor binding domain of SARS-CoV-2: a molecular modeling approach. J Biomol Struct Dyn 2023:1-15. [PMID: 38115191 DOI: 10.1080/07391102.2023.2291165] [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: 05/29/2023] [Accepted: 09/09/2023] [Indexed: 12/21/2023]
Abstract
The omicron (B.1.19) variant of contagious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is considered a variant of concern (VOC) due to its increased transmissibility and highly infectious nature. The spike receptor-binding domain (RBD) is a hotspot of mutations and is regarded as a prominent target for screening drug candidates owing to its crucial role in viral entry and immune evasion. To date, no effective therapy or antivirals have been reported; therefore, there is an urgent need for rapid screening of antivirals. An extensive molecular modelling study has been performed with the primary goal to assess the inhibition potential of natural flavonoids as inhibitors against RBD from a manually curated library. Out of 40 natural flavonoids, five natural flavonoids, namely tomentin A (-8.7 kcal/mol), tomentin C (-8.6 kcal/mol), hyperoside (-8.4 kcal/mol), catechin gallate (-8.3 kcal/mol), and corylifol A (-8.2 kcal/mol), have been considered as the top-ranked compounds based on their binding affinity and molecular interaction profiling. The state-of-the-art molecular dynamics (MD) simulations of these top-ranked compounds in complex with RBD exhibited stable dynamics and structural compactness patterns on 200 nanoseconds. Additionally, complexes of these molecules demonstrated favorable free binding energies and affirmed the docking and simulation results. Moreover, the post-simulation validation of these interacted flavonoids using principal component analysis (PCA) revealed stable interaction patterns with RBD. The integrated results suggest that tomentin A, tomentin C, hyperoside, catechin gallate, and corylifol A might be effective against the emerging variants of SARS-CoV-2 and should be further evaluated using in-vitro and in-vivo experiments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anuj Kumar
- Laboratory of Immunity, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Canada
- Department of Paediatrics, IWK Health Center, Canadian Centre for Vaccinology (CCfV), Halifax, Canada
| | - Mansi Dutt
- Laboratory of Immunity, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Canada
- Department of Paediatrics, IWK Health Center, Canadian Centre for Vaccinology (CCfV), Halifax, Canada
| | - Budheswar Dehury
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Gustavo Sganzerla Martinez
- Laboratory of Immunity, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Canada
- Department of Paediatrics, IWK Health Center, Canadian Centre for Vaccinology (CCfV), Halifax, Canada
| | - Cynthia L Swan
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Canada
| | - Alyson A Kelvin
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Christopher D Richardson
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Canada
- Department of Paediatrics, IWK Health Center, Canadian Centre for Vaccinology (CCfV), Halifax, Canada
| | - David J Kelvin
- Laboratory of Immunity, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Canada
- Department of Paediatrics, IWK Health Center, Canadian Centre for Vaccinology (CCfV), Halifax, Canada
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7
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Swan CL, Dushimiyimana V, Ndishimye P, Buchanan R, Yourkowski A, Semafara S, Nsanzimana S, Francis ME, Thivierge B, Lew J, Facciuolo A, Gerdts V, Falzarano D, Sjaarda C, Kelvin DJ, Bitunguhari L, Kelvin AA. Third COVID-19 vaccine dose boosts antibody function in Rwandans with high HIV viral load. iScience 2023; 26:107959. [PMID: 37810226 PMCID: PMC10558770 DOI: 10.1016/j.isci.2023.107959] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 06/28/2023] [Revised: 08/18/2023] [Accepted: 09/14/2023] [Indexed: 10/10/2023] Open
Abstract
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) causing COVID-19 (coronavirus disease 2019) poses a greater health risk to immunocompromized individuals including people living with HIV (PLWH). However, most studies on PLWH have been conducted in higher-income countries. We investigated the post-vaccination antibody responses of PLWH in Rwanda by collecting peripheral blood from participants after receiving a second or third COVID-19 vaccine. Virus-binding antibodies as well as antibody neutralization ability against all major SARS-CoV-2 variants of concern were analyzed. We found that people with high HIV viral loads and two COVID-19 vaccine doses had lower levels of binding antibodies that were less virus neutralizing and less cross-reactive compared to control groups. A third vaccination increased neutralizing antibody titers. Our data suggest that people with high HIV viral loads require a third dose of vaccine to neutralize SARS-CoV-2 virus and new variants as they emerge.
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Affiliation(s)
- Cynthia L. Swan
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | | | - Pacifique Ndishimye
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
- African Institute for Mathematical Sciences, Kigali, Rwanda
| | - Rachelle Buchanan
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Anthony Yourkowski
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Sage Semafara
- Rwanda Network of the People living with HIV (RRP+), Kigali, Rwanda
| | | | - Magen E. Francis
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Brittany Thivierge
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Jocelyne Lew
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Antonio Facciuolo
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Volker Gerdts
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Darryl Falzarano
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Calvin Sjaarda
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON K7L 3N6, Canada
- Queen’s Genomics Lab at Ongwanada (Q-GLO), Ongwanada Resource Centre, Kingston, ON K7M 8A6, Canada
| | - David J. Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | | | - Alyson A. Kelvin
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
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Zoroddu S, Sanna L, Bordoni V, Lyu W, Murineddu G, Pinna GA, Forcales SV, Sala A, Kelvin DJ, Bagella L. RNAseq Analysis of Novel 1,3,4-Oxadiazole Chalcogen Analogues Reveals Anti-Tubulin Properties on Cancer Cell Lines. Int J Mol Sci 2023; 24:11263. [PMID: 37511023 PMCID: PMC10379353 DOI: 10.3390/ijms241411263] [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: 05/16/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
1,3,4-Oxadiazole derivatives are among the most studied anticancer drugs. Previous studies have analyzed the action of different 1,3,4-oxadiazole derivatives and their effects on cancer cells. This study investigated the characterization of two new compounds named 6 and 14 on HeLa and PC-3 cancer cell lines. Based on the previously obtained IC50, cell cycle effects were monitored by flow cytometry. RNA sequencing (RNAseq) was performed to identify differentially expressed genes, followed by functional annotation using gene ontology (GO), KEGG signaling pathway enrichment, and protein-protein interaction (PPI) network analyses. The tubulin polymerization assay was used to analyze the interaction of both compounds with tubulin. The results showed that 6 and 14 strongly inhibited the proliferation of cancer cells by arresting them in the G2/M phase of the cell cycle. Transcriptome analysis showed that exposure of HeLa and PC-3 cells to the compounds caused a marked reprograming of gene expression. Functional enrichment analysis indicated that differentially expressed genes were significantly enriched throughout the cell cycle and cancer-related biological processes. Furthermore, PPI network, hub gene, and CMap analyses revealed that compounds 14 and 6 shared target genes with established microtubule inhibitors, indicating points of similarity between the two molecules and microtubule inhibitors in terms of the mechanism of action. They were also able to influence the polymerization process of tubulin, suggesting the potential of these new compounds to be used as efficient chemotherapeutic agents.
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Affiliation(s)
- Stefano Zoroddu
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100 Sassari, Italy
| | - Luca Sanna
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100 Sassari, Italy
| | - Valentina Bordoni
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100 Sassari, Italy
| | - Weidong Lyu
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, Shantou 515031, China
| | - Gabriele Murineddu
- Department of Medicine, Surgery and Pharmacy, University of Sassari, 07100 Sassari, Italy
| | - Gerard A Pinna
- Department of Medicine, Surgery and Pharmacy, University of Sassari, 07100 Sassari, Italy
| | - Sonia Vanina Forcales
- Department of Pathology and Experimental Therapeutics, School of Medicine, Health Science Campus of Bellvitge, University of Barcelona, Carrer de la Feixa Llarga, s/n, Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Arturo Sala
- Centre for Inflammation Research and Translational Medicine (CIRTM), Department of Life Sciences, Brunel University, London UB8 3PH, UK
| | - David J Kelvin
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, Shantou 515031, China
- Department of Microbiology and Immunology, Dalhousie University, 6299 South St, Halifax, NS B3H 4R2, Canada
| | - Luigi Bagella
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100 Sassari, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Centre for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
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Sganzerla Martinez G, Kelvin DJ. Convergence in Mobility Data Sets From Apple, Google, and Meta. JMIR Public Health Surveill 2023; 9:e44286. [PMID: 37347516 DOI: 10.2196/44286] [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: 11/14/2022] [Revised: 02/09/2023] [Accepted: 05/26/2023] [Indexed: 06/23/2023] Open
Abstract
BACKGROUND The higher movement of people was one of the variables that contributed to the spread of the infectious agent SARS-CoV-2 during the COVID-19 pandemic. Governments worldwide responded to the virus by implementing measures that would restrict people's movements, and consequently, the spread of the disease. During the onset of the pandemic, the technology companies Apple, Google, and Meta used their infrastructure to anonymously gather mobility reports from their users. OBJECTIVE This study aims to compare mobility data reports collected by Apple, Google, and Meta (formerly Facebook) during the COVID-19 pandemic and a major winter storm in Texas in 2021. We aim to explore the hypothesis that different people exhibit similar mobility trends during dramatic events and to emphasize the importance of this type of data for public health measures. The study also aims to promote evidence for companies to continue releasing mobility trends data, given that all 3 companies have discontinued these services. METHODS In this study, we collected mobility data spanning from 2020 to 2022 from 3 major tech companies: Apple, Google, and Meta. Our analysis focused on 58 countries that are common to all 3 databases, enabling us to conduct a comprehensive global-scale analysis. By using the winter storm that occurred in Texas in 20201 as a benchmark, we were able to assess the robustness of the mobility data obtained from the 3 companies and ensure the integrity of our findings. RESULTS Our study revealed convergence in the mobility trends observed across different companies during the onset of significant disasters, such as the first year of the COVID-19 pandemic and the winter storm that impacted Texas in 2021. Specifically, we observed strong positive correlations (r=0.96) in the mobility data collected from different tech companies during the first year of the pandemic. Furthermore, our analysis of mobility data during the 2021 winter storm in Texas showed a similar convergence of trends. Additionally, we found that periods of stay-at-home orders were reflected in the data, with record-low mobility and record-high stay-at-home figures. CONCLUSIONS Our findings provide valuable insights into the ways in which major disruptive events can impact patterns of human mobility; moreover, the convergence of data across distinct methodologies highlights the potential value of leveraging mobility data from multiple sources for informing public health decision-making. Therefore, we conclude that the use of mobility data is an asset for health authorities to consider during natural disasters, as we determined that the data sets from 3 companies yielded convergent mobility patterns. Comparatively, data obtained from a single source would be limited, and therefore, more difficult to interpret, requiring careful analysis.
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Affiliation(s)
- Gustavo Sganzerla Martinez
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
- Department of Pediatrics, Izaak Walton Killam Health Center, Canadian Center for Vaccinology, Halifax, NS, Canada
| | - David J Kelvin
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
- Department of Pediatrics, Izaak Walton Killam Health Center, Canadian Center for Vaccinology, Halifax, NS, Canada
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10
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Shukla R, Chandra A, Kumar A, Kandpal P, Avashthi H, Goel VK, Qamar I, Singh N, Kelvin DJ, Singh TR. Repurposing of drugs against methyltransferase as potential Zika virus therapies. Sci Rep 2023; 13:7870. [PMID: 37188743 PMCID: PMC10184974 DOI: 10.1038/s41598-023-33341-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
In recent years, the outbreak of infectious disease caused by Zika Virus (ZIKV) has posed a major threat to global public health, calling for the development of therapeutics to treat ZIKV disease. Several possible druggable targets involved in virus replication have been identified. In search of additional potential inhibitors, we screened 2895 FDA-approved compounds using Non-Structural Protein 5 (NS5) as a target utilizing virtual screening of in-silco methods. The top 28 compounds with the threshold of binding energy -7.2 kcal/mol value were selected and were cross-docked on the three-dimensional structure of NS5 using AutoDock Tools. Of the 2895 compounds screened, five compounds (Ceforanide, Squanavir, Amcinonide, Cefpiramide, and Olmesartan_Medoxomil) ranked highest based on filtering of having the least negative interactions with the NS5 and were selected for Molecular Dynamic Simulations (MDS) studies. Various parameters such as RMSD, RMSF, Rg, SASA, PCA and binding free energy were calculated to validate the binding of compounds to the target, ZIKV-NS5. The binding free energy was found to be -114.53, -182.01, -168.19, -91.16, -122.56, and -150.65 kJ mol-1 for NS5-SFG, NS5-Ceforanide, NS5-Squanavir, NS5-Amcinonide, NS5-Cefpiramide, and NS5-Ol_Me complexes respectively. The binding energy calculations suggested Cefpiramide and Olmesartan_Medoxomil (Ol_Me) as the most stable compounds for binding to NS5, indicating a strong rationale for their use as lead compounds for development of ZIKV inhibitors. As these drugs have been evaluated on pharmacokinetics and pharmacodynamics parameters only, in vitro and in vivo testing and their impact on Zika viral cell culture may suggest their clinical trials on ZIKV patients.
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Affiliation(s)
- Rohit Shukla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, Solan, Himachal Pradesh, 173234, India
- Centre for Excellence in Healthcare Technologies and Informatics (CEHTI), Jaypee University of Information Technology (JUIT), Waknaghat, Solan, Himachal Pradesh, 173234, India
| | - Anshuman Chandra
- School of Biotechnology, Gautam Buddha University, Gautam Buddh Nagar, Greater Noida, Uttar Pradesh, 201312, India
- School of Physical Science, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Anuj Kumar
- Laboratory of Immunity, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, IWK Health Center, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, Canada
- Department of Pediatrics, IWK Health Center, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, Canada
- European Virus Bioinformatics Center, Leutragraben 1, Jena, Germany
| | | | - Himanshu Avashthi
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Pusa, New Delhi, India
| | - Vijay Kumar Goel
- School of Physical Science, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Imteyaz Qamar
- School of Biotechnology, Gautam Buddha University, Gautam Buddh Nagar, Greater Noida, Uttar Pradesh, 201312, India
| | - Nagendra Singh
- School of Biotechnology, Gautam Buddha University, Gautam Buddh Nagar, Greater Noida, Uttar Pradesh, 201312, India.
| | - David J Kelvin
- Laboratory of Immunity, Shantou University Medical College, Shantou, China.
- Department of Microbiology and Immunology, IWK Health Center, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, Canada.
- Department of Pediatrics, IWK Health Center, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, Canada.
| | - Tiratha Raj Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, Solan, Himachal Pradesh, 173234, India.
- Centre for Excellence in Healthcare Technologies and Informatics (CEHTI), Jaypee University of Information Technology (JUIT), Waknaghat, Solan, Himachal Pradesh, 173234, India.
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Dutt M, Kumar A, Rout M, Dehury B, Martinez G, Ndishimye P, Kelvin AA, Kelvin DJ. Drug repurposing for Mpox: Discovery of small molecules as potential inhibitors against DNA-dependent RNA polymerase using molecular modeling approach. J Cell Biochem 2023; 124:701-715. [PMID: 36946432 PMCID: PMC10473176 DOI: 10.1002/jcb.30397] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 01/12/2023] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/23/2023]
Abstract
Mpox (formerly Monkeypox), a zoonotic illness caused by the Mpox virus, belongs to the Orthopoxvirus genus in the family Poxviridae. To design and develop effective antiviral therapeutics against DNA viruses, the DNA-dependent RNA polymerase (DdRp) of poxviruses has emerged as a promising drug target. In the present study, we modeled the three-dimensional (3D) structure of DdRp using a template-based homology approach. After modeling, virtual screening was performed to probe the molecular interactions between 1755 Food and Drug Administration-approved small molecule drugs (≤500 molecular weight) and the DdRp of Mpox. Based on the binding affinity and molecular interaction patterns, five drugs, lumacaftor (-11.7 kcal/mol), conivaptan (-11.7 kcal/mol), betulinic acid (-11.6 kcal/mol), fluspirilene (-11.3 kcal/mol), and imatinib (-11.2 kcal/mol), have been ranked as the top drug compounds interacting with Mpox DdRp. Complexes of these shortlisted drugs with DdRp were further evaluated using state-of-the-art all-atoms molecular dynamics (MD) simulations on 200 nanoseconds followed by principal component analysis (PCA). MD simulations and PCA results revealed highly stable interactions of these small drugs with DdRp. After due validation in wet-lab using available in vitro and in vivo experiments, these repurposed drugs can be further utilized for the treatment of contagious Mpox virus. The outcome of this study may establish a solid foundation to screen repurposed and natural compounds as potential antiviral therapeutics against different highly pathogenic viruses.
