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Jaiswal S, Kumar M, Mandeep, Sunita, Singh Y, Shukla P. Systems Biology Approaches for Therapeutics Development Against COVID-19. Front Cell Infect Microbiol 2020; 10:560240. [PMID: 33194800 PMCID: PMC7655984 DOI: 10.3389/fcimb.2020.560240] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/29/2020] [Indexed: 12/13/2022] Open
Abstract
Understanding the systems biology approaches for promoting the development of new therapeutic drugs is attaining importance nowadays. The threat of COVID-19 outbreak needs to be vanished for global welfare, and every section of research is focusing on it. There is an opportunity for finding new, quick, and accurate tools for developing treatment options, including the vaccine against COVID-19. The review at this moment covers various aspects of pathogenesis and host factors for exploring the virus target and developing suitable therapeutic solutions through systems biology tools. Furthermore, this review also covers the extensive details of multiomics tools i.e., transcriptomics, proteomics, genomics, lipidomics, immunomics, and in silico computational modeling aiming towards the study of host-virus interactions in search of therapeutic targets against the COVID-19.
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Affiliation(s)
- Shweta Jaiswal
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Mohit Kumar
- Soil Microbial Ecology and Environmental Toxicology Laboratory, Department of Zoology, University of Delhi, Delhi, India
- Department of Zoology, Hindu College, University of Delhi, Delhi, India
| | - Mandeep
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Sunita
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Yogendra Singh
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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Gómez-Rial J, Sánchez-Batán S, Rivero-Calle I, Pardo-Seco J, Martinón-Martínez JM, Salas A, Martinón-Torres F. Rotavirus infection beyond the gut. Infect Drug Resist 2018; 12:55-64. [PMID: 30636886 PMCID: PMC6307677 DOI: 10.2147/idr.s186404] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The landscape of rotavirus (RV) infection has changed substantially in recent years. Autoimmune triggering has been added to clinical spectrum of this pathology, which is now known to be much broader than diarrhea. The impact of RV vaccines in these other conditions is becoming a growing field of research. The importance of host genetic background in RV susceptibility has been revealed, therefore increasing our understanding of vaccine effectiveness and giving some clues about the limited efficacy of RV vaccines in low-income settings. Also, interaction of RV with intestinal microbiota seems to play a key role in the process of infection vaccine effect. This article reviews current findings on the extraintestinal impact of RV infection and their widening clinical picture, and the recently described mechanisms of host susceptibility to infection and vaccine effectiveness. RV infection is a systemic disease with clinical and pathophysiological implications beyond the gut. We propose an “iceberg” model for this pathology with almost hidden clinical implications away from the gastrointestinal tract and eventually triggering the development of autoimmune diseases. Impact of current vaccines is being influenced by host genetics and gut microbiota interactions and these factors must be taken into account in the development of public health programs.
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Affiliation(s)
- José Gómez-Rial
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago de Compostela (SERGAS), Galicia, Spain, .,Laboratorio de Inmunología, Servicio de Análisis Clínicos, Hospital Clínico Universitario de Santiago de Compostela (SERGAS), Galicia, Spain
| | - Sonia Sánchez-Batán
- Laboratorio de Inmunología, Servicio de Análisis Clínicos, Hospital Clínico Universitario de Santiago de Compostela (SERGAS), Galicia, Spain
| | - Irene Rivero-Calle
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago de Compostela (SERGAS), Galicia, Spain, .,Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela (SERGAS), Galicia, Spain,
| | - Jacobo Pardo-Seco
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago de Compostela (SERGAS), Galicia, Spain,
| | - José María Martinón-Martínez
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago de Compostela (SERGAS), Galicia, Spain,
| | - Antonio Salas
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago de Compostela (SERGAS), Galicia, Spain, .,Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forense, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago de Compostela (SERGAS), Galicia, Spain
| | - Federico Martinón-Torres
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago de Compostela (SERGAS), Galicia, Spain, .,Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela (SERGAS), Galicia, Spain,
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Gale P. Using thermodynamic parameters to calibrate a mechanistic dose-response for infection of a host by a virus. MICROBIAL RISK ANALYSIS 2018; 8:1-13. [PMID: 32289059 PMCID: PMC7103988 DOI: 10.1016/j.mran.2018.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/29/2017] [Accepted: 01/03/2018] [Indexed: 05/21/2023]
Abstract