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Affiliation(s)
- Mansi Dutt
- Department of Microbiology and Immunology, Department of Paediatrics, IWK Health Center, Canadian Centre for Vaccinology (CCfV), Faculty of MedicineDalhousie UniversityHalifaxCanada
| | - Anuj Kumar
- Department of Microbiology and Immunology, Department of Paediatrics, IWK Health Center, Canadian Centre for Vaccinology (CCfV), Faculty of MedicineDalhousie UniversityHalifaxCanada
- European Virus Bioinformatics CenterJenaGermany
| | - Madhusmita Rout
- Bioinformatics DivisionICMR‐Regional Medical Research CentreBhubaneswarOdishaIndia
| | - Budheswar Dehury
- Bioinformatics DivisionICMR‐Regional Medical Research CentreBhubaneswarOdishaIndia
| | - Gustavo Martinez
- Department of Microbiology and Immunology, Department of Paediatrics, IWK Health Center, Canadian Centre for Vaccinology (CCfV), Faculty of MedicineDalhousie UniversityHalifaxCanada
| | - Pacifique Ndishimye
- Department of Microbiology and Immunology, Department of Paediatrics, IWK Health Center, Canadian Centre for Vaccinology (CCfV), Faculty of MedicineDalhousie UniversityHalifaxCanada
| | - Alyson A. Kelvin
- Vaccine and Infectious Disease Organization (VIDO)University of SaskatchewanSaskatoonSaskatchewanCanada
- Department of Biochemistry, Microbiology, and ImmunologyUniversity of SaskatchewanSaskatoonSaskatchewanCanada
| | - David J. Kelvin
- Department of Microbiology and Immunology, Department of Paediatrics, IWK Health Center, Canadian Centre for Vaccinology (CCfV), Faculty of MedicineDalhousie UniversityHalifaxCanada
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Bermejo-Martin JF, García-Mateo N, Motos A, Resino S, Tamayo L, Ryan Murua P, Bustamante-Munguira E, Gallego Curto E, Úbeda-Iglesias A, de la Torre MDC, Estella Á, Campos-Fernández S, Martínez Varela I, Pérez-García F, Socias L, López Messa J, Vidal-Cortés P, Sagredo Meneses V, González-Rivera M, Carbonell N, de Gonzalo-Calvo D, Martín Delgado MC, Valdivia LJ, Martín-López C, Jorge García RN, Maseda E, Loza-Vázquez A, Kelvin DJ, Barbé F, Torres A. Effect of viral storm in patients admitted to intensive care units with severe COVID-19 in Spain: a multicentre, prospective, cohort study. Lancet Microbe 2023:S2666-5247(23)00041-1. [PMID: 37116517 PMCID: PMC10129133 DOI: 10.1016/s2666-5247(23)00041-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 01/09/2023] [Accepted: 02/08/2023] [Indexed: 04/30/2023]
Abstract
BACKGROUND The contribution of the virus to the pathogenesis of severe COVID-19 is still unclear. We aimed to evaluate associations between viral RNA load in plasma and host response, complications, and deaths in critically ill patients with COVID-19. METHODS We did a prospective cohort study across 23 hospitals in Spain. We included patients aged 18 years or older with laboratory-confirmed SARS-CoV-2 infection who were admitted to an intensive care unit between March 16, 2020, and Feb 27, 2021. RNA of the SARS-CoV-2 nucleocapsid region 1 (N1) was quantified in plasma samples collected from patients in the first 48 h following admission, using digital PCR. Patients were grouped on the basis of N1 quantity: VIR-N1-Zero (<1 N1 copies per mL), VIR-N1-Low (1-2747 N1 copies per mL), and VIR-N1-Storm (>2747 N1 copies per mL). The primary outcome was all-cause death within 90 days after admission. We evaluated odds ratios (ORs) for the primary outcome between groups using a logistic regression analysis. FINDINGS 1068 patients met the inclusion criteria, of whom 117 had insufficient plasma samples and 115 had key information missing. 836 patients were included in the analysis, of whom 403 (48%) were in the VIR-N1-Low group, 283 (34%) were in the VIR-N1-Storm group, and 150 (18%) were in the VIR-N1-Zero group. Overall, patients in the VIR-N1-Storm group had the most severe disease: 266 (94%) of 283 patients received invasive mechanical ventilation (IMV), 116 (41%) developed acute kidney injury, 180 (65%) had secondary infections, and 148 (52%) died within 90 days. Patients in the VIR-N1-Zero group had the least severe disease: 81 (54%) of 150 received IMV, 34 (23%) developed acute kidney injury, 47 (32%) had secondary infections, and 26 (17%) died within 90 days (OR for death 0·30, 95% CI 0·16-0·55; p<0·0001, compared with the VIR-N1-Storm group). 106 (26%) of 403 patients in the VIR-N1-Low group died within 90 days (OR for death 0·39, 95% CI 0·26-0·57; p<0·0001, compared with the VIR-N1-Storm group). INTERPRETATION The presence of a so-called viral storm is associated with increased all-cause death in patients admitted to the intensive care unit with severe COVID-19. Preventing this viral storm could help to reduce poor outcomes. Viral storm could be an enrichment marker for treatment with antivirals or purification devices to remove viral components from the blood. FUNDING Instituto de Salud Carlos III, Canadian Institutes of Health Research, Li Ka-Shing Foundation, Research Nova Scotia, and European Society of Clinical Microbiology and Infectious Diseases. TRANSLATION For the Spanish translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- Jesús F Bermejo-Martin
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, Gerencia Regional de Salud de Castilla y León, Salamanca, Spain; Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Research Unit, Hospital Universitario Rio Hortega, Gerencia Regional de Salud de Castilla y León, Valladolid, Spain; School of Medicine, Universidad de Salamanca, Salamanca, Spain.
| | - Nadia García-Mateo
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, Gerencia Regional de Salud de Castilla y León, Salamanca, Spain
| | - Anna Motos
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Department of Pulmonology, Hospital Clinic de Barcelona, Institut D Investigacions August Pi I Sunyer (IDIBAPS), Universidad de Barcelona, Barcelona, Spain
| | - Salvador Resino
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Viral Infection and Immunity Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Luis Tamayo
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Critical Care Medicine Service, Hospital Universitario Rio Hortega, Gerencia Regional de Salud de Castilla y León, Valladolid, Spain
| | - Pablo Ryan Murua
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Internal Medicine Service, Hospital Infanta Leonor, Madrid, Spain
| | - Elena Bustamante-Munguira
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Critical Care Medicine Service, Hospital Clínico Universitario de Valladolid, Gerencia Regional de Salud de Castilla y León, Valladolid, Spain
| | - Elena Gallego Curto
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Critical Care Medicine Service, Hospital San Pedro de Alcántara, Cáceres, Spain
| | | | | | - Ángel Estella
- Intensive Care Unit, Hospital Universitario de Jerez, Departamento de Medicina Universidad de Cádiz, INiBICA, Cádiz, Spain
| | - Sandra Campos-Fernández
- Critical Care Medicine Service, Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | | | - Felipe Pérez-García
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Clinical Microbiology Service, Hospital Universitario Príncipe de Asturias, Alcalá de Henares, Spain; Biomedicine and Biotechnology Department, Faculty of Medicine, Universidad de Alcalá, Alcalá de Henares, Spain
| | | | - Juan López Messa
- Critical Care Medicine Service, Complejo Asistencial Universitario de Palencia, Palencia, Spain
| | - Pablo Vidal-Cortés
- Intensive Care Unit, Complejo Hospitalario Universitario de Ourense, Ourense, Spain
| | | | | | - Nieves Carbonell
- Intensive Care Unit, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - David de Gonzalo-Calvo
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain
| | | | | | | | | | - Emilio Maseda
- Anesthesiology and Reanimation Service, Hospital Universitario de la Paz, Madrid, Spain
| | - Ana Loza-Vázquez
- Critical Care Medicine Service, Hospital Universitario Nuestra Señora de Valme, Sevilla, Spain
| | - David J Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Canadian Center for Vaccinology, Dalhousie University, Halifax, NS, Canada; Laboratory of Immunity, Shantou University Medical College, Shantou, Guangdong, China
| | - Ferrán Barbé
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain
| | - Antoni Torres
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Department of Pulmonology, Hospital Clinic de Barcelona, Institut D Investigacions August Pi I Sunyer (IDIBAPS), Universidad de Barcelona, Barcelona, Spain
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13
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Li C, Zhang J, Wu Q, Kumar A, Pan G, Kelvin DJ. Nifuroxazide Activates the Parthanatos to Overcome TMPRSS2:ERG Fusion-Positive Prostate Cancer. Mol Cancer Ther 2023; 22:306-316. [PMID: 36622760 PMCID: PMC9978883 DOI: 10.1158/1535-7163.mct-22-0159] [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: 03/05/2022] [Revised: 08/24/2022] [Accepted: 12/30/2022] [Indexed: 01/10/2023]
Abstract
Fusion of the E-26 transformation-specific (ETS)-related gene (ERG) with transmembrane serine protease 2 (TMPRSS2) is a crucial step in the occurrence and progression of approximately 50% of prostate cancers. Despite significant progress in drug discovery, ERG inhibitors have yet to be approved for the clinical treatment of prostate cancer. In this study, we used computer-aided drug design (CADD)-based virtual screening to screen for potential inhibitors of ERG. In vivo and in vitro methods revealed that nifuroxazide (NFZ) inhibited the proliferation of a TMPRSS2:ERG fusion-positive prostate cancer cell line (VCaP) with an IC50 lower than that of ERG-negative prostate cancer cell lines (LNCaP, DU145, and WPMY cells). Poly [ADP-ribose] polymerase 1, the critical mediator of parthanatos, is known to bind ERG and is required for ERG-mediated transcription. NFZ blocked this interaction and overly activated PARP1, leading to cell death that was reduced by olaparib, a PARP1 inhibitor. These results show that NFZ inhibits ERG, leading to parthanatic cell death.
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Affiliation(s)
- Chengxun Li
- Laboratory of Immunity, Shantou University Medical College, Guangdong, China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jiale Zhang
- Laboratory of Immunity, Shantou University Medical College, Guangdong, China
| | - Qiming Wu
- Laboratory of Immunity, Shantou University Medical College, Guangdong, China
| | - Anuj Kumar
- Laboratory of Immunity, Shantou University Medical College, Guangdong, China
- Department of Microbiology and Immunology, Faculty of Medicine, Canadian Center for Vaccinology, Dalhousie University, Halifax, NS, Canada
| | - Guihong Pan
- Laboratory of Immunity, Shantou University Medical College, Guangdong, China
| | - David J. Kelvin
- Laboratory of Immunity, Shantou University Medical College, Guangdong, China
- Department of Microbiology and Immunology, Faculty of Medicine, Canadian Center for Vaccinology, Dalhousie University, Halifax, NS, Canada
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Guangdong, China
- Corresponding Author: David J. Kelvin, Laboratory of Immunity, Shantou University Medical College, Guangdong, China. E-mail:
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14
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Zeng TS, Yang DS, Kelvin AA, Kelvin DJ. Host Transcriptome Analysis of Ferret Tissues Following Henipavirus Infection. Methods Mol Biol 2023; 2682:281-299. [PMID: 37610589 DOI: 10.1007/978-1-0716-3283-3_20] [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] [Indexed: 08/24/2023]
Abstract
Ferrets are commonly used as experimental models of infection for a variety of viruses due to their susceptibility to human respiratory viruses and the close resemblance of pathological outcomes found in human infections. Even though ferret-specific reagents are limited, the use of ferrets as a preclinical experimental model of infection has gained considerable interest since the publication of the ferret transcriptome and draft ferret genome. These advances have made it feasible to easily perform whole-genome gene expression analysis in the ferret infection model. Here, we describe methods for genome-wide gene expression analysis using RNA sequence (RNAseq) data obtained from the lung and brain tissues obtained from experimental infections of Hendra (HeV) and Nipah (NiV) viruses in ferrets. We provide detailed methods for RNAseq and representative data for host gene expression profiles of the lung tissues that show early activation of interferon pathways and later activation of inflammation-related pathways.
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Affiliation(s)
- Tian S Zeng
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - D S Yang
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - A A Kelvin
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - David J Kelvin
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada.
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15
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Sganzerla Martinez G, Hewins B, LeBlanc JJ, Ndishimye P, Toloue Ostadgavahi A, Kelvin DJ. Evaluating the effectiveness of lockdowns and restrictions during SARS-CoV-2 variant waves in the Canadian province of Nova Scotia. Front Public Health 2023; 11:1142602. [PMID: 37181684 PMCID: PMC10174067 DOI: 10.3389/fpubh.2023.1142602] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/30/2023] [Indexed: 05/16/2023] Open
Abstract
Introduction After the initial onset of the SARS-CoV-2 pandemic, the government of Canada and provincial health authorities imposed restrictive policies to limit virus transmission and mitigate disease burden. In this study, the pandemic implications in the Canadian province of Nova Scotia (NS) were evaluated as a function of the movement of people and governmental restrictions during successive SARS-CoV-2 variant waves (i.e., Alpha through Omicron). Methods Publicly available data obtained from community mobility reports (Google), the Bank of Canada Stringency Index, the "COVID-19 Tracker" service, including cases, hospitalizations, deaths, and vaccines, population mobility trends, and governmental response data were used to relate the effectiveness of policies in controlling movement and containing multiple waves of SARS-CoV-2. Results Our results indicate that the SARS-CoV-2 pandemic inflicted low burden in NS in the initial 2 years of the pandemic. In this period, we identified reduced mobility patterns in the population. We also observed a negative correlation between public transport (-0.78), workplace (-0.69), retail and recreation (-0.68) and governmental restrictions, indicating a tight governmental control of these movement patterns. During the initial 2 years, governmental restrictions were high and the movement of people low, characterizing a 'seek-and-destroy' approach. Following this phase, the highly transmissible Omicron (B.1.1.529) variant began circulating in NS at the end of the second year, leading to increased cases, hospitalizations, and deaths. During this Omicron period, unsustainable governmental restrictions and waning public adherence led to increased population mobility, despite increased transmissibility (26.41-fold increase) and lethality (9.62-fold increase) of the novel variant. Discussion These findings suggest that the low initial burden caused by the SARS-CoV-2 pandemic was likely a result of enhanced restrictions to contain the movement of people and consequently, the spread of the disease. Easing public health restrictions (as measured by a decline in the BOC index) during periods of high transmissibility of circulating COVID-19 variants contributed to community spread, despite high levels of immunization in NS.
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Affiliation(s)
- Gustavo Sganzerla Martinez
- Department of Microbiology and Immunology, Faculty of Medicine, Canadian Center for Vaccinology, Dalhousie University, Halifax, NS, Canada
- Laboratory of Immunity, Shantou University Medical College, Shantou, Guangdong, China
- Department of Pediatrics, Izaak Walton Killan (IWK) Health Center, Canandian Center for Vaccinology, Halifax, NS, Canada
| | - Benjamin Hewins
- Department of Microbiology and Immunology, Faculty of Medicine, Canadian Center for Vaccinology, Dalhousie University, Halifax, NS, Canada
- Laboratory of Immunity, Shantou University Medical College, Shantou, Guangdong, China
- Department of Pediatrics, Izaak Walton Killan (IWK) Health Center, Canandian Center for Vaccinology, Halifax, NS, Canada
| | - Jason J. LeBlanc
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
- Division of Infectious Diseases, Department of Medicine, Dalhousie University, Halifax, NS, Canada
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, NS, Canada
| | - Pacifique Ndishimye
- Department of Microbiology and Immunology, Faculty of Medicine, Canadian Center for Vaccinology, Dalhousie University, Halifax, NS, Canada
- Laboratory of Immunity, Shantou University Medical College, Shantou, Guangdong, China
- Department of Pediatrics, Izaak Walton Killan (IWK) Health Center, Canandian Center for Vaccinology, Halifax, NS, Canada
| | - Ali Toloue Ostadgavahi
- Department of Microbiology and Immunology, Faculty of Medicine, Canadian Center for Vaccinology, Dalhousie University, Halifax, NS, Canada
- Laboratory of Immunity, Shantou University Medical College, Shantou, Guangdong, China
- Department of Pediatrics, Izaak Walton Killan (IWK) Health Center, Canandian Center for Vaccinology, Halifax, NS, Canada
| | - David J. Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Canadian Center for Vaccinology, Dalhousie University, Halifax, NS, Canada
- Laboratory of Immunity, Shantou University Medical College, Shantou, Guangdong, China
- Department of Pediatrics, Izaak Walton Killan (IWK) Health Center, Canandian Center for Vaccinology, Halifax, NS, Canada
- *Correspondence: David J. Kelvin,
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Hewins B, Richardson C, Rubino S, Kelvin A, Toloue Ostadgavahi A, Kelvin DJ. Molecular mechanisms responsible for SARS-CoV-2 antibody waning and vaccine escape in Omicron sublineages BA.4 and BA.5. J Infect Dev Ctries 2022; 16:1122-1125. [DOI: 10.3855/jidc.17010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 06/29/2022] [Indexed: 10/31/2022] Open
Abstract
Mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome continue to threaten the global landscape of the coronavirus disease 2019 (COVID-19) pandemic. The Omicron variant (B.1.1.529) rapidly displaced previous ‘variants of concern’ (VoC) in 2021 due to its high rate of transmissibility and multitude of mutations. This global influx of infections saturated healthcare systems, overwhelmed testing capacity and case reporting, and increased the COVID-19 death toll. Global health leaders are now being faced with the most transmissible COVID-19 variants yet, the Omicron sublineages BA.4 and BA.5, which contain additional spike protein (S) mutations from previous Omicron and VoC serotypes. With universally observed antibody waning, increasing vaccine-variant mismatch, and resuming international travel, the stage is set for unprecedented levels of breakthrough infections and superspreading events. In this paper, we raise awareness to these novel variants and provide context for the high likelihood of an upcoming wave of infection capable of inflicting significant disease burden on a global scale.
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17
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Kumar A, Sharma M, Richardson CD, Kelvin DJ. Potential of Natural Alkaloids From Jadwar ( Delphinium denudatum) as Inhibitors Against Main Protease of COVID-19: A Molecular Modeling Approach. Front Mol Biosci 2022; 9:898874. [PMID: 35620478 PMCID: PMC9127362 DOI: 10.3389/fmolb.2022.898874] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 03/18/2022] [Accepted: 04/08/2022] [Indexed: 02/05/2023] Open
Abstract
The ongoing pandemic coronavirus disease (COVID-19) caused by a novel corona virus, namely, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has had a major impact on global public health. COVID-19 cases continue to increase across the globe with high mortality rates in immunocompromised patients. There is still a pressing demand for drug discovery and vaccine development against this highly contagious disease. To design and develop antiviral drugs against COVID-19, the main protease (Mpro) has emerged as one of the important drug targets. In this context, the present work explored Jadwar (Delphinium denudatum)-derived natural alkaloids as potential inhibitors against Mpro of SARS-CoV-2 by employing a combination of molecular docking and molecular dynamic simulation-based methods. Molecular docking and interaction profile analysis revealed strong binding on the Mpro functional domain with four natural alkaloids viz. panicutine (-7.4 kcal/mol), vilmorrianone (-7.0 kcal/mol), denudatine (-6.0 kcal/mol), and condelphine (-5.9 kcal/mol). The molecular docking results evaluated by using the MD simulations on 200 nanoseconds confirmed highly stable interactions of these compounds with the Mpro. Additionally, mechanics/generalized Born/Poisson-Boltzmann surface area (MM/G/P/BSA) free energy calculations also affirmed the docking results. Natural alkaloids explored in the present study possess the essential drug-likeness properties, namely, absorption, distribution, metabolism, and excretion (ADME), and are in accordance with Lipinski's rule of five. The results of this study suggest that these four bioactive molecules, namely, condelphine, denudatine, panicutine, and vilmorrianone, might be effective candidates against COVID-19 and can be further investigated using a number of experimental methods.