Assessing the risk of infection from emerging viruses or of existing viruses jumping the species barrier into novel hosts is limited by the lack of dose response data. The initial stages of the infection of a host by a virus involve a series of specific contact interactions between molecules in the host and on the virus surface. The strength of the interaction is quantified in the literature by the dissociation constant (Kd) which is determined experimentally and is specific for a given virus molecule/host molecule combination. Here, two stages of the initial infection process of host intestinal cells are modelled, namely escape of the virus in the oral challenge dose from the innate host defenses (e.g. mucin proteins in mucus) and the subsequent binding of any surviving virus to receptor molecules on the surface of the host epithelial cells. The strength of virus binding to host cells and to mucins may be quantified by the association constants, Ka and Kmucin, respectively. Here, a mechanistic dose-response model for the probability of infection of a host by a given virus dose is constructed using Ka and Kmucin which may be derived from published Kd values taking into account the number of specific molecular interactions. It is shown that the effectiveness of the mucus barrier is determined not only by the amount of mucin but also by the magnitude of Kmucin. At very high Kmucin values, slight excesses of mucin over virus are sufficient to remove all the virus according to the model. At lower Kmucin values, high numbers of virus may escape even with large excesses of mucin. The output from the mechanistic model is the probability (p1) of infection by a single virion which is the parameter used in conventional dose-response models to predict the risk of infection of the host from the ingested dose. It is shown here how differences in Ka (due to molecular differences in an emerging virus strain or new host) affect p1, and how these differences in Ka may be quantified in terms of two thermodynamic parameters, namely enthalpy and entropy. This provides the theoretical link between sequencing data and risk of infection. Lack of data on entropy is a limitation at present and may also affect our interpretation of Kd in terms of infectivity. It is concluded that thermodynamic approaches have a major contribution to make in developing dose-response models for emerging viruses.
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Key Words
- Asp, aspartate
- CRD, carbohydrate-recognition domain
- Cr, host cell receptor
- Dose-response
- EBOV, Zaire ebolavirus
- Enthalpy
- Entropy
- G, Gibbs free energy
- GI, gastrointestinal
- GP, glycoprotein
- H, enthalpy
- HA, haemagglutinin
- HBGA, histoblood group antigen
- HeV, Hendra virus
- Ka, Kmucin, association constants
- Kd, dissociation constant for two molecules bound to each other
- L, Avogadro number
- M, molar (moles dm−3)
- MBP, mannose binding protein
- MERS-CoV, MERS coronavirus
- MRA, microbiological risk assessment
- Mucin
- NPC1, Niemann-Pick C1 protein
- NiV, Nipah virus
- NoV, norovirus
- PL, phospholipid
- PRR, pathogen recognition receptor
- Phe, phenylalanine
- R, ideal gas constant
- S, entropy
- SPR, surface plasmon resonance
- T, temperature
- TIM-1, T-cell immunoglobulin and mucin domain protein 1
- VSV, vesicular stomatitis virus
- Virus
- k, on/off rate constant
- n, number of GP/Cr molecular contacts per virus/host cell binding
- pfu, plaque-forming unit
- ΔGa, change in Gibbs free energy on association of virus and cell
- ΔHa, change in enthalpy on association of virus and cell
- ΔSa, change in entropy on association of virus and cell
- ΔΔHa, change in ΔHa
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Hill AA, Crotta M, Wall B, Good L, O'Brien SJ, Guitian J. Towards an integrated food safety surveillance system: a simulation study to explore the potential of combining genomic and epidemiological metadata. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160721. [PMID: 28405360 PMCID: PMC5383817 DOI: 10.1098/rsos.160721] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 02/27/2017] [Indexed: 05/05/2023]
Abstract
Foodborne infection is a result of exposure to complex, dynamic food systems. The efficiency of foodborne infection is driven by ongoing shifts in genetic machinery. Next-generation sequencing technologies can provide high-fidelity data about the genetics of a pathogen. However, food safety surveillance systems do not currently provide similar high-fidelity epidemiological metadata to associate with genetic data. As a consequence, it is rarely possible to transform genetic data into actionable knowledge that can be used to genuinely inform risk assessment or prevent outbreaks. Big data approaches are touted as a revolution in decision support, and pose a potentially attractive method for closing the gap between the fidelity of genetic and epidemiological metadata for food safety surveillance. We therefore developed a simple food chain model to investigate the potential benefits of combining 'big' data sources, including both genetic and high-fidelity epidemiological metadata. Our results suggest that, as for any surveillance system, the collected data must be relevant and characterize the important dynamics of a system if we are to properly understand risk: this suggests the need to carefully consider data curation, rather than the more ambitious claims of big data proponents that unstructured and unrelated data sources can be combined to generate consistent insight. Of interest is that the biggest influencers of foodborne infection risk were contamination load and processing temperature, not genotype. This suggests that understanding food chain dynamics would probably more effectively generate insight into foodborne risk than prescribing the hazard in ever more detail in terms of genotype.