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Affiliation(s)
- Anuj Kumar
- Laboratory of Immunity, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - Mansi Sharma
- Laboratory of Immunity, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - Christopher D. Richardson
- Department of Microbiology and Immunology, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - David J. Kelvin
- Laboratory of Immunity, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, Canada
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18
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Hewins B, Rahman M, Bermejo-Martin JF, Kelvin AA, Richardson CD, Rubino S, Kumar A, Ndishimye P, Toloue Ostadgavahi A, Mahmud-Al-Rafat A, Kelvin DJ. Alpha, Beta, Delta, Omicron, and SARS-CoV-2 Breakthrough Cases: Defining Immunological Mechanisms for Vaccine Waning and Vaccine-Variant Mismatch. Front Virol 2022. [DOI: 10.3389/fviro.2022.849936] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The COVID-19 pandemic, caused by the SARS-CoV-2 coronavirus, is responsible for over 400 million cases and over 5. 5 million deaths worldwide. In response to widespread SARS-CoV-2 infection, immunization of the global population has approached 60% one dose and 54% full dose vaccination status. Emerging data indicates decreasing circulating antibody levels as well as decreases in other immune correlates in vaccinated individuals. Complicating the determination of vaccine effectiveness is the concomitant emergence of novel SARS-CoV-2 variants with substantial antigenic differences from the ancestral D614G strain. The Omicron variant (B.1.1.529) spike protein has over 30 mutations compared with the D614G spike protein, which was used to design most SARS-CoV-2 vaccines in use today. Therefore, breakthrough cases of SARS-CoV-2 infections or severe disease in fully vaccinated individuals must be interpreted with caution taking into consideration vaccine waning and the degree of vaccine variant-mismatch resulting in adaptive immune evasion by novel emerging SARS-CoV-2 variants.
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19
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Mahmud-Al-Rafat A, Hewins B, Mannan A, Kelvin DJ, Billah MM. COVID-19 vaccine inequity, dependency, and production capability in low-income and middle-income countries: the case of Bangladesh. Lancet Infect Dis 2022; 22:310-312. [PMID: 35101243 PMCID: PMC8798084 DOI: 10.1016/s1473-3099(22)00028-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/20/2021] [Accepted: 01/11/2022] [Indexed: 02/05/2023]
Affiliation(s)
- Abdullah Mahmud-Al-Rafat
- Department of Microbiology and Immunology, Canadian Center for Vaccinology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Benjamin Hewins
- Department of Microbiology and Immunology, Canadian Center for Vaccinology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Adnan Mannan
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - David J Kelvin
- Department of Microbiology and Immunology, Canadian Center for Vaccinology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada; Laboratory of Immunity, Shantou University Medical College, Guangdong, China
| | - Md Morsaline Billah
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh.
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20
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Martin‐Vicente M, Almansa R, Martínez I, Tedim AP, Bustamante E, Tamayo L, Aldecoa C, Gómez JM, Renedo G, Berezo JÁ, Cedeño JA, Mamolar N, García Olivares P, Herrán‐Monge R, Cicuendez R, Enríquez P, Ortega A, Jorge N, Doncel C, de la Fuente A, Bustamante‐Munguira J, Muñoz‐Gómez MJ, González‐Rivera M, Puertas C, Más V, Vázquez M, Pérez‐García F, Rico‐Feijoo J, Martín S, Motos A, Fernandez‐Barat L, Eiros JM, Dominguez‐Gil M, Ferrer R, Barbé F, Trapiello W, Kelvin DJ, Bermejo‐Martin JF, Resino S, Torres A. Low anti-SARS-CoV-2 S antibody levels predict increased mortality and dissemination of viral components in the blood of critical COVID-19 patients. J Intern Med 2022; 291:232-240. [PMID: 34611927 PMCID: PMC8661581 DOI: 10.1111/joim.13386] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Anti-SARS-CoV-2 S antibodies prevent viral replication. Critically ill COVID-19 patients show viral material in plasma, associated with a dysregulated host response. If these antibodies influence survival and viral dissemination in ICU-COVID patients is unknown. PATIENTS/METHODS We studied the impact of anti-SARS-CoV-2 S antibodies levels on survival, viral RNA-load in plasma, and N-antigenaemia in 92 COVID-19 patients over ICU admission. RESULTS Frequency of N-antigenaemia was >2.5-fold higher in absence of antibodies. Antibodies correlated inversely with viral RNA-load in plasma, representing a protective factor against mortality (adjusted HR [CI 95%], p): (S IgM [AUC ≥ 60]: 0.44 [0.22; 0.88], 0.020); (S IgG [AUC ≥ 237]: 0.31 [0.16; 0.61], <0.001). Viral RNA-load in plasma and N-antigenaemia predicted increased mortality: (N1-viral load [≥2.156 copies/ml]: 2.25 [1.16; 4.36], 0.016); (N-antigenaemia: 2.45 [1.27; 4.69], 0.007). CONCLUSIONS Low anti-SARS-CoV-2 S antibody levels predict mortality in critical COVID-19. Our findings support that these antibodies contribute to prevent systemic dissemination of SARS-CoV-2.
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Affiliation(s)
- María Martin‐Vicente
- Unidad de Infección Viral e InmunidadCentro Nacional de MicrobiologíaInstituto de Salud Carlos IIIMajadahondaSpain
| | - Raquel Almansa
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Hospital Universitario Río HortegaGerencia Regional de SaludValladolidSpain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
| | - Isidoro Martínez
- Unidad de Infección Viral e InmunidadCentro Nacional de MicrobiologíaInstituto de Salud Carlos IIIMajadahondaSpain
| | - Ana P. Tedim
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Hospital Universitario Río HortegaGerencia Regional de SaludValladolidSpain
| | - Elena Bustamante
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Intensive Care UnitHospital Clínico Universitario de Valladolid, Gerencia Regional de SaludValladolidSpain
| | - Luis Tamayo
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Intensive Care UnitHospital Universitario Rio Hortega, Gerencia Regional de SaludValladolidSpain
| | - César Aldecoa
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Department of AnesthesiologyFacultad de Medicina de ValladolidValladolidSpain
- Anesthesiology and Reanimation ServiceHospital Universitario Rio Hortega, Gerencia Regional de SaludValladolidSpain
| | - José Manuel Gómez
- Intensive Care Unit. Hospital General Universitario Gregorio Marañón, Calle del Dr. EsquerdoMadridSpain
| | - Gloria Renedo
- Intensive Care UnitHospital Clínico Universitario de Valladolid, Gerencia Regional de SaludValladolidSpain
| | - Jose Ángel Berezo
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Intensive Care UnitHospital Universitario Rio Hortega, Gerencia Regional de SaludValladolidSpain
| | - Jamil Antonio Cedeño
- Intensive Care Unit. Hospital General Universitario Gregorio Marañón, Calle del Dr. EsquerdoMadridSpain
| | - Nuria Mamolar
- Intensive Care UnitHospital Clínico Universitario de Valladolid, Gerencia Regional de SaludValladolidSpain
| | - Pablo García Olivares
- Intensive Care Unit. Hospital General Universitario Gregorio Marañón, Calle del Dr. EsquerdoMadridSpain
| | - Rubén Herrán‐Monge
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Intensive Care UnitHospital Universitario Rio Hortega, Gerencia Regional de SaludValladolidSpain
| | - Ramón Cicuendez
- Intensive Care UnitHospital Clínico Universitario de Valladolid, Gerencia Regional de SaludValladolidSpain
| | - Pedro Enríquez
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Intensive Care UnitHospital Universitario Rio Hortega, Gerencia Regional de SaludValladolidSpain
| | - Alicia Ortega
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Hospital Universitario Río HortegaGerencia Regional de SaludValladolidSpain
| | - Noelia Jorge
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Hospital Universitario Río HortegaGerencia Regional de SaludValladolidSpain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
| | - Cristina Doncel
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Hospital Universitario Río HortegaGerencia Regional de SaludValladolidSpain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
| | - Amanda de la Fuente
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Hospital Universitario Río HortegaGerencia Regional de SaludValladolidSpain
| | - Juan Bustamante‐Munguira
- Department of Cardiovascular SurgeryHospital Clínico Universitario de Valladolid, Gerencia Regional de SaludValladolidSpain
| | - María José Muñoz‐Gómez
- Unidad de Infección Viral e InmunidadCentro Nacional de MicrobiologíaInstituto de Salud Carlos IIIMajadahondaSpain
| | | | - Carolina Puertas
- Department of Laboratory MedicineHospital General Universitario Gregorio MarañónMadridSpain
| | - Vicente Más
- Unidad de Biología ViralCentro Nacional de MicrobiologíaInstituto de Salud Carlos IIIMadridSpain
| | - Mónica Vázquez
- Unidad de Biología ViralCentro Nacional de MicrobiologíaInstituto de Salud Carlos IIIMadridSpain
| | - Felipe Pérez‐García
- Servicio de Microbiología ClínicaHospital Universitario Príncipe de AsturiasMadridSpain
| | - Jesús Rico‐Feijoo
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Anesthesiology and Reanimation ServiceHospital Universitario Rio Hortega, Gerencia Regional de SaludValladolidSpain
| | - Silvia Martín
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Anesthesiology and Reanimation ServiceHospital Universitario Rio Hortega, Gerencia Regional de SaludValladolidSpain
| | - Anna Motos
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
- Department of PulmonologyHospital Clinic de BarcelonaUniversidad de BarcelonaInstitut D investigacions August Pi I Sunyer (IDIBAPS)BarcelonaSpain
| | - Laia Fernandez‐Barat
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
- Department of PulmonologyHospital Clinic de BarcelonaUniversidad de BarcelonaInstitut D investigacions August Pi I Sunyer (IDIBAPS)BarcelonaSpain
| | - Jose María Eiros
- Microbiology ServiceHospital Universitario Río Hortega, Gerencia Regional de SaludValladolidSpain
| | - Marta Dominguez‐Gil
- Microbiology ServiceHospital Universitario Río Hortega, Gerencia Regional de SaludValladolidSpain
| | - Ricard Ferrer
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
- Intensive Care DepartmentVall d'Hebron Hospital Universitari, SODIR Research GroupVall d'Hebron Institut de RecercaBarcelonaSpain
| | - Ferrán Barbé
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
- Respiratory DepartmentInstitut Ricerca Biomedica de LleidaLleidaSpain
| | - Wysali Trapiello
- Clinical Analysis ServiceHospital Clínico Universitario de Valladolid, Gerencia Regional de SaludValladolidSpain
| | - David J. Kelvin
- Department of Microbiology and ImmunologyFaculty of MedicineCanadian Center for Vaccinology CCfVDalhousie UniversityHalifaxNova ScotiaCanada
- Laboratory of ImmunityShantou University Medical CollegeShantouGuangdongChina
| | - Jesús F. Bermejo‐Martin
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Hospital Universitario Río HortegaGerencia Regional de SaludValladolidSpain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
| | - Salvador Resino
- Unidad de Infección Viral e InmunidadCentro Nacional de MicrobiologíaInstituto de Salud Carlos IIIMajadahondaSpain
| | - Antoni Torres
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
- Department of PulmonologyHospital Clinic de BarcelonaUniversidad de BarcelonaInstitut D investigacions August Pi I Sunyer (IDIBAPS)BarcelonaSpain
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21
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Grandi N, Paglietti B, Cusano R, Ibba G, Lai V, Piu C, Angioj F, Serra C, Kelvin DJ, Tramontano E, Rubino S. Genomic Snapshot of SARS-CoV-2 in Migrants Entering Through Mediterranean Sea Routes. Front Public Health 2022; 10:846115. [PMID: 35309205 PMCID: PMC8927662 DOI: 10.3389/fpubh.2022.846115] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/07/2022] [Indexed: 02/05/2023] Open
Abstract
In December 2019, a novel coronavirus emerged in Wuhan, China, rapidly spreading into a global pandemic. Italy was the first European country to experience SARS-CoV-2 epidemic, and one of the most severely affected during the first wave of diffusion. In contrast to the general restriction of people movements in Europe, the number of migrants arriving at Italian borders via the Mediterranean Sea route in the summer of 2020 had increased dramatically, representing a possible, uncontrolled source for the introduction of novel SARS-CoV-2 variants. Importantly, most of the migrants came from African countries showing limited SARS-CoV-2 epidemiological surveillance. In this study, we characterized the SARS-CoV-2 genome isolated from an asymptomatic migrant arrived in Sardinia via the Mediterranean route in September 2020, in comparison with SARS-CoV-2 isolates arrived in Sicily through the Libyan migration route; with SARS-CoV-2 isolates circulating in Sardinia during 2020; and with viral genomes reported in African countries during the same summer. Results showed that our sequence is not phylogenetically related to isolates from migrants arriving in Sicily, nor to isolates circulating in Sardinia territory, having greater similarity to SARS-CoV-2 genomes reported in countries known for being sites of migrant embarkation to Italy. This is in line with the hypothesis that most SARS-CoV-2 infections among migrants have been acquired prior to embarking to Italy, possibly during the travel to or the stay in crowded Libyan immigrant camps. Overall, these observations underline the importance of dedicated SARS-CoV-2 surveillance of migrants arriving in Italy and in Europe through the Mediterranean routes.
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Affiliation(s)
- Nicole Grandi
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Bianca Paglietti
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- SC Microbiologia e Virologia, Azienda Ospedaliero Universitaria Sassari, Sassari, Italy
- *Correspondence: Bianca Paglietti
| | - Roberto Cusano
- Center for Advanced Studies, Research and Development in Sardinia (CRS4), Science and Technology Park Polaris, Cagliari, Italy
| | - Gabriele Ibba
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- SC Microbiologia e Virologia, Azienda Ospedaliero Universitaria Sassari, Sassari, Italy
| | - Vincenzo Lai
- SC Microbiologia e Virologia, Azienda Ospedaliero Universitaria Sassari, Sassari, Italy
| | - Claudia Piu
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- SC Microbiologia e Virologia, Azienda Ospedaliero Universitaria Sassari, Sassari, Italy
| | - Flavia Angioj
- SC Microbiologia e Virologia, Azienda Ospedaliero Universitaria Sassari, Sassari, Italy
| | - Caterina Serra
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- SC Microbiologia e Virologia, Azienda Ospedaliero Universitaria Sassari, Sassari, Italy
| | - David J. Kelvin
- Department of Microbiology and Immunology, Canadian Center for Vaccinology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, Shantou, China
| | - Enzo Tramontano
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale Delle Ricerche, Cagliari, Italy
| | - Salvatore Rubino
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- SC Microbiologia e Virologia, Azienda Ospedaliero Universitaria Sassari, Sassari, Italy
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22
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Shukla R, Kumar A, Kelvin DJ, Singh TR. Disruption of DYRK1A-induced hyperphosphorylation of amyloid-beta and tau protein in Alzheimer's disease: An integrative molecular modeling approach. Front Mol Biosci 2022; 9:1078987. [PMID: 36741918 PMCID: PMC9892649 DOI: 10.3389/fmolb.2022.1078987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/20/2022] [Indexed: 01/20/2023] Open
Abstract
Alzheimer's disease (AD) is a neurological disorder caused by the abnormal accumulation of hyperphosphorylated proteins. Dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) is a dual phosphorylation enzyme which phosphorylates the amyloid-β (Aβ) and neurofibrillary tangles (NFTs). A high throughput virtual screening approach was applied to screen a library of 98,071 compounds against DYRK1A using different programs including AutoDock Vina, Smina, and idock. Based on the binding affinities, we selected 330 compounds for absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis. Various pharmacokinetics parameters were predicted using the admetSAR server, and based on the pharmacokinetics results, 14 compounds were selected for cross-docking analysis using AutoDock. Cross-docking analysis revealed four compounds, namely, ZINC3843365 (-11.07 kcal/mol-1), ZINC2123081 (-10.93 kcal/mol-1), ZINC5220992 (-10.63 kcal/mol-1), and ZINC68569602 (-10.35 kcal/mol-1), which had the highest negative affinity scores compared to the 10 other molecules analyzed. Density functional theory (DFT) analysis was conducted for all the four top-ranked compounds. The molecular interaction stability of these four compounds with DYRK1A has been evaluated using molecular dynamics (MD) simulations on 100 nanoseconds followed by principal component analysis (PCA) and binding free energy calculations. The Gibbs free energy landscape analysis suggested the metastable state and folding pattern of selected docking complexes. Based on the present study outcome, we propose four antagonists, viz., ZINC3843365, ZINC2123081, ZINC5220992, and ZINC68569602 as potential inhibitors against DYRK1A and to reduce the amyloid-β and neurofibrillary tangle burden. These screened molecules can be further investigated using a number of in vitro and in vivo experiments.
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Affiliation(s)
- Rohit Shukla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, Himachal Pradesh, India
- Centre for Excellence in Healthcare Technologies and Informatics (CEHTI), Jaypee University of Information Technology (JUIT), Waknaghat, Himachal Pradesh, India
| | - Anuj Kumar
- Laboratory of Immunity, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - David J. Kelvin
- Laboratory of Immunity, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
- *Correspondence: David J. Kelvin, ; Tiratha Raj Singh,
| | - Tiratha Raj Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, Himachal Pradesh, India
- Centre for Excellence in Healthcare Technologies and Informatics (CEHTI), Jaypee University of Information Technology (JUIT), Waknaghat, Himachal Pradesh, India
- *Correspondence: David J. Kelvin, ; Tiratha Raj Singh,
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23
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Bordoni V, Sanna L, Lyu W, Avitabile E, Zoroddu S, Medici S, Kelvin DJ, Bagella L. Silver Nanoparticles Derived by Artemisia arborescens Reveal Anticancer and Apoptosis-Inducing Effects. Int J Mol Sci 2021; 22:ijms22168621. [PMID: 34445327 PMCID: PMC8395306 DOI: 10.3390/ijms22168621] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 07/12/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 02/05/2023] Open
Abstract
The fight against cancer is one of the main challenges for medical research. Recently, nanotechnology has made significant progress, providing possibilities for developing innovative nanomaterials to overcome the common limitations of current therapies. In this context, silver nanoparticles (AgNPs) represent a promising nano-tool able to offer interesting applications for cancer research. Following this path, we combined the silver proprieties with Artemisia arborescens characteristics, producing novel nanoparticles called Artemisia-AgNPs. A "green" synthesis method was performed to produce Artemisia-AgNPs, using Artemisia arborescens extracts. This kind of photosynthesis is an eco-friendly, inexpensive, and fast approach. Moreover, the bioorganic molecules of plant extracts improved the biocompatibility and efficacy of Artemisia-AgNPs. The Artemisia-AgNPs were fully characterized and tested to compare their effects on various cancer cell lines, in particular HeLa and MCF-7. Artemisia-AgNPs treatment showed dose-dependent growth inhibition of cancer cells. Moreover, we evaluated their impact on the cell cycle, observing a G1 arrest mediated by Artemisia-AgNPs treatment. Using a clonogenic assay after treatment, we observed a complete lack of cell colonies, which demonstrated cell reproducibility death. To have a broader overview on gene expression impact, we performed RNA-sequencing, which demonstrated the potential of Artemisia-AgNPs as a suitable candidate tool in cancer research.
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Affiliation(s)
- Valentina Bordoni
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100 Sassari, Italy; (V.B.); (L.S.); (W.L.); (E.A.); (S.Z.)
| | - Luca Sanna
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100 Sassari, Italy; (V.B.); (L.S.); (W.L.); (E.A.); (S.Z.)
| | - Weidong Lyu
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100 Sassari, Italy; (V.B.); (L.S.); (W.L.); (E.A.); (S.Z.)
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, Shantou 515011, China;
| | - Elisabetta Avitabile
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100 Sassari, Italy; (V.B.); (L.S.); (W.L.); (E.A.); (S.Z.)
| | - Stefano Zoroddu
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100 Sassari, Italy; (V.B.); (L.S.); (W.L.); (E.A.); (S.Z.)
| | - Serenella Medici
- Department of Chemistry and Pharmacy, University of Sassari, Via Muroni 23, 07100 Sassari, Italy;
| | - David J. Kelvin
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, Shantou 515011, China;
- Department of Microbiology and Immunology, Dalhousie University, 6299 South St, Halifax, NS B3H 4R2, Canada
| | - Luigi Bagella
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100 Sassari, Italy; (V.B.); (L.S.); (W.L.); (E.A.); (S.Z.)
- Centre for Biotechnology, Sbarro Institute for Cancer Research and Molecular Medicine, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
- Correspondence:
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24
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Foley MK, Searle SD, Toloue A, Booth R, Falkenham A, Falzarano D, Rubino S, Francis ME, McNeil M, Richardson C, LeBlanc J, Oldford S, Gerdts V, Andrew MK, McNeil SA, Clarke B, Rockwood K, Kelvin DJ, Kelvin AA. Centenarians and extremely old people living with frailty can elicit durable SARS-CoV-2 spike specific IgG antibodies with virus neutralization functions following virus infection as determined by serological study. EClinicalMedicine 2021; 37:100975. [PMID: 34222846 PMCID: PMC8235995 DOI: 10.1016/j.eclinm.2021.100975] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/21/2021] [Accepted: 06/04/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The SARS-CoV-2 (Severe Acute Respiratory Syndrome coronavirus 2) has led to more than 165 million COVID-19 cases and >3.4 million deaths worldwide. Epidemiological analysis has revealed that the risk of developing severe COVID-19 increases with age. Despite a disproportionate number of older individuals and long-term care facilities being affected by SARS-CoV-2 and COVID-19, very little is understood about the immune responses and development of humoral immunity in the extremely old person after SARS-CoV-2 infection. Here we conducted a serological study to investigate the development of humoral immunity in centenarians following a SARS-CoV-2 outbreak in a long-term care facility. METHODS Extreme aged individuals and centenarians who were residents in a long-term care facility and infected with or exposed to SARS-CoV-2 were investigated between April and June 2020 for the development of antibodies to SARS-CoV-2. Blood samples were collected from positive and bystander individuals 30 and 60 days after original diagnosis of SARS-CoV-2 infection. Plasma was used to quantify IgG, IgA, and IgM isotypes and subsequent subclasses of antibodies specific for SARS-CoV-2 spike protein. The function of anti-spike was then assessed by virus neutralization assays against the native SARS-CoV-2 virus. FINDINGS Fifteen long-term care residents were investigated for SARS-CoV-2 infection. All individuals had a Clinical Frailty scale score ≥5 and were of extreme older age or were centenarians. Six women with a median age of 98.8 years tested positive for SARS-CoV-2. Anti-spike IgG antibody titers were the highest titers observed in our cohort with all IgG positive individuals having virus neutralization ability. Additionally, 5 out of the 6 positive participants had a robust IgA anti-SARS-CoV-2 response. In all 5, antibodies were detected after 60 days from initial diagnosis.
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Affiliation(s)
- Mary K. Foley
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Samuel D. Searle
- Divsion of Geriatrics, Department of Medicine, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
- MRC Unit for Lifelong Health and Ageing, University College London, London, Gower Street, WC1E 6BT, England United Kingdom
| | - Ali Toloue
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Ryan Booth
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Alec Falkenham
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Darryl Falzarano
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, S7N 5E3, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Salvatore Rubino
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy
| | - Magen E. Francis
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, S7N 5E3, Canada
| | - Mara McNeil
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Christopher Richardson
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Jason LeBlanc
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
- Department of Medicine, Faculty of Medicine, Dalhousie University, University, Halifax, Nova Scotia, B3H 4R2, Canada
- Canadian Centre for Vaccinology, IWK Health Centre, Nova Scotia, Halifax, B3K 6R8 Canada
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Faculty of Medicine, Dalhousie University, Nova Scotia, Halifax, B3H 4R2, Canada
| | - Sharon Oldford
- Canadian Centre for Vaccinology, IWK Health Centre, Nova Scotia, Halifax, B3K 6R8 Canada
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Faculty of Medicine, Dalhousie University, Nova Scotia, Halifax, B3H 4R2, Canada
| | - Volker Gerdts
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, S7N 5E3, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Melissa K. Andrew
- Divsion of Geriatrics, Department of Medicine, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Shelly A. McNeil
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, S7N 5E3, Canada
| | - Barry Clarke
- Department of Family Medicine, Dalhousie University, Nova Scotia, Halifax, B3H 4R2, Canada
| | - Kenneth Rockwood
- Divsion of Geriatrics, Department of Medicine, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - David J. Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
- Canadian Centre for Vaccinology, IWK Health Centre, Nova Scotia, Halifax, B3K 6R8 Canada
- Laboratory of Immunity, Shantou University Medical College, 22 Xinling Rd, Jinping, Shantou, China
| | - Alyson A. Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, S7N 5E3, Canada
- Canadian Centre for Vaccinology, IWK Health Centre, Nova Scotia, Halifax, B3K 6R8 Canada
- Department of Pediatrics, Faculty of Medicine, Dalhousie University, Halifax, NS B3K 6R8, Canada
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25
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Tedim AP, Almansa R, Domínguez‐Gil M, González‐Rivera M, Micheloud D, Ryan P, Méndez R, Blanca‐López N, Pérez‐García F, Bustamante E, Gómez JM, Doncel C, Trapiello W, Kelvin AA, Booth R, Ostadgavahi AT, Oneizat R, Puertas C, Barbé F, Ferrer R, Menéndez R, Bermejo‐Martin JF, Eiros JM, Kelvin DJ, Torres A. Comparison of real-time and droplet digital PCR to detect and quantify SARS-CoV-2 RNA in plasma. Eur J Clin Invest 2021; 51:e13501. [PMID: 33512013 PMCID: PMC7995030 DOI: 10.1111/eci.13501] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/13/2021] [Accepted: 01/25/2021] [Indexed: 02/05/2023]
Abstract
BACKGROUND The presence of SARS-CoV-2 RNA in plasma has been linked to disease severity and mortality. We compared RT-qPCR to droplet digital PCR (ddPCR) to detect SARS-CoV-2 RNA in plasma from COVID-19 patients (mild, moderate, and critical disease). METHODS The presence/concentration of SARS-CoV-2 RNA in plasma was compared in three groups of COVID-19 patients (30 outpatients, 30 ward patients and 30 ICU patients) using both RT-qPCR and ddPCR. Plasma was obtained in the first 24h following admission, and RNA was extracted using eMAG. ddPCR was performed using Bio-Rad SARS-CoV-2 detection kit, and RT-qPCR was performed using GeneFinder™ COVID-19 Plus RealAmp Kit. Statistical analysis was performed using Statistical Package for the Social Science. RESULTS SARS-CoV-2 RNA was detected, using ddPCR and RT-qPCR, in 91% and 87% of ICU patients, 27% and 23% of ward patients and 3% and 3% of outpatients. The concordance of the results obtained by both methods was excellent (Cohen's kappa index = 0.953). RT-qPCR was able to detect 34/36 (94.4%) patients positive for viral RNA in plasma by ddPCR. Viral RNA load was higher in ICU patients compared with the other groups (P < .001), by both ddPCR and RT-qPCR. AUC analysis revealed Ct values (RT-qPCR) and viral RNA load values (ddPCR) can similarly differentiate between patients admitted to wards and to the ICU (AUC of 0.90 and 0.89, respectively). CONCLUSION Both methods yielded similar prevalence of RNAemia between groups, with ICU patients showing the highest (>85%). RT-qPCR was as useful as ddPCR to detect and quantify SARS-CoV-2 RNAemia in plasma.
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Affiliation(s)
- Ana P. Tedim
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de SalamancaSalamancaSpain
- Hospital Universitario Río HortegaValladolidSpain
| | - Raquel Almansa
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de SalamancaSalamancaSpain
- Hospital Universitario Río HortegaValladolidSpain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIAv. de Monforte de LemosMadridSpain
| | | | | | - Dariela Micheloud
- Emergency DepartmentHospital General Universitario Gregorio MarañónMadridSpain
| | - Pablo Ryan
- Hospital Universitario Infanta LeonorMadridSpain
| | - Raúl Méndez
- Pulmonology ServiceHospital Universitario y Politécnico de La FeAvinguda de Fernando Abril MartorellSpain
| | | | - Felipe Pérez‐García
- Servicio de Microbiología ClínicaHospital Universitario Príncipe de AsturiasMadridSpain
| | - Elena Bustamante
- Intensive Care UnitHospital Clínico Universitario de Valladolid. Av. Ramón y CajalValladolidSpain
| | - José Manuel Gómez
- Intensive Care Unit. Hospital General Universitario Gregorio MarañónMadridSpain
| | - Cristina Doncel
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de SalamancaSalamancaSpain
- Hospital Universitario Río HortegaValladolidSpain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIAv. de Monforte de LemosMadridSpain
| | - Wysali Trapiello
- Clinical Analysis Service. HospitalClínico Universitario de ValladolidAv. Ramón y CajalValladolidSpain
| | - Alyson A. Kelvin
- Department of Microbiology and ImmunologyFaculty of MedicineCanadian Center for Vaccinology CCfVDalhousie UniversityHalifaxNova ScotiaCanada
- Laboratory of ImmunityShantou University Medical CollegeJinping, ShantouChina
| | - Ryan Booth
- Department of Microbiology and ImmunologyFaculty of MedicineCanadian Center for Vaccinology CCfVDalhousie UniversityHalifaxNova ScotiaCanada
- Laboratory of ImmunityShantou University Medical CollegeJinping, ShantouChina
| | - Ali Toloue Ostadgavahi
- Department of Microbiology and ImmunologyFaculty of MedicineCanadian Center for Vaccinology CCfVDalhousie UniversityHalifaxNova ScotiaCanada
- Laboratory of ImmunityShantou University Medical CollegeJinping, ShantouChina
| | - Ruth Oneizat
- Microbiology ServiceHospital Universitario Rio HortegaValladolidSpain
| | - Carolina Puertas
- Department of Laboratory MedicineHospital General Universitario Gregorio MarañónMadridSpain
| | - Ferrán Barbé
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIAv. de Monforte de LemosMadridSpain
- Respiratory DepartmentInstitut Ricerca Biomedica de LleidaAv. Alcalde Rovira RoureLleidaSpain
| | - Ricard Ferrer
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIAv. de Monforte de LemosMadridSpain
- Intensive Care DepartmentSODIR Research GroupVall d’Hebron Hospital UniversitariVall d’Hebron Institut de RecercaBarcelonaSpain
| | - Rosario Menéndez
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIAv. de Monforte de LemosMadridSpain
- Pulmonology ServiceHospital Universitario y Politécnico de La FeAvinguda de Fernando Abril MartorellSpain
| | - Jesús F Bermejo‐Martin
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de SalamancaSalamancaSpain
- Hospital Universitario Río HortegaValladolidSpain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIAv. de Monforte de LemosMadridSpain
| | - José María Eiros
- Microbiology ServiceHospital Universitario Rio HortegaValladolidSpain
| | - David J Kelvin
- Department of Microbiology and ImmunologyFaculty of MedicineCanadian Center for Vaccinology CCfVDalhousie UniversityHalifaxNova ScotiaCanada
- Laboratory of ImmunityShantou University Medical CollegeJinping, ShantouChina
| | - Antoni Torres
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIAv. de Monforte de LemosMadridSpain
- Department of PulmonologyInstitut D investigacions August Pi I Sunyer (IDIBAPS)Hospital Clinic de BarcelonaUniversidad de BarcelonaBarcelonaSpain
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26
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Almansa R, Tedim AP, de la Fuente A, Eiros JM, Kelvin DJ, Torres A, Bermejo-Martin JF. Combining immunomodulators and antivirals for COVID-19 - Authors' reply. Lancet Microbe 2021; 2:e234. [PMID: 34100005 PMCID: PMC8172165 DOI: 10.1016/s2666-5247(21)00115-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Raquel Almansa
- Group for Biomedical Research in Sepsis, Instituto de Investigación Biomédica de Salamanca, Gerencia Regional de Salud, Paseo de San Vicente, 37007 Salamanca, Spain
- Research Unit, Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Ana P Tedim
- Group for Biomedical Research in Sepsis, Instituto de Investigación Biomédica de Salamanca, Gerencia Regional de Salud, Paseo de San Vicente, 37007 Salamanca, Spain
- Research Unit, Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid, Spain
| | - Amanda de la Fuente
- Group for Biomedical Research in Sepsis, Instituto de Investigación Biomédica de Salamanca, Gerencia Regional de Salud, Paseo de San Vicente, 37007 Salamanca, Spain
- Research Unit, Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid, Spain
| | - Jose María Eiros
- Microbiology Service, Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid, Spain
- Research Unit, Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid, Spain
| | - David J Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Canadian Center for Vaccinology, Dalhousie University, Halifax, NS, Canada
- Laboratory of Immunity, Shantou University Medical College, Jinping, Shantou, Guangdong, China
| | - Antoni Torres
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Department of Pulmonology, Hospital Clinic de Barcelona, Universidad de Barcelona, Institut D investigacions August Pi I Sunyer, Barcelona, Spain
| | - Jesus F Bermejo-Martin
- Group for Biomedical Research in Sepsis, Instituto de Investigación Biomédica de Salamanca, Gerencia Regional de Salud, Paseo de San Vicente, 37007 Salamanca, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
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27
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Bermejo-Martin JF, Almansa R, Tedim AP, de la Fuente A, Eiros JM, Torres A, Kelvin DJ. Mounting evidence of impaired viral control in severe COVID-19. Lancet Microbe 2021; 2:e228-e229. [PMID: 33880456 PMCID: PMC8049594 DOI: 10.1016/s2666-5247(21)00084-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Jesus F Bermejo-Martin
- Group for Biomedical Research in Sepsis, Instituto de Investigación Biomédica de Salamanca, Gerencia Regional de Salud, Salamanca 37007, Spain
- Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid 47012, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Raquel Almansa
- Group for Biomedical Research in Sepsis, Instituto de Investigación Biomédica de Salamanca, Gerencia Regional de Salud, Salamanca 37007, Spain
- Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid 47012, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Ana P Tedim
- Group for Biomedical Research in Sepsis, Instituto de Investigación Biomédica de Salamanca, Gerencia Regional de Salud, Salamanca 37007, Spain
- Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid 47012, Spain
| | - Amanda de la Fuente
- Group for Biomedical Research in Sepsis, Instituto de Investigación Biomédica de Salamanca, Gerencia Regional de Salud, Salamanca 37007, Spain
- Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid 47012, Spain
| | - Jose María Eiros
- Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid 47012, Spain
| | - Antoni Torres
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid 28029, Spain
- Department of Pulmonology, Institut D investigacions August Pi I Sunyer, Hospital Clinic de Barcelona, Universidad de Barcelona, Barcelona, Spain
| | - David J Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Canadian Center for Vaccinology, Dalhousie University, Halifax, NS, Canada
- Laboratory of Immunity, Shantou University Medical College, Guangdong, China
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Weidong L, Sanna L, Bordoni V, Tiansheng Z, Chengxun L, Murineddu G, Pinna GA, Kelvin DJ, Bagella L. Target identification of a novel unsymmetrical 1,3,4-oxadiazole derivative with antiproliferative properties. J Cell Physiol 2021; 236:3789-3799. [PMID: 33089499 DOI: 10.1002/jcp.30120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/22/2020] [Accepted: 10/10/2020] [Indexed: 02/05/2023]
Abstract
1,3,4-Oxadiazole derivatives are widely used in research on antineoplastic drugs. Recently, we discovered a novel unsymmetrical 1,3,4-oxadiazole compound with antiproliferative properties called 2j. To further investigate its possible targets and molecular mechanisms, RNA-seq was performed and the differentially expressed genes (DEGs) were obtained after treatment. Data were analyzed using functional (Gene Ontology term) and pathway (Kyoto Encyclopedia of Genes and Genomes) enrichment of the DEGs. The hub genes were determined by the analysis of protein-protein interaction networks. The connectivity map (CMap) information provided insight into the model action of antitumor small molecule drugs. Hub genes have been identified through function gene networks using STRING analysis. The small molecular targets obtained by CMap comparison showed that 2j is a tubulin inhibitor and it acts mainly affecting tumor cells through the cell cycle, FoxO signaling pathway, apoptotic, and p53 signaling pathways. The possible targets of 2j could be TUBA1A and TUBA4A. Molecular docking results indicated that 2j interacts at the colchicine-binding site on tubulin.