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Affiliation(s)
| | - M. Crotta
- Royal Veterinary College, University of London, London, UK
| | - B. Wall
- Royal Veterinary College, University of London, London, UK
| | - L. Good
- Royal Veterinary College, University of London, London, UK
| | - S. J. O'Brien
- NIHR Health Protection Research Unit in Gastrointestinal Infections, UK
| | - J. Guitian
- Royal Veterinary College, University of London, London, UK
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Gale P. Could Bat Cell Temperature and Filovirus Filament Length Explain the Emergence of Ebola Virus in Mammals? Predictions of a Thermodynamic Model. Transbound Emerg Dis 2016; 64:1676-1693. [PMID: 27670273 DOI: 10.1111/tbed.12580] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Indexed: 02/07/2023]
Abstract
The host reservoir of Zaire ebolavirus (EBOV) remains elusive. One suggestion is that EBOV emerges in mammals when the precursor virus jumps from mayflies (or other riverine insects) to insectivorous bats. However, this does not fit with the current view that filoviruses cannot infect arthropods. Here, it is first argued that the evidence that arthropods are refractory is not definitive. Second, it is proposed that a combination of filovirus filament length and the high temperature (~42°C) experienced by an insect virus ingested by a flying bat, together with the large number of insects eaten by bats (e.g. during an ephemeral mass emergence of mayflies), facilitate jumping the species barrier. The length of a filovirus filament is related to the number of genome copies (GC). Predictions from a preliminary thermodynamic model developed here suggest that filament length could greatly affect EBOV infectivity to mammalian cells with infectivity peaking for filaments of a certain length. Importantly, the infectivity to mammals of even short filaments may be more than one million-fold higher than that for the single GC virion. Third, it is proposed that at the high temperature within the bat, the phospholipid phosphatidylserine in the virus envelope promotes filament formation through fusion of single GC particles within the ingested insect, thus hugely increasing their infectivity to bats. Forth, according to the thermodynamic model, increasing the temperature from 27°C (insect cell temperature at average air temperature in Guinea, West Africa) to 42°C (bat) could increase the affinity of the filaments for bat cells by 1-2 orders of magnitude, while having no effect on the binding affinity of the single GC virions. The thermodynamic model developed here is supported by the counterintuitive observation that high glycoprotein densities on the EBOV surface reduce its infectivity in contrast to other viruses such as HIV.
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Affiliation(s)
- P Gale
- Independent Scientist, Tilehurst, Reading, Berkshire, UK
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Snary EL, Swart AN, Hald T. Quantitative Microbiological Risk Assessment and Source Attribution for Salmonella: Taking it Further. RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2016; 36:433-6. [PMID: 27002671 DOI: 10.1111/risa.12605] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Affiliation(s)
- Emma L Snary
- Department of Epidemiological Sciences, Animal & Plant Health Agency (APHA) Weybridge, New Haw, Addlestone, Surrey, UK
| | - Arno N Swart
- RIVM - Centre for Infectious Disease Control, BA Bilthoven, The Netherlands
| | - Tine Hald
- Food-DTU - National Food Institute, Technical University of Denmark, Denmark
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Soumpasis I, Knapp L, Pitt T. A proof-of-concept model for the identification of the key events in the infection process with specific reference to Pseudomonas aeruginosa in corneal infections. Infect Ecol Epidemiol 2015; 5:28750. [PMID: 26546946 PMCID: PMC4636861 DOI: 10.3402/iee.v5.28750] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 10/16/2015] [Accepted