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Affiliation(s)
- Lyu Weidong
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Laboratory of Immunity, Shantou University Medical College, Shantou, Guangdong, China
| | - Luca Sanna
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Valentina Bordoni
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Zeng Tiansheng
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Laboratory of Immunity, Shantou University Medical College, Shantou, Guangdong, China
| | - Li Chengxun
- Laboratory of Immunity, Shantou University Medical College, Shantou, Guangdong, China
| | - Gabriele Murineddu
- Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy
| | - Gerard A Pinna
- Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy
| | - David J Kelvin
- Laboratory of Immunity, Shantou University Medical College, Shantou, Guangdong, China
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Luigi Bagella
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, Pennsylvania, USA
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29
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Zeng T, Fedeli MA, Tanda F, Wang Y, Yang D, Xue B, Jia L, Palmieri G, Sechi LA, Kelvin DJ. Whole-exome Sequencing of Prostate Cancer in Sardinian Identify Recurrent UDP-glucuronosyltransferase Amplifications. J Cancer 2021; 12:438-450. [PMID: 33391440 PMCID: PMC7738997 DOI: 10.7150/jca.48433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 05/20/2020] [Accepted: 10/25/2020] [Indexed: 02/05/2023] Open
Abstract
Globally, prostate cancer is the third most common cancer in the world, and the second most common cancer in men. However, rates for incidence and mortality vary considerably with race, ethnicity, and geography. Over 97 significantly mutated genes that have been identified in prostate cancer; however, a lack of genomic prostate cancer studies focusing on different racial and ethnic groups and racial mixing pose a serious challenge to universalize these findings. The Sardinian population is an isolated Mediterranean population that has a high frequency of centenarians and a much lower incidence of prostate cancer than found in males in mainland Europe. Here, we conducted a genomic prostate cancer study on a Sardinian cohort diagnosed with local prostate cancer. Our data reveals a low rate of ERG fusion in Sardinian prostate cancer. Interestingly, we identified a novel BTBD7-SLC2A5 fusion that occurred in 13% of the patients. We also found that the UGT2B4 on 4q13.2 was amplified in 20% of the Sardinian patients but rarely amplified in patients of other population. These observations underscore the importance of the inter-population molecular heterogeneity of prostate cancer. In addition, we examined the expression of UGT2B4 in 497 prostate cancer patients derived from The Cancer Genome Atlas database. We found that high expression of UGT2B4 was associated with low-grade prostate cancer and upregulation of UGT2B4 in tumors was associated with upregulation of metabolism pathways such as 'de novo' IMP biosynthetic process, glutamine and monocarboxylic acid metabolism. These data provide insight into clinical relevance and functional mechanism of UGT2B4. Further understanding functional mechanism of UGT2B4 amplification and BTBD7-SLC2A5 fusion will aid in developing drugs to benefit the prostate cancer patients.
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Affiliation(s)
- Tiansheng Zeng
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, Shantou Guangdong, China
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Maria Antonietta Fedeli
- Department of Scienze Mediche Chirurgiche e Sperimentali, first affiliated Hospital of 33445Sassari University
| | - Francesco Tanda
- Department of Scienze Mediche Chirurgiche e Sperimentali, first affiliated Hospital of 33445Sassari University
| | - Yuyong Wang
- Department of Urology, affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, China
| | - Dongsheng Yang
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, Shantou Guangdong, China
| | - Bei Xue
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, Shantou Guangdong, China
| | - Lisha Jia
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, Shantou Guangdong, China
| | - Giuseppe Palmieri
- Institute of Genetic and Biomedical Research (IRGB), Head, National Research Council (CNR), 07100 Sassari, Italy
| | - Leonardo A Sechi
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- ✉ Corresponding authors: J. Kelvin, E-mail: ; and Leonardo A. Sechi, E-mail: . Co-corresponding authors equally contributed to this work
| | - David J. Kelvin
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, Shantou Guangdong, China
- Department of Scienze Mediche Chirurgiche e Sperimentali, first affiliated Hospital of 33445Sassari University
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
- Canadian Center for Vaccinology, IWK, Halifax, Nova Scotia, Canada
- ✉ Corresponding authors: J. Kelvin, E-mail: ; and Leonardo A. Sechi, E-mail: . Co-corresponding authors equally contributed to this work
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30
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Bermejo-Martin JF, González-Rivera M, Almansa R, Micheloud D, Tedim AP, Domínguez-Gil M, Resino S, Martín-Fernández M, Ryan Murua P, Pérez-García F, Tamayo L, Lopez-Izquierdo R, Bustamante E, Aldecoa C, Gómez JM, Rico-Feijoo J, Orduña A, Méndez R, Fernández Natal I, Megías G, González-Estecha M, Carriedo D, Doncel C, Jorge N, Ortega A, de la Fuente A, Del Campo F, Fernández-Ratero JA, Trapiello W, González-Jiménez P, Ruiz G, Kelvin AA, Ostadgavahi AT, Oneizat R, Ruiz LM, Miguéns I, Gargallo E, Muñoz I, Pelegrin S, Martín S, García Olivares P, Cedeño JA, Ruiz Albi T, Puertas C, Berezo JÁ, Renedo G, Herrán R, Bustamante-Munguira J, Enríquez P, Cicuendez R, Blanco J, Abadia J, Gómez Barquero J, Mamolar N, Blanca-López N, Valdivia LJ, Fernández Caso B, Mantecón MÁ, Motos A, Fernandez-Barat L, Ferrer R, Barbé F, Torres A, Menéndez R, Eiros JM, Kelvin DJ. Viral RNA load in plasma is associated with critical illness and a dysregulated host response in COVID-19. Crit Care 2020; 24:691. [PMID: 33317616 PMCID: PMC7734467 DOI: 10.1186/s13054-020-03398-0] [Citation(s) in RCA: 157] [Impact Index Per Article: 39.3] [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: 09/03/2020] [Accepted: 11/18/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND COVID-19 can course with respiratory and extrapulmonary disease. SARS-CoV-2 RNA is detected in respiratory samples but also in blood, stool and urine. Severe COVID-19 is characterized by a dysregulated host response to this virus. We studied whether viral RNAemia or viral RNA load in plasma is associated with severe COVID-19 and also to this dysregulated response. METHODS A total of 250 patients with COVID-19 were recruited (50 outpatients, 100 hospitalized ward patients and 100 critically ill). Viral RNA detection and quantification in plasma was performed using droplet digital PCR, targeting the N1 and N2 regions of the SARS-CoV-2 nucleoprotein gene. The association between SARS-CoV-2 RNAemia and viral RNA load in plasma with severity was evaluated by multivariate logistic regression. Correlations between viral RNA load and biomarkers evidencing dysregulation of host response were evaluated by calculating the Spearman correlation coefficients. RESULTS The frequency of viral RNAemia was higher in the critically ill patients (78%) compared to ward patients (27%) and outpatients (2%) (p < 0.001). Critical patients had higher viral RNA loads in plasma than non-critically ill patients, with non-survivors showing the highest values. When outpatients and ward patients were compared, viral RNAemia did not show significant associations in the multivariate analysis. In contrast, when ward patients were compared with ICU patients, both viral RNAemia and viral RNA load in plasma were associated with critical illness (OR [CI 95%], p): RNAemia (3.92 [1.183-12.968], 0.025), viral RNA load (N1) (1.962 [1.244-3.096], 0.004); viral RNA load (N2) (2.229 [1.382-3.595], 0.001). Viral RNA load in plasma correlated with higher levels of chemokines (CXCL10, CCL2), biomarkers indicative of a systemic inflammatory response (IL-6, CRP, ferritin), activation of NK cells (IL-15), endothelial dysfunction (VCAM-1, angiopoietin-2, ICAM-1), coagulation activation (D-Dimer and INR), tissue damage (LDH, GPT), neutrophil response (neutrophils counts, myeloperoxidase, GM-CSF) and immunodepression (PD-L1, IL-10, lymphopenia and monocytopenia). CONCLUSIONS SARS-CoV-2 RNAemia and viral RNA load in plasma are associated with critical illness in COVID-19. Viral RNA load in plasma correlates with key signatures of dysregulated host responses, suggesting a major role of uncontrolled viral replication in the pathogenesis of this disease.
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Affiliation(s)
- Jesús F Bermejo-Martin
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Milagros González-Rivera
- Department of Laboratory Medicine, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
- Department of Medicine, Faculty of Medicine, Universidad Complutense de Madrid, Plaza de Ramón y Cajal, s/n, 28040, Madrid, Spain
| | - Raquel Almansa
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Dariela Micheloud
- Emergency Department, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Ana P Tedim
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Marta Domínguez-Gil
- Microbiology Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Salvador Resino
- Viral Infection and Immunity Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. de Pozuelo, 28, 28222, Majadahonda, Spain
| | - Marta Martín-Fernández
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Pablo Ryan Murua
- Hospital Universitario Infanta Leonor, Av. Gran Vía del Este, 80, 28031, Madrid, Spain
| | - Felipe Pérez-García
- Servicio de Microbiología Clínica, Hospital Universitario Príncipe de Asturias, Carr. de Alcalá, s/n, 28805, Madrid, Spain
| | - Luis Tamayo
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Intensive Care Unit, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Raúl Lopez-Izquierdo
- Emergency Department, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Elena Bustamante
- Intensive Care Unit, Hospital Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - César Aldecoa
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Department of Anesthesiology, Facultad de Medicina de Valladolid, Av. Ramón y Cajal, 47005, Valladolid, Spain
- Anesthesiology and Reanimation Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - José Manuel Gómez
- Intensive Care Unit, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Jesús Rico-Feijoo
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Anesthesiology and Reanimation Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Antonio Orduña
- Microbiology Service, Hospital Clinico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Raúl Méndez
- Pulmonology Service, Hospital Universitario y Politécnico de La Fe, Avinguda de Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Isabel Fernández Natal
- Clinical Microbiology Department, Complejo Asistencial Universitario de León, Calle Altos de Nava, s/n, 24001, León, Spain
| | - Gregoria Megías
- Microbiology Service, Hospital Universitario de Burgos, Av. Islas Baleares, 3, 09006, Burgos, Spain
| | - Montserrat González-Estecha
- Department of Laboratory Medicine, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
- Department of Medicine, Faculty of Medicine, Universidad Complutense de Madrid, Plaza de Ramón y Cajal, s/n, 28040, Madrid, Spain
| | - Demetrio Carriedo
- Intensive Care Unit, Complejo Asistencial Universitario de León, Calle Altos de nava, s/n, 24001, León, Spain
| | - Cristina Doncel
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Noelia Jorge
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Alicia Ortega
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Amanda de la Fuente
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Félix Del Campo
- Pneumology Service, Hospital Universitario Río Hortega/Biomedical Engineering Group, Universidad de Valladolid, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | | | - Wysali Trapiello
- Clinical Analysis Service. Hospital, Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Paula González-Jiménez
- Pulmonology Service, Hospital Universitario y Politécnico de La Fe, Avinguda de Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Guadalupe Ruiz
- Clinical Analysis Service. Hospital, Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Alyson A Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Canadian Center for Vaccinology CCfV, Dalhousie University, Halifax, NS, B3H 4R2, Canada
- Laboratory of Immunity, Shantou University Medical College, 22 Xinling Rd., Jinping, Shantou, Guangdong, China
| | - Ali Toloue Ostadgavahi
- Department of Microbiology and Immunology, Faculty of Medicine, Canadian Center for Vaccinology CCfV, Dalhousie University, Halifax, NS, B3H 4R2, Canada
- Laboratory of Immunity, Shantou University Medical College, 22 Xinling Rd., Jinping, Shantou, Guangdong, China
| | - Ruth Oneizat
- Microbiology Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Luz María Ruiz
- Microbiology Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Iria Miguéns
- Emergency Department, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Esther Gargallo
- Emergency Department, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Ioana Muñoz
- Emergency Department, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Sara Pelegrin
- Anesthesiology and Reanimation Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Silvia Martín
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Anesthesiology and Reanimation Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Pablo García Olivares
- Intensive Care Unit, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Jamil Antonio Cedeño
- Intensive Care Unit, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Tomás Ruiz Albi
- Pneumology Service, Hospital Universitario Río Hortega/Biomedical Engineering Group, Universidad de Valladolid, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Carolina Puertas
- Department of Laboratory Medicine, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Jose Ángel Berezo
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Intensive Care Unit, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Gloria Renedo
- Intensive Care Unit, Hospital Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Rubén Herrán
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Intensive Care Unit, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Juan Bustamante-Munguira
- Department of Cardiovascular Surgery, Hospital Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Pedro Enríquez
- Intensive Care Unit, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Ramón Cicuendez
- Intensive Care Unit, Hospital Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Jesús Blanco
- Intensive Care Unit, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Jesica Abadia
- Infectious Diseases Clinic, Internal Medicine Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Julia Gómez Barquero
- Infectious Diseases Clinic, Internal Medicine Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Nuria Mamolar
- Intensive Care Unit, Hospital Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Natalia Blanca-López
- Hospital Universitario Infanta Leonor, Av. Gran Vía del Este, 80, 28031, Madrid, Spain
| | - Luis Jorge Valdivia
- Intensive Care Unit, Complejo Asistencial Universitario de León, Calle Altos de nava, s/n, 24001, León, Spain
| | - Belén Fernández Caso
- Clinical Microbiology Department, Complejo Asistencial Universitario de León, Calle Altos de Nava, s/n, 24001, León, Spain
| | - María Ángeles Mantecón
- Microbiology Service, Hospital Universitario de Burgos, Av. Islas Baleares, 3, 09006, Burgos, Spain
| | - Anna Motos
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
- Department of Pulmonology, Hospital Clinic de Barcelona, Institut D Investigacions August Pi I Sunyer (IDIBAPS), Universidad de Barcelona, Carrer del Rosselló, 149, 08036, Barcelona, Spain
| | - Laia Fernandez-Barat
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
- Department of Pulmonology, Hospital Clinic de Barcelona, Institut D Investigacions August Pi I Sunyer (IDIBAPS), Universidad de Barcelona, Carrer del Rosselló, 149, 08036, Barcelona, Spain
| | - Ricard Ferrer
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
- Intensive Care Department, Vall d'Hebron Hospital Universitari, SODIR Research Group, Vall d'Hebron Institut de Recerca, Passeig de la Vall d'Hebron, 119, 08035, Barcelona, Spain
| | - Ferrán Barbé
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
- Respiratory Department, Institut Ricerca Biomedica de Lleida, Av. Alcalde Rovira Roure, 80, 25198, Lleida, Spain
| | - Antoni Torres
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
- Department of Pulmonology, Hospital Clinic de Barcelona, Institut D Investigacions August Pi I Sunyer (IDIBAPS), Universidad de Barcelona, Carrer del Rosselló, 149, 08036, Barcelona, Spain
| | - Rosario Menéndez
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
- Pulmonology Service, Hospital Universitario y Politécnico de La Fe, Avinguda de Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - José María Eiros
- Microbiology Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - David J Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Canadian Center for Vaccinology CCfV, Dalhousie University, Halifax, NS, B3H 4R2, Canada.
- Laboratory of Immunity, Shantou University Medical College, 22 Xinling Rd., Jinping, Shantou, Guangdong, China.
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Bermejo-Martin JF, González-Rivera M, Almansa R, Micheloud D, Tedim AP, Domínguez-Gil M, Resino S, Martín-Fernández M, Ryan Murua P, Pérez-García F, Tamayo L, Lopez-Izquierdo R, Bustamante E, Aldecoa C, Gómez JM, Rico-Feijoo J, Orduña A, Méndez R, Fernández Natal I, Megías G, González-Estecha M, Carriedo D, Doncel C, Jorge N, Ortega A, de la Fuente A, Del Campo F, Fernández-Ratero JA, Trapiello W, González-Jiménez P, Ruiz G, Kelvin AA, Ostadgavahi AT, Oneizat R, Ruiz LM, Miguéns I, Gargallo E, Muñoz I, Pelegrin S, Martín S, García Olivares P, Cedeño JA, Ruiz Albi T, Puertas C, Berezo JÁ, Renedo G, Herrán R, Bustamante-Munguira J, Enríquez P, Cicuendez R, Blanco J, Abadia J, Gómez Barquero J, Mamolar N, Blanca-López N, Valdivia LJ, Fernández Caso B, Mantecón MÁ, Motos A, Fernandez-Barat L, Ferrer R, Barbé F, Torres A, Menéndez R, Eiros JM, Kelvin DJ. Viral RNA load in plasma is associated with critical illness and a dysregulated host response in COVID-19. Crit Care 2020; 24:691. [PMID: 33317616 DOI: 10.1186/s13054‐020‐03398‐0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/18/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND COVID-19 can course with respiratory and extrapulmonary disease. SARS-CoV-2 RNA is detected in respiratory samples but also in blood, stool and urine. Severe COVID-19 is characterized by a dysregulated host response to this virus. We studied whether viral RNAemia or viral RNA load in plasma is associated with severe COVID-19 and also to this dysregulated response. METHODS A total of 250 patients with COVID-19 were recruited (50 outpatients, 100 hospitalized ward patients and 100 critically ill). Viral RNA detection and quantification in plasma was performed using droplet digital PCR, targeting the N1 and N2 regions of the SARS-CoV-2 nucleoprotein gene. The association between SARS-CoV-2 RNAemia and viral RNA load in plasma with severity was evaluated by multivariate logistic regression. Correlations between viral RNA load and biomarkers evidencing dysregulation of host response were evaluated by calculating the Spearman correlation coefficients. RESULTS The frequency of viral RNAemia was higher in the critically ill patients (78%) compared to ward patients (27%) and outpatients (2%) (p < 0.001). Critical patients had higher viral RNA loads in plasma than non-critically ill patients, with non-survivors showing the highest values. When outpatients and ward patients were compared, viral RNAemia did not show significant associations in the multivariate analysis. In contrast, when ward patients were compared with ICU patients, both viral RNAemia and viral RNA load in plasma were associated with critical illness (OR [CI 95%], p): RNAemia (3.92 [1.183-12.968], 0.025), viral RNA load (N1) (1.962 [1.244-3.096], 0.004); viral RNA load (N2) (2.229 [1.382-3.595], 0.001). Viral RNA load in plasma correlated with higher levels of chemokines (CXCL10, CCL2), biomarkers indicative of a systemic inflammatory response (IL-6, CRP, ferritin), activation of NK cells (IL-15), endothelial dysfunction (VCAM-1, angiopoietin-2, ICAM-1), coagulation activation (D-Dimer and INR), tissue damage (LDH, GPT), neutrophil response (neutrophils counts, myeloperoxidase, GM-CSF) and immunodepression (PD-L1, IL-10, lymphopenia and monocytopenia). CONCLUSIONS SARS-CoV-2 RNAemia and viral RNA load in plasma are associated with critical illness in COVID-19. Viral RNA load in plasma correlates with key signatures of dysregulated host responses, suggesting a major role of uncontrolled viral replication in the pathogenesis of this disease.
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Affiliation(s)
- Jesús F Bermejo-Martin
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Milagros González-Rivera
- Department of Laboratory Medicine, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
- Department of Medicine, Faculty of Medicine, Universidad Complutense de Madrid, Plaza de Ramón y Cajal, s/n, 28040, Madrid, Spain
| | - Raquel Almansa
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Dariela Micheloud
- Emergency Department, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Ana P Tedim
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Marta Domínguez-Gil
- Microbiology Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Salvador Resino
- Viral Infection and Immunity Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. de Pozuelo, 28, 28222, Majadahonda, Spain
| | - Marta Martín-Fernández
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Pablo Ryan Murua
- Hospital Universitario Infanta Leonor, Av. Gran Vía del Este, 80, 28031, Madrid, Spain
| | - Felipe Pérez-García
- Servicio de Microbiología Clínica, Hospital Universitario Príncipe de Asturias, Carr. de Alcalá, s/n, 28805, Madrid, Spain
| | - Luis Tamayo
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Intensive Care Unit, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Raúl Lopez-Izquierdo
- Emergency Department, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Elena Bustamante
- Intensive Care Unit, Hospital Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - César Aldecoa
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Department of Anesthesiology, Facultad de Medicina de Valladolid, Av. Ramón y Cajal, 47005, Valladolid, Spain
- Anesthesiology and Reanimation Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - José Manuel Gómez
- Intensive Care Unit, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Jesús Rico-Feijoo
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Anesthesiology and Reanimation Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Antonio Orduña
- Microbiology Service, Hospital Clinico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Raúl Méndez
- Pulmonology Service, Hospital Universitario y Politécnico de La Fe, Avinguda de Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Isabel Fernández Natal
- Clinical Microbiology Department, Complejo Asistencial Universitario de León, Calle Altos de Nava, s/n, 24001, León, Spain
| | - Gregoria Megías
- Microbiology Service, Hospital Universitario de Burgos, Av. Islas Baleares, 3, 09006, Burgos, Spain
| | - Montserrat González-Estecha
- Department of Laboratory Medicine, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
- Department of Medicine, Faculty of Medicine, Universidad Complutense de Madrid, Plaza de Ramón y Cajal, s/n, 28040, Madrid, Spain
| | - Demetrio Carriedo
- Intensive Care Unit, Complejo Asistencial Universitario de León, Calle Altos de nava, s/n, 24001, León, Spain
| | - Cristina Doncel
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Noelia Jorge
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Alicia Ortega
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Amanda de la Fuente
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Félix Del Campo
- Pneumology Service, Hospital Universitario Río Hortega/Biomedical Engineering Group, Universidad de Valladolid, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | | | - Wysali Trapiello
- Clinical Analysis Service. Hospital, Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Paula González-Jiménez
- Pulmonology Service, Hospital Universitario y Politécnico de La Fe, Avinguda de Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Guadalupe Ruiz
- Clinical Analysis Service. Hospital, Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Alyson A Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Canadian Center for Vaccinology CCfV, Dalhousie University, Halifax, NS, B3H 4R2, Canada
- Laboratory of Immunity, Shantou University Medical College, 22 Xinling Rd., Jinping, Shantou, Guangdong, China
| | - Ali Toloue Ostadgavahi
- Department of Microbiology and Immunology, Faculty of Medicine, Canadian Center for Vaccinology CCfV, Dalhousie University, Halifax, NS, B3H 4R2, Canada
- Laboratory of Immunity, Shantou University Medical College, 22 Xinling Rd., Jinping, Shantou, Guangdong, China
| | - Ruth Oneizat
- Microbiology Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Luz María Ruiz
- Microbiology Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Iria Miguéns
- Emergency Department, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Esther Gargallo
- Emergency Department, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Ioana Muñoz
- Emergency Department, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Sara Pelegrin
- Anesthesiology and Reanimation Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Silvia Martín
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Anesthesiology and Reanimation Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Pablo García Olivares
- Intensive Care Unit, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Jamil Antonio Cedeño
- Intensive Care Unit, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Tomás Ruiz Albi
- Pneumology Service, Hospital Universitario Río Hortega/Biomedical Engineering Group, Universidad de Valladolid, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Carolina Puertas
- Department of Laboratory Medicine, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Jose Ángel Berezo
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Intensive Care Unit, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Gloria Renedo
- Intensive Care Unit, Hospital Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Rubén Herrán
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Intensive Care Unit, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Juan Bustamante-Munguira
- Department of Cardiovascular Surgery, Hospital Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Pedro Enríquez
- Intensive Care Unit, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Ramón Cicuendez
- Intensive Care Unit, Hospital Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Jesús Blanco
- Intensive Care Unit, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Jesica Abadia
- Infectious Diseases Clinic, Internal Medicine Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Julia Gómez Barquero
- Infectious Diseases Clinic, Internal Medicine Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Nuria Mamolar
- Intensive Care Unit, Hospital Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Natalia Blanca-López
- Hospital Universitario Infanta Leonor, Av. Gran Vía del Este, 80, 28031, Madrid, Spain
| | - Luis Jorge Valdivia
- Intensive Care Unit, Complejo Asistencial Universitario de León, Calle Altos de nava, s/n, 24001, León, Spain
| | - Belén Fernández Caso
- Clinical Microbiology Department, Complejo Asistencial Universitario de León, Calle Altos de Nava, s/n, 24001, León, Spain
| | - María Ángeles Mantecón
- Microbiology Service, Hospital Universitario de Burgos, Av. Islas Baleares, 3, 09006, Burgos, Spain
| | - Anna Motos
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
- Department of Pulmonology, Hospital Clinic de Barcelona, Institut D Investigacions August Pi I Sunyer (IDIBAPS), Universidad de Barcelona, Carrer del Rosselló, 149, 08036, Barcelona, Spain
| | - Laia Fernandez-Barat
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
- Department of Pulmonology, Hospital Clinic de Barcelona, Institut D Investigacions August Pi I Sunyer (IDIBAPS), Universidad de Barcelona, Carrer del Rosselló, 149, 08036, Barcelona, Spain
| | - Ricard Ferrer
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
- Intensive Care Department, Vall d'Hebron Hospital Universitari, SODIR Research Group, Vall d'Hebron Institut de Recerca, Passeig de la Vall d'Hebron, 119, 08035, Barcelona, Spain
| | - Ferrán Barbé
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
- Respiratory Department, Institut Ricerca Biomedica de Lleida, Av. Alcalde Rovira Roure, 80, 25198, Lleida, Spain
| | - Antoni Torres
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
- Department of Pulmonology, Hospital Clinic de Barcelona, Institut D Investigacions August Pi I Sunyer (IDIBAPS), Universidad de Barcelona, Carrer del Rosselló, 149, 08036, Barcelona, Spain
| | - Rosario Menéndez
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
- Pulmonology Service, Hospital Universitario y Politécnico de La Fe, Avinguda de Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - José María Eiros
- Microbiology Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - David J Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Canadian Center for Vaccinology CCfV, Dalhousie University, Halifax, NS, B3H 4R2, Canada.
- Laboratory of Immunity, Shantou University Medical College, 22 Xinling Rd., Jinping, Shantou, Guangdong, China.
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Bermejo-Martin JF, Almansa R, Torres A, González-Rivera M, Kelvin DJ. COVID-19 as a cardiovascular disease: the potential role of chronic endothelial dysfunction. Cardiovasc Res 2020; 116:e132-e133. [PMID: 32420587 PMCID: PMC7314234 DOI: 10.1093/cvr/cvaa140] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Jesús F Bermejo-Martin
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca (IBSAL), Paseo de San Vicente, 58-182, 37007 Salamanca, Spain
- Hospital Universitario Río Hortega de Valladolid. Calle Dulzaina, 2, 47012 Valladolid, Spain
- Centro de Investigación Biomedica En Red-Enfermedades Respiratorias, Instituto de Salud Carlos III, Av. de Monforte de Lemos, 5, 28029, Madrid, Spain
- Corresponding author: Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca (IBSAL), Paseo de San Vicente, 58-182, 37007 Salamanca, Spain. Tel: +34 648 56 34 36,
| | - Raquel Almansa
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca (IBSAL), Paseo de San Vicente, 58-182, 37007 Salamanca, Spain
- Hospital Universitario Río Hortega de Valladolid. Calle Dulzaina, 2, 47012 Valladolid, Spain
- Centro de Investigación Biomedica En Red-Enfermedades Respiratorias, Instituto de Salud Carlos III, Av. de Monforte de Lemos, 5, 28029, Madrid, Spain
| | - Antoni Torres
- Centro de Investigación Biomedica En Red-Enfermedades Respiratorias, Instituto de Salud Carlos III, Av. de Monforte de Lemos, 5, 28029, Madrid, Spain
- Department of Pneumology, Institut Clinic del Tórax, Hospital Clinic of Barcelona – Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB) – SGR 911 – Carrer de Villarroel, 170, 08036 Barcelona, Spain
| | - Milagros González-Rivera
- Biochemistry Service. Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007 Madrid, Spain
| | - David J Kelvin
- Department of Microbiology and Immunology, Canadian Centre for Vaccinology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
- Laboratory of Immunity Shantou University Medical College, 22 Xinling Rd, Jinping, Shantou, Guangdong, China
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Chessa D, Murgia M, Sias E, Deligios M, Mazzarello V, Fiamma M, Rovina D, Carenti G, Ganau G, Pintore E, Fiori M, Kay GL, Ponzeletti A, Cappuccinelli P, Kelvin DJ, Wain J, Rubino S. Metagenomics and microscope revealed T. trichiura and other intestinal parasites in a cesspit of an Italian nineteenth century aristocratic palace. Sci Rep 2020; 10:12656. [PMID: 32728085 PMCID: PMC7391740 DOI: 10.1038/s41598-020-69497-8] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 07/08/2020] [Indexed: 11/09/2022] Open
Abstract
This study evidenced the presence of parasites in a cesspit of an aristocratic palace of nineteenth century in Sardinia (Italy) by the use of classical paleoparasitological techniques coupled with next-generation sequencing. Parasite eggs identified by microscopy included helminth genera pathogenic for humans and animals: the whipworm Trichuris sp., the roundworm Ascaris sp., the flatworm Dicrocoelium sp. and the fish tapeworm Diphyllobothrium sp. In addition, 18S rRNA metabarcoding and metagenomic sequencing analysis allowed the first description in Sardinia of aDNA of the human specific T. trichiura species and Ascaris genus. Their presence is important for understanding the health conditions, hygiene habits, agricultural practices and the diet of the local inhabitants in the period under study.
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Affiliation(s)
- Daniela Chessa
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - Manuela Murgia
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy.
| | - Emanuela Sias
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - Massimo Deligios
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - Vittorio Mazzarello
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - Maura Fiamma
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - Daniela Rovina
- Superintendence Archaeology of Sardinia, 07100, Sassari, Italy
| | - Gabriele Carenti
- Department of Nature and Environmental Sciences, University of Sassari, 07100, Sassari, Italy
| | - Giulia Ganau
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - Elisabetta Pintore
- Department of Veterinary Medicine, University of Sassari, 07100, Sassari, Italy
| | | | - Gemma L Kay
- Bob Champion Research and Educational Building, University of East Anglia, Norwich Research Park, Norwich, UK
- The Quadram Institute, Norwich Research Park, Norwich, UK
| | | | - Piero Cappuccinelli
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - David J Kelvin
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - John Wain
- Bob Champion Research and Educational Building, University of East Anglia, Norwich Research Park, Norwich, UK
- The Quadram Institute, Norwich Research Park, Norwich, UK
| | - Salvatore Rubino
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
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Hou YJ, Okuda K, Edwards CE, Martinez DR, Asakura T, Dinnon KH, Kato T, Lee RE, Yount BL, Mascenik TM, Chen G, Olivier KN, Ghio A, Tse LV, Leist SR, Gralinski LE, Schäfer A, Dang H, Gilmore R, Nakano S, Sun L, Fulcher ML, Livraghi-Butrico A, Nicely NI, Cameron M, Cameron C, Kelvin DJ, de Silva A, Margolis DM, Markmann A, Bartelt L, Zumwalt R, Martinez FJ, Salvatore SP, Borczuk A, Tata PR, Sontake V, Kimple A, Jaspers I, O'Neal WK, Randell SH, Boucher RC, Baric RS. SARS-CoV-2 Reverse Genetics Reveals a Variable Infection Gradient in the Respiratory Tract. Cell 2020; 182:429-446.e14. [PMID: 32526206 DOI: 10.1016/j.cell.2020.05] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/11/2020] [Accepted: 05/20/2020] [Indexed: 05/26/2023]
Abstract
The mode of acquisition and causes for the variable clinical spectrum of coronavirus disease 2019 (COVID-19) remain unknown. We utilized a reverse genetics system to generate a GFP reporter virus to explore severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogenesis and a luciferase reporter virus to demonstrate sera collected from SARS and COVID-19 patients exhibited limited cross-CoV neutralization. High-sensitivity RNA in situ mapping revealed the highest angiotensin-converting enzyme 2 (ACE2) expression in the nose with decreasing expression throughout the lower respiratory tract, paralleled by a striking gradient of SARS-CoV-2 infection in proximal (high) versus distal (low) pulmonary epithelial cultures. COVID-19 autopsied lung studies identified focal disease and, congruent with culture data, SARS-CoV-2-infected ciliated and type 2 pneumocyte cells in airway and alveolar regions, respectively. These findings highlight the nasal susceptibility to SARS-CoV-2 with likely subsequent aspiration-mediated virus seeding to the lung in SARS-CoV-2 pathogenesis. These reagents provide a foundation for investigations into virus-host interactions in protective immunity, host susceptibility, and virus pathogenesis.
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Affiliation(s)
- Yixuan J Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenichi Okuda
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Caitlin E Edwards
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David R Martinez
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Takanori Asakura
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth H Dinnon
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Takafumi Kato
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rhianna E Lee
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Boyd L Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Teresa M Mascenik
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gang Chen
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth N Olivier
- Laboratory of Chronic Airway Infection, Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrew Ghio
- National Health and Environmental Effects Research Laboratory, Environmental Protection Agency, Chapel Hill, NC, USA
| | - Longping V Tse
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lisa E Gralinski
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hong Dang
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rodney Gilmore
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Satoko Nakano
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ling Sun
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - M Leslie Fulcher
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Nathan I Nicely
- Protein Expression and Purification Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mark Cameron
- Department of Population and Quantitative Health Science, Case Western Reserve University, Cleveland, OH, USA
| | - Cheryl Cameron
- Department of Nutrition, Case Western Reserve University, Cleveland, OH, USA
| | - David J Kelvin
- Department of Microbiology and Immunology, Canadian Center for Vaccinology, Dalhousie University, Halifax, NS, Canada; Laboratory of Immunology, Shantou University Medical College, Shantou, Guangdong, China
| | - Aravinda de Silva
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David M Margolis
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alena Markmann
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Luther Bartelt
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ross Zumwalt
- Department of Pathology, University of New Mexico, Albuquerque, NM, USA
| | - Fernando J Martinez
- Division of Pulmonary and Critical Care Medicine, Joan & Sanford I. Weill Medical College of Cornell University, New York, NY, USA
| | - Steven P Salvatore
- Department of Pathology, Joan & Sanford I. Weill Medical College of Cornell University, New York, NY, USA
| | - Alain Borczuk
- Department of Pathology, Joan & Sanford I. Weill Medical College of Cornell University, New York, NY, USA
| | - Purushothama R Tata
- Department of Cell Biology, Regeneration Next Initiative, Duke University Medical Center, Durham, NC, USA
| | - Vishwaraj Sontake
- Department of Cell Biology, Regeneration Next Initiative, Duke University Medical Center, Durham, NC, USA
| | - Adam Kimple
- Department of Otolaryngology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ilona Jaspers
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wanda K O'Neal
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott H Randell
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Richard C Boucher
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Hou YJ, Okuda K, Edwards CE, Martinez DR, Asakura T, Dinnon KH, Kato T, Lee RE, Yount BL, Mascenik TM, Chen G, Olivier KN, Ghio A, Tse LV, Leist SR, Gralinski LE, Schäfer A, Dang H, Gilmore R, Nakano S, Sun L, Fulcher ML, Livraghi-Butrico A, Nicely NI, Cameron M, Cameron C, Kelvin DJ, de Silva A, Margolis DM, Markmann A, Bartelt L, Zumwalt R, Martinez FJ, Salvatore SP, Borczuk A, Tata PR, Sontake V, Kimple A, Jaspers I, O'Neal WK, Randell SH, Boucher RC, Baric RS. SARS-CoV-2 Reverse Genetics Reveals a Variable Infection Gradient in the Respiratory Tract. Cell 2020; 182:429-446.e14. [PMID: 32526206 PMCID: PMC7250779 DOI: 10.1016/j.cell.2020.05.042] [Citation(s) in RCA: 1039] [Impact Index Per Article: 259.8] [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: 04/24/2020] [Revised: 05/11/2020] [Accepted: 05/20/2020] [Indexed: 02/06/2023]
Abstract
The mode of acquisition and causes for the variable clinical spectrum of coronavirus disease 2019 (COVID-19) remain unknown. We utilized a reverse genetics system to generate a GFP reporter virus to explore severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogenesis and a luciferase reporter virus to demonstrate sera collected from SARS and COVID-19 patients exhibited limited cross-CoV neutralization. High-sensitivity RNA in situ mapping revealed the highest angiotensin-converting enzyme 2 (ACE2) expression in the nose with decreasing expression throughout the lower respiratory tract, paralleled by a striking gradient of SARS-CoV-2 infection in proximal (high) versus distal (low) pulmonary epithelial cultures. COVID-19 autopsied lung studies identified focal disease and, congruent with culture data, SARS-CoV-2-infected ciliated and type 2 pneumocyte cells in airway and alveolar regions, respectively. These findings highlight the nasal susceptibility to SARS-CoV-2 with likely subsequent aspiration-mediated virus seeding to the lung in SARS-CoV-2 pathogenesis. These reagents provide a foundation for investigations into virus-host interactions in protective immunity, host susceptibility, and virus pathogenesis.
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Affiliation(s)
- Yixuan J Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenichi Okuda
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Caitlin E Edwards
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David R Martinez
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Takanori Asakura
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth H Dinnon
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Takafumi Kato
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rhianna E Lee
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Boyd L Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Teresa M Mascenik
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gang Chen
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth N Olivier
- Laboratory of Chronic Airway Infection, Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrew Ghio
- National Health and Environmental Effects Research Laboratory, Environmental Protection Agency, Chapel Hill, NC, USA
| | - Longping V Tse
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lisa E Gralinski
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hong Dang
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rodney Gilmore
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Satoko Nakano
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ling Sun
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - M Leslie Fulcher
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Nathan I Nicely
- Protein Expression and Purification Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mark Cameron
- Department of Population and Quantitative Health Science, Case Western Reserve University, Cleveland, OH, USA
| | - Cheryl Cameron
- Department of Nutrition, Case Western Reserve University, Cleveland, OH, USA
| | - David J Kelvin
- Department of Microbiology and Immunology, Canadian Center for Vaccinology, Dalhousie University, Halifax, NS, Canada; Laboratory of Immunology, Shantou University Medical College, Shantou, Guangdong, China
| | - Aravinda de Silva
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David M Margolis
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alena Markmann
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Luther Bartelt
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ross Zumwalt
- Department of Pathology, University of New Mexico, Albuquerque, NM, USA
| | - Fernando J Martinez
- Division of Pulmonary and Critical Care Medicine, Joan & Sanford I. Weill Medical College of Cornell University, New York, NY, USA
| | - Steven P Salvatore
- Department of Pathology, Joan & Sanford I. Weill Medical College of Cornell University, New York, NY, USA
| | - Alain Borczuk
- Department of Pathology, Joan & Sanford I. Weill Medical College of Cornell University, New York, NY, USA
| | - Purushothama R Tata
- Department of Cell Biology, Regeneration Next Initiative, Duke University Medical Center, Durham, NC, USA
| | - Vishwaraj Sontake
- Department of Cell Biology, Regeneration Next Initiative, Duke University Medical Center, Durham, NC, USA
| | - Adam Kimple
- Department of Otolaryngology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ilona Jaspers
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wanda K O'Neal
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott H Randell
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Richard C Boucher
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Abstract
Human endogenous retroviruses (HERVs) are derived from exogenous retrovirus infections in the evolution of primates and account for about 8% of the human genome. They were considered as silent passengers within our genomes for a long time, however, reactivation of HERVs has been associated with tumors and autoimmune diseases, especially the HERV-K (HML-2) family, the most recent integration groups with the least number of mutations and the most biologically active to encode functional retroviral proteins and produce retrovirus-like particles. Increasing studies are committed to determining the potential role of HERV-K (HML-2) in pathogenicity. Although there is still no evidence for HERV-K (HML-2) as a direct cause of diseases, aberrant expression profiles of the HERV-K (HML-2) transcripts and their regulatory function to their proximal host-genes were identified in different diseases. In this review, we summarized the advances between HERV-K (HML-2) and diseases to provide basis for further studies on the causal relationship between HERV-K (HML-2) and diseases. We recommended more attention to polymorphic integrated HERV-K (HML-2) loci which could be genetic causative factors and be associated with inter-individual differences in tumorigenesis and autoimmune diseases.
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Affiliation(s)
- Bei Xue
- Division of Immunology, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, Canadian Center for Vaccinology, Dalhousie University, Halifax, NS, Canada
| | - Leonardo A. Sechi
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Mediterranean Center for Disease Control, University of Sassari, Sassari, Italy
| | - David J. Kelvin
- Division of Immunology, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, Canadian Center for Vaccinology, Dalhousie University, Halifax, NS, Canada
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
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37
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Andrew M, Searle SD, McElhaney JE, McNeil SA, Clarke B, Rockwood K, Kelvin DJ. COVID-19, frailty and long-term care: Implications for policy and practice. J Infect Dev Ctries 2020; 14:428-432. [PMID: 32525825 DOI: 10.3855/jidc.13003] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [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: 05/09/2020] [Accepted: 05/16/2020] [Indexed: 10/31/2022] Open
Abstract
Older adults have been disproportionately affected by the COVID-19 pandemic, with many outbreaks occurring in Long Term Care Facilities (LTCFs). We discuss this vulnerability among LTCF residents using an ecological framework, on levels spanning from the individual to families and caregivers, institutions, health services and systems, communities, and contextual government policies. Challenges abound for fully understanding the burden of COVID-19 in LTCF, including differences in nomenclature, data collection systems, cultural differences, varied social welfare models, and (often) under-resourcing of the LTC sector. Registration of cases and deaths may be limited by testing capacity and policy, record-keeping and reporting procedures. Hospitalization and death rates may be inaccurate depending on atypical presentations and whether or not residents' goals of care include escalation of care and transfer to hospital. Given the important contribution of frailty, use of the Clinical Frailty Scale (CFS) is discussed as a readily implementable measure, as are lessons learned from the study of frailty in relation to influenza. Biomarkers hold emerging promise in helping to predict disease severity and address the puzzle of why some frail LTCF residents are resilient to COVID-19, either remaining test-negative despite exposure or having asymptomatic infection, while others experience the full range of illness severity including critical illness and death. Strong and coordinated surveillance and research focused on LTCFs and their frail residents is required. These efforts should include widespread assessment of frailty using feasible and readily implementable tools such as the CFS, and rigorous reporting of morbidity and mortality in LTCFs.
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Affiliation(s)
- Melissa Andrew
- Department of Medicine (Geriatrics), Dalhousie University, Halifax, Canada.
| | - Samuel D Searle
- Department of Medicine (Geriatrics), Dalhousie University, Halifax, Canada.
| | | | - Shelly A McNeil
- Department of Medicine (Infectious Diseases), Dalhousie University, Halifax, Canada.
| | - Barry Clarke
- Department of Family Medicine, Dalhousie University, Halifax, Canada.
| | - Kenneth Rockwood
- Department of Medicine (Geriatrics), Dalhousie University, Halifax, Canada.
| | - David J Kelvin
- Department of Microbiology and Immunology, Dalhousie, Halifax, Canada.
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Xue B, Zeng T, Jia L, Yang D, Lin SL, Sechi LA, Kelvin DJ. Identification of the distribution of human endogenous retroviruses K (HML-2) by PCR-based target enrichment sequencing. Retrovirology 2020; 17:10. [PMID: 32375827 PMCID: PMC7201656 DOI: 10.1186/s12977-020-00519-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 01/16/2020] [Accepted: 04/23/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Human endogenous retroviruses (HERVs), suspected to be transposition-defective, may reshape the transcriptional network of the human genome by regulatory elements distributed in their long terminal repeats (LTRs). HERV-K (HML-2), the most preserved group with the least number of accumulated of mutations, has been associated with aberrant gene expression in tumorigenesis and autoimmune diseases. Because of the high sequence similarity between different HERV-Ks, current methods have limitations in providing genome-wide mapping specific for individual HERV-K (HML-2) members, a major barrier in delineating HERV-K (HML-2) function. RESULTS In an attempt to obtain detailed distribution information of HERV-K (HML-2), we utilized a PCR-based target enrichment sequencing protocol for HERV-K (HML-2) (PTESHK) loci, which not only maps the presence of reference loci, but also identifies non-reference loci, enabling determination of the genome-wide distribution of HERV-K (HML-2) loci. Here we report on the genomic data obtained from three individuals. We identified a total of 978 loci using this method, including 30 new reference loci and 5 non-reference loci. Among the 3 individuals in our study, 14 polymorphic HERV-K (HML-2) loci were identified, and solo-LTR330 and N6p21.32 were identified as polymorphic for the first time. CONCLUSIONS Interestingly, PTESHK provides an approach for the identification of the genome-wide distribution of HERV-K (HML-2) and can be used for the identification of polymorphic loci. Since polymorphic HERV-K (HML-2) integrations are suspected to be related to various diseases, PTESHK can supplement other emerging techniques in accessing polymorphic HERV-K (HML-2) elements in cancer and autoimmune diseases.
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Affiliation(s)
- Bei Xue
- Division of Immunology, Shantou University Medical College, Shantou, China
- The Department of Microbiology and Immunology, Dalhousie University, Halifax, Canada
- Canadian Center for Vaccinology, Dalhousie University, Halifax, Canada
| | - Tiansheng Zeng
- Division of Immunology, Shantou University Medical College, Shantou, China
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Lisha Jia
- Division of Immunology, Shantou University Medical College, Shantou, China
| | - Dongsheng Yang
- Division of Immunology, Shantou University Medical College, Shantou, China
| | - Stanley L Lin
- Division of Immunology, Shantou University Medical College, Shantou, China
| | - Leonardo A Sechi
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy.
| | - David J Kelvin
- Division of Immunology, Shantou University Medical College, Shantou, China.
- The Department of Microbiology and Immunology, Dalhousie University, Halifax, Canada.
- Canadian Center for Vaccinology, Dalhousie University, Halifax, Canada.
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy.
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Bermejo-Martin JF, Almansa R, Menéndez R, Mendez R, Kelvin DJ, Torres A. Lymphopenic community acquired pneumonia as signature of severe COVID-19 infection. J Infect 2020; 80:e23-e24. [PMID: 32145214 PMCID: PMC7133663 DOI: 10.1016/j.jinf.2020.02.029] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 02/27/2020] [Accepted: 02/28/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Jesús F Bermejo-Martin
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca (IBSAL), Paseo de San Vicente, 58-182, 37007 Salamanca, Spain; Hospital Universitario Río Hortega de Valladolid. Calle Dulzaina, 2, 47012 Valladolid, Spain; Centro de Investigación Biomedica En Red-Enfermedades Respiratorias, Instituto de Salud Carlos III, Av. de Monforte de Lemos, 5, 28029, Madrid, Spain.
| | - Raquel Almansa
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca (IBSAL), Paseo de San Vicente, 58-182, 37007 Salamanca, Spain; Hospital Universitario Río Hortega de Valladolid. Calle Dulzaina, 2, 47012 Valladolid, Spain; Centro de Investigación Biomedica En Red-Enfermedades Respiratorias, Instituto de Salud Carlos III, Av. de Monforte de Lemos, 5, 28029, Madrid, Spain
| | - Rosario Menéndez
- Centro de Investigación Biomedica En Red-Enfermedades Respiratorias, Instituto de Salud Carlos III, Av. de Monforte de Lemos, 5, 28029, Madrid, Spain; Pulmonology Service, University and Polytechnic Hospital La Fe, Avinguda de Fernando Abril Martorell, 106, 46026 València, Spain
| | - Raúl Mendez
- Pulmonology Service, University and Polytechnic Hospital La Fe, Avinguda de Fernando Abril Martorell, 106, 46026 València, Spain
| | - David J Kelvin
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada; Division of Immunity Shantou University Medical College, 22 Xinling Rd, Jinping, Shantou, Guangdong, China
| | - Antoni Torres
- Centro de Investigación Biomedica En Red-Enfermedades Respiratorias, Instituto de Salud Carlos III, Av. de Monforte de Lemos, 5, 28029, Madrid, Spain; Department of Pneumology, Institut Clinic del Tórax, Hospital Clinic of Barcelona - Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB) - SGR 911- Carrer de Villarroel, 170, 08036 Barcelona, Spain
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40
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Wu L, Zeng T, Deligios M, Milanesi L, Langille MGI, Zinellu A, Rubino S, Carru C, Kelvin DJ. Age-Related Variation of Bacterial and Fungal Communities in Different Body Habitats across the Young, Elderly, and Centenarians in Sardinia. mSphere 2020; 5:5/1/e00558-19. [PMID: 32102941 PMCID: PMC7045387 DOI: 10.1128/msphere.00558-19] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [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: 07/31/2019] [Accepted: 12/15/2019] [Indexed: 02/05/2023] Open
Abstract
Human body microbes interact with the host, forming microbial communities that are in continual flux during the aging process. Previous studies have mostly focused on surveying a single body habitat to determine the age-related variation in the bacterial and fungal communities. A more comprehensive understanding of the variation in the human microbiota and mycobiota across multiple body habitats related to aging is still unclear. To obtain an integrated view of the spatial distribution of microbes in a specific Mediterranean population across a wide age range, we surveyed the bacterial and fungal communities in the skin, oral cavity, and gut in the young, elderly, and centenarians in Sardinia using 16S rRNA gene and internal transcribed spacer 1 (ITS1) sequencing. We found that the distribution and correlation of bacterial and fungal communities in Sardinians were largely determined by body site. In each age group, the bacterial and fungal communities found in the skin were significantly different in structure. In the oral cavity, age had a marginal impact on the structures of the bacterial and fungal communities. Furthermore, the gut bacterial communities in centenarians clustered separately from those of the young and elderly, while the fungal communities in the gut habitat could not be separated by host age.IMPORTANCE Site-specific microbial communities are recognized as important factors in host health and disease. To better understand how the human microbiota potentially affects and is affected by its host during the aging process, the fundamental issue to address is the distribution of microbiota related to age. Here, we show an integrated view of the spatial distribution of microbes in a specific Mediterranean population (Sardinians) across a wide age range. Our study indicates that age plays a critical role in shaping the human microbiota in a habitat-dependent manner. The dynamic age-related microbiota changes we observed across multiple body sites may provide possibilities for modulating microbe communities to maintain or improve health during aging.
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Affiliation(s)
- Lu Wu
- Division of Immunology International Institute of Infection and Immunity, Shantou University Medical College, Shantou, Guangdong, China
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Tiansheng Zeng
- Division of Immunology International Institute of Infection and Immunity, Shantou University Medical College, Shantou, Guangdong, China
| | - Massimo Deligios
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Luciano Milanesi
- Institute of Biomedical Technologies, National Research Council of Italy, Segrate, Italy
| | - Morgan G I Langille
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Angelo Zinellu
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Salvatore Rubino
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Ciriaco Carru
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - David J Kelvin
- Division of Immunology International Institute of Infection and Immunity, Shantou University Medical College, Shantou, Guangdong, China
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
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Affiliation(s)
- David J Kelvin
- International Institute of Infection and Immunity, Shantou University Medical College, Shantou, Guangdong, China; and Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada. Canadian Centre for Vaccinology, IWK Health Centre, Halifax, Nova Scotia, Canada. Senior editor, JIDC.
| | - Salvatore Rubino
- Dipartimento di Scienze Biomediche, Universita' degli Studi di Sassari, Sassari, Italy. Editor-in-Chief, JIDC.
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Ralph R, Lew J, Zeng T, Francis M, Xue B, Roux M, Toloue Ostadgavahi A, Rubino S, Dawe NJ, Al-Ahdal MN, Kelvin DJ, Richardson CD, Kindrachuk J, Falzarano D, Kelvin AA. 2019-nCoV (Wuhan virus), a novel Coronavirus: human-to-human transmission, travel-related cases, and vaccine readiness. J Infect Dev Ctries 2020; 14:3-17. [PMID: 32088679 DOI: 10.3855/jidc.12425] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [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: 01/20/2020] [Accepted: 01/23/2020] [Indexed: 02/05/2023] Open
Abstract
On 31 December 2019 the Wuhan Health Commission reported a cluster of atypical pneumonia cases that was linked to a wet market in the city of Wuhan, China. The first patients began experiencing symptoms of illness in mid-December 2019. Clinical isolates were found to contain a novel coronavirus with similarity to bat coronaviruses. As of 28 January 2020, there are in excess of 4,500 laboratory-confirmed cases, with > 100 known deaths. As with the SARS-CoV, infections in children appear to be rare. Travel-related cases have been confirmed in multiple countries and regions outside mainland China including Germany, France, Thailand, Japan, South Korea, Vietnam, Canada, and the United States, as well as Hong Kong and Taiwan. Domestically in China, the virus has also been noted in several cities and provinces with cases in all but one provinence. While zoonotic transmission appears to be the original source of infections, the most alarming development is that human-to-human transmission is now prevelant. Of particular concern is that many healthcare workers have been infected in the current epidemic. There are several critical clinical questions that need to be resolved, including how efficient is human-to-human transmission? What is the animal reservoir? Is there an intermediate animal reservoir? Do the vaccines generated to the SARS-CoV or MERS-CoV or their proteins offer protection against 2019-nCoV? We offer a research perspective on the next steps for the generation of vaccines. We also present data on the use of in silico docking in gaining insight into 2019-nCoV Spike-receptor binding to aid in therapeutic development. Diagnostic PCR protocols can be found at https://www.who.int/health-topics/coronavirus/laboratory-diagnostics-for-novel-coronavirus.
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Affiliation(s)
- Robyn Ralph
- Vaccine and Infectious Disease Organization - International Vaccine Centre (VIDO-InterVac), Saskatoon, Saskatchewan, Canada.
| | - Jocelyne Lew
- Vaccine and Infectious Disease Organization - International Vaccine Centre (VIDO-InterVac), Saskatoon, Saskatchewan, Canada.
| | - Tiansheng Zeng
- International Institute of Infection and Immunity, Shantou University Medical College, Shantou, Guangdong, China.
| | - Magie Francis
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada.
| | - Bei Xue
- International Institute of Infection and Immunity, Shantou University Medical College, Shantou, Guangdong, China.
| | - Melissa Roux
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada.
| | - Ali Toloue Ostadgavahi
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada.
| | - Salvatore Rubino
- Sezione di Microbiologia Sperimentale e Clinica, Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy.
| | - Nicholas J Dawe
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada.
| | - Mohammed N Al-Ahdal
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
| | - David J Kelvin
- International Institute of Infection and Immunity, Shantou University Medical College, Shantou, Guangdong, China.
| | - Christopher D Richardson
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada.
| | - Jason Kindrachuk
- Laboratory of Emerging and Re-Emerging Viruses, Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.
| | - Darryl Falzarano
- Vaccine and Infectious Disease Organization - International Vaccine Centre (VIDO-InterVac), Saskatoon, Saskatchewan, Canada.
| | - Alyson Anne Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada.
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Wu L, Zeng T, Zinellu A, Rubino S, Kelvin DJ, Carru C. A Cross-Sectional Study of Compositional and Functional Profiles of Gut Microbiota in Sardinian Centenarians. mSystems 2019; 4:4/4/e00325-19. [PMID: 31289141 PMCID: PMC6616150 DOI: 10.1128/msystems.00325-19] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [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: 05/22/2019] [Accepted: 06/18/2019] [Indexed: 02/05/2023] Open
Abstract
Sardinia, Italy, has a high prevalence of residents who live more than 100 years. The reasons for longevity in this isolated region are currently unknown. Gut microbiota may hold a clue. To explore the role gut microbiota may play in healthy aging and longevity, we used metagenomic sequencing to determine the compositional and functional differences in gut microbiota associated with populations of different ages in Sardinia. Our data revealed that the gut microbiota of both young and elderly Sardinians shared similar taxonomic and functional profiles. A different pattern was found in centenarians. Within the centenarian group, the gut microbiota was correlated with the functional independence measurement of the host. Centenarians had a higher diversity of core microbiota species and microbial genes than those in the young and elderly. We found that the gut microbiota in Sardinian centenarians displayed a rearranged taxonomic pattern compared with those of the young and elderly, featured by depletion of Faecalibacterium prausnitzii and Eubacterium rectale and enriched for Methanobrevibacter smithii and Bifidobacterium adolescentis Moreover, functional analysis revealed that the microbiota in centenarians had high capacity for central metabolism, especially glycolysis and fermentation to short-chain fatty acids (SCFAs), although the gut microbiota in centenarians was low in genes encoding enzymes involved in degradation of carbohydrates, including fibers and galactose.IMPORTANCE The gut microbiota has been proposed as a promising determinant for human health. Centenarians as a model for extreme aging may help us understand the correlation of gut microbiota with healthy aging and longevity. Here we confirmed that centenarians had microbiota elements usually associated with benefits to health. Our finding of a high capacity of glycolysis and related SCFA production represented a healthy microbiome and environment that is regarded as beneficial for host gut epithelium. The low abundance of genes encoding components of pathways involved in carbohydrate degradation was also found in the gut microbiota of Sardinian centenarians and is often associated with poor gut health. Overall, our study here represents an expansion of previous research investigating the age-related changes in gut microbiota. Furthermore, our study provides a new prospective for potential targets for gut microbiota intervention directed at limiting gut inflammation and pathology and enhancing a healthy gut barrier.
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Affiliation(s)
- Lu Wu
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, Shantou, Guangdong, China
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Tiansheng Zeng
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, Shantou, Guangdong, China
| | - Angelo Zinellu
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Salvatore Rubino
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - David J Kelvin
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, Shantou, Guangdong, China
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Canada
| | - Ciriaco Carru
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
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Jovel J, Lin Z, O'keefe S, Willows S, Wang W, Zhang G, Patterson J, Moctezuma-Velázquez C, Kelvin DJ, Ka-Shu Wong G, Mason AL. A Survey of Molecular Heterogeneity in Hepatocellular Carcinoma. Hepatol Commun 2018; 2:941-955. [PMID: 30094405 PMCID: PMC6078210 DOI: 10.1002/hep4.1197] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 04/11/2018] [Accepted: 04/17/2018] [Indexed: 12/24/2022] Open
Abstract
Understanding the heterogeneity of dysregulated pathways associated with the development of hepatocellular carcinoma (HCC) may provide prognostic and therapeutic avenues for disease management. As HCC involves a complex process of genetic and epigenetic modifications, we evaluated expression of both polyadenylated transcripts and microRNAs from HCC and liver samples derived from two cohorts of patients undergoing either partial hepatic resection or liver transplantation. Copy number variants were inferred from whole genome low‐pass sequencing data, and a set of 56 cancer‐related genes were screened using an oncology panel assay. HCC was associated with marked transcriptional deregulation of hundreds of protein‐coding genes. In the partially resected livers, diminished transcriptional activity was observed in genes associated with drug catabolism and increased expression in genes related to inflammatory responses and cell proliferation. Moreover, several long noncoding RNAs and microRNAs not previously linked with HCC were found to be deregulated. In liver transplant recipients, down‐regulation of genes involved in energy production and up‐regulation of genes associated with glycolysis were detected. Numerous copy number variants events were observed, with hotspots on chromosomes 1 and 17. Amplifications were more common than deletions and spanned regions containing genes potentially involved in tumorigenesis. Colony stimulating factor 1 receptor (CSF1R), fibroblast growth factor receptor 3 (FGFR3), fms‐like tyrosine kinase 3 (FLT3), nucleolar phosphoprotein B23 (NPM1), platelet‐derived growth factor receptor alpha polypeptide (PDGFRA), phosphatase and tensin homolog (PTEN), G‐protein‐coupled receptors‐like receptor Smoothened (SMO), and tumor protein P53 (TP53) were mutated in all tumors; another 26 cancer‐related genes were mutated with variable penetrance. Conclusion: Our results underscore the marked molecular heterogeneity between HCC tumors and reinforce the notion that precision medicine approaches are needed for management of individual HCC. These data will serve as a resource to generate hypotheses for further research to improve our understanding of HCC biology. (Hepatology Communications 2018; 00:000‐000)
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Affiliation(s)
- Juan Jovel
- Department of Medicine University of Alberta Edmonton Canada
| | - Zhen Lin
- Department of Medicine University of Alberta Edmonton Canada
| | - Sandra O'keefe
- Department of Medicine University of Alberta Edmonton Canada
| | - Steven Willows
- Department of Medicine University of Alberta Edmonton Canada
| | - Weiwei Wang
- Department of Medicine University of Alberta Edmonton Canada
| | - Guangzhi Zhang
- Department of Medicine University of Alberta Edmonton Canada
| | | | | | - David J Kelvin
- Division of Experimental Therapeutics University Health Network Toronto Canada
| | - Gane Ka-Shu Wong
- Department of Medicine University of Alberta Edmonton Canada.,Department of Biological Sciences University of Alberta Edmonton Canada.,BGI-Shenzhen Shenzhen China
| | - Andrew L Mason
- Department of Medicine University of Alberta Edmonton Canada
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Leon AJ, Borisevich V, Boroumand N, Seymour R, Nusbaum R, Escaffre O, Xu L, Kelvin DJ, Rockx B. Host gene expression profiles in ferrets infected with genetically distinct henipavirus strains. PLoS Negl Trop Dis 2018; 12:e0006343. [PMID: 29538374 PMCID: PMC5868854 DOI: 10.1371/journal.pntd.0006343] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 03/26/2018] [Accepted: 02/24/2018] [Indexed: 02/05/2023] Open
Abstract
Henipavirus infection causes severe respiratory and neurological disease in humans that can be fatal. To characterize the pathogenic mechanisms of henipavirus infection in vivo, we performed experimental infections in ferrets followed by genome-wide gene expression analysis of lung and brain tissues. The Hendra, Nipah-Bangladesh, and Nipah-Malaysia strains caused severe respiratory and neurological disease with animals succumbing around 7 days post infection. Despite the presence of abundant viral shedding, animal-to-animal transmission did not occur. The host gene expression profiles of the lung tissue showed early activation of interferon responses and subsequent expression of inflammation-related genes that coincided with the clinical deterioration. Additionally, the lung tissue showed unchanged levels of lymphocyte markers and progressive downregulation of cell cycle genes and extracellular matrix components. Infection in the brain resulted in a limited breadth of the host responses, which is in accordance with the immunoprivileged status of this organ. Finally, we propose a model of the pathogenic mechanisms of henipavirus infection that integrates multiple components of the host responses.
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Affiliation(s)
- Alberto J. Leon
- Division of Experimental Therapeutics, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Viktoriya Borisevich
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States of America
- Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX, United States of America
- Institute of Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Nahal Boroumand
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Robert Seymour
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States of America
- Institute of Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Rebecca Nusbaum
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Olivier Escaffre
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Luoling Xu
- Division of Experimental Therapeutics, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - David J. Kelvin
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Canada
- International Institute of Infection and Immunity, Shantou University Medical College, Shantou, PRC
- * E-mail: (DJK); (BR)
| | - Barry Rockx
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States of America
- Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX, United States of America
- Institute of Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, United States of America
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
- * E-mail: (DJK); (BR)
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Abstract
Influenza viruses cause mild to severe respiratory infections in humans. Due to efficient means of transmission, the viruses infect human population on a large scale. Apart from vaccines, antiviral drugs are used to control infection; neuraminidase inhibitors are thought to be the first choice of treatment, particularly for severe cases. Rapidly evolving and emerging influenza viruses with increased frequency of viral resistance to these drugs stress the need to explore novel antiviral compounds. In this study, we investigated antiviral activity of ginseng extract and ginsenosides, the ginseng-derived triterpene and saponin compounds, against 2009 pandemic H1N1 virus in vitro and in vivo. Our data showed that treatment of mice with ginsenosides protected the animals from lethal 2009 pandemic H1N1 infection and lowered viral titers in animal lungs. Mechanistic studies revealed that ginsenosides interact with viral hemagglutinin protein and prevent the attachment of virus with α 2-3' sialic acid receptors present on host cell surfaces. The interference in the viral attachment process subsequently minimizes viral entry into the cells and decreases the severity of the viral infection. We also describe that sugar moieties present in ginsenosides are indispensible for their attachment with viral HA protein. On the basis of our observations, we can say that ginsenosides are promising candidates for the development of antiviral drugs for influenza viruses.
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Affiliation(s)
- Wei Dong
- Division of Immunology, International Institute of Infection and Immunity, University Health Network & Shantou University Medical College, Shantou, China
| | - Amber Farooqui
- Division of Immunology, International Institute of Infection and Immunity, University Health Network & Shantou University Medical College, Shantou, China
- Division of Experimental Therapeutics, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou, China
| | - Alberto J. Leon
- Division of Immunology, International Institute of Infection and Immunity, University Health Network & Shantou University Medical College, Shantou, China
- Division of Experimental Therapeutics, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - David J. Kelvin
- Division of Immunology, International Institute of Infection and Immunity, University Health Network & Shantou University Medical College, Shantou, China
- Division of Experimental Therapeutics, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou, China
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Deptartment of Immunology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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Bermejo-Martin JF, Andaluz-Ojeda D, Almansa R, Gandía F, Gómez-Herreras JI, Gomez-Sanchez E, Heredia-Rodríguez M, Eiros JM, Kelvin DJ, Tamayo E. Defining immunological dysfunction in sepsis: A requisite tool for precision medicine. J Infect 2016; 72:525-36. [PMID: 26850357 DOI: 10.1016/j.jinf.2016.01.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [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: 12/15/2015] [Revised: 01/24/2016] [Accepted: 01/26/2016] [Indexed: 02/05/2023]
Abstract
OBJECTIVES Immunological dysregulation is now recognised as a major pathogenic event in sepsis. Stimulation of immune response and immuno-modulation are emerging approaches for the treatment of this disease. Defining the underlying immunological alterations in sepsis is important for the design of future therapies with immuno-modulatory drugs. METHODS Clinical studies evaluating the immunological response in adult patients with Sepsis and published in PubMed were reviewed to identify features of immunological dysfunction. For this study we used key words related with innate and adaptive immunity. RESULTS Ten major features of immunological dysfunction (FID) were identified involving quantitative and qualitative alterations of [antigen presentation](FID1), [T and B lymphocytes] (FID2), [natural killer cells] (FID3), [relative increase in T regulatory cells] (FID4), [increased expression of PD-1 and PD-ligand1](FID5), [low levels of immunoglobulins](FID6), [low circulating counts of neutrophils and/or increased immature forms in non survivors](FID7), [hyper-cytokinemia] (FID8), [complement consumption] (FID9), [defective bacterial killing by neutrophil extracellular traps](FID10). CONCLUSIONS This review article identified ten major features associated with immunosuppression and immunological dysregulation in sepsis. Assessment of these features could help in utilizing precision medicine for the treatment of sepsis with immuno-modulatory drugs.
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Affiliation(s)
- Jesús F Bermejo-Martin
- Infection and Immunity Medical Investigation Unit (IMI), Hospital Clínico Universitario de Valladolid, SACYL/IECSCYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain; Grupo de Investigación Biomédica en Cuidados Críticos (BioCritic), Hospital Clínico Universitario de Valladolid, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain.
| | - David Andaluz-Ojeda
- Grupo de Investigación Biomédica en Cuidados Críticos (BioCritic), Hospital Clínico Universitario de Valladolid, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain; Servicio de Medicina Intensiva, Hospital Clínico Universitario de Valladolid, SACYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain.
| | - Raquel Almansa
- Infection and Immunity Medical Investigation Unit (IMI), Hospital Clínico Universitario de Valladolid, SACYL/IECSCYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain; Grupo de Investigación Biomédica en Cuidados Críticos (BioCritic), Hospital Clínico Universitario de Valladolid, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain.
| | - Francisco Gandía
- Grupo de Investigación Biomédica en Cuidados Críticos (BioCritic), Hospital Clínico Universitario de Valladolid, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain; Servicio de Medicina Intensiva, Hospital Clínico Universitario de Valladolid, SACYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain.
| | - Jose Ignacio Gómez-Herreras
- Grupo de Investigación Biomédica en Cuidados Críticos (BioCritic), Hospital Clínico Universitario de Valladolid, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain; Servicio de Anestesiología y Reanimación, Hospital Clínico Universitario de Valladolid, SACYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain.
| | - Esther Gomez-Sanchez
- Grupo de Investigación Biomédica en Cuidados Críticos (BioCritic), Hospital Clínico Universitario de Valladolid, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain; Servicio de Anestesiología y Reanimación, Hospital Clínico Universitario de Valladolid, SACYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain.
| | - María Heredia-Rodríguez
- Grupo de Investigación Biomédica en Cuidados Críticos (BioCritic), Hospital Clínico Universitario de Valladolid, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain; Servicio de Anestesiología y Reanimación, Hospital Clínico Universitario de Valladolid, SACYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain.
| | - Jose Maria Eiros
- Grupo de Investigación Biomédica en Cuidados Críticos (BioCritic), Hospital Clínico Universitario de Valladolid, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain.
| | - David J Kelvin
- Division of Experimental Therapeutics, Toronto General Hospital Research Institute, University Health Network, 200 Elizabeth Street, Toronto, ON M5G 2C4, Canada; Sezione di Microbiologia Sperimentale e Clinica, Dipartimento di Scienze Biomediche, Universita' degli Studi di Sassari, Piazza Università, 21, 07100 Sassari SS, Italy; International Institute of Infection and Immunity, Shantou University Medical College, 22 Xinling Road, Shantou, 515041 Guangdong Province, PR China.
| | - Eduardo Tamayo
- Grupo de Investigación Biomédica en Cuidados Críticos (BioCritic), Hospital Clínico Universitario de Valladolid, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain; Servicio de Anestesiología y Reanimación, Hospital Clínico Universitario de Valladolid, SACYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain.
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Farooqui A, Liu W, Zeng T, Liu Y, Zhang L, Khan A, Wu X, Wu R, Wu S, Huang L, Cai Y, Kelvin AA, Paquette SG, Hu K, Zheng N, Chen H, Xu S, Lin C, Sun P, Yao Z, Wang J, Ma H, Zhu Z, Lin P, Chen W, Fang X, Bermejo-Martin JF, Leon AJ, Kelvin DJ. Probable Hospital Cluster of H7N9 Influenza Infection. N Engl J Med 2016; 374:596-8. [PMID: 26863372 DOI: 10.1056/nejmc1505359] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
| | | | | | - Yisu Liu
- Shantou University Medical College, Shantou, China
| | - Li Zhang
- Shantou University Medical College, Shantou, China
| | - Adnan Khan
- Shantou University Medical College, Shantou, China
| | - Xiuming Wu
- Second Affiliated Hospital, Shantou, China
| | - Renhua Wu
- Second Affiliated Hospital, Shantou, China
| | - Suwu Wu
- Shantou Central Hospital, Shantou, China
| | | | - Yingmu Cai
- First Affiliated Hospital, Shantou, China
| | | | | | - Kezhao Hu
- Second Affiliated Hospital, Shantou, China
| | | | | | - Sheng Xu
- Second Affiliated Hospital, Shantou, China
| | | | - Peng Sun
- Second Affiliated Hospital, Shantou, China
| | | | - Jun Wang
- Second Affiliated Hospital, Shantou, China
| | - Huanjie Ma
- Second Affiliated Hospital, Shantou, China
| | | | | | | | | | | | | | - David J Kelvin
- International Institute of Infection and Immunity, Shantou, China.
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Zhang Z, Huang T, Yu F, Liu X, Zhao C, Chen X, Kelvin DJ, Gu J. Infectious Progeny of 2009 A (H1N1) Influenza Virus Replicated in and Released from Human Neutrophils. Sci Rep 2015; 5:17809. [PMID: 26639836 PMCID: PMC4671072 DOI: 10.1038/srep17809] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 11/06/2015] [Indexed: 02/05/2023] Open
Abstract
Various reports have indicated that a number of viruses could infect neutrophils, but the multiplication of viruses in neutrophils was abortive. Based on our previous finding that avian influenza viral RNA and proteins were present in the nucleus of infected human neutrophils in vivo, we investigated the possibility of 2009 A (H1N1) influenza viral synthesis in infected neutrophils and possible release of infectious progeny from host cells. In this study we found that human neutrophils in vitro without detectable level of sialic acid expression could be infected by this virus strain. We also show that the infected neutrophils can not only synthesize 2009 A (H1N1) viral mRNA and proteins, but also produce infectious progeny. These findings suggest that infectious progeny of 2009 A (H1N1) influenza virus could be replicated in and released from human neutrophils with possible clinical implications.
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Affiliation(s)
- Zhang Zhang
- Department of Pathology and Provincial Key Laboratory of Infectious Diseases and Immunopathology, Collaborative and Creative Center, Shantou University Medical College, Shantou, Guangdong, 515041, China
| | - Tao Huang
- Department of Pathology and Provincial Key Laboratory of Infectious Diseases and Immunopathology, Collaborative and Creative Center, Shantou University Medical College, Shantou, Guangdong, 515041, China
| | - Feiyuan Yu
- Department of Pathology and Provincial Key Laboratory of Infectious Diseases and Immunopathology, Collaborative and Creative Center, Shantou University Medical College, Shantou, Guangdong, 515041, China
| | - Xingmu Liu
- Department of Pathology and Provincial Key Laboratory of Infectious Diseases and Immunopathology, Collaborative and Creative Center, Shantou University Medical College, Shantou, Guangdong, 515041, China
| | - Conghui Zhao
- Department of Pathology, Beijing University Health Science Center, Beijing, 100083, China
| | - Xueling Chen
- Department of Pathology and Provincial Key Laboratory of Infectious Diseases and Immunopathology, Collaborative and Creative Center, Shantou University Medical College, Shantou, Guangdong, 515041, China
| | - David J. Kelvin
- Division of Experimental Therapeutics, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Universita’ degli Studi di Sassari, Sezione di Microbiologia Sperimentale e Clinica, Dipartimento di Scienze Biomediche, Viale San Pietro 43/b, 07100 Sassari, Italia
- International Institute of Infection and Immunity, Shantou University Medical College, Shantou, Guangdong, China
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Jiang Gu
- Department of Pathology and Provincial Key Laboratory of Infectious Diseases and Immunopathology, Collaborative and Creative Center, Shantou University Medical College, Shantou, Guangdong, 515041, China
- Department of Pathology, Beijing University Health Science Center, Beijing, 100083, China
- Translational Medicine Center, Second Affiliated Hospital, Shantou University Medical College, Shantou, China
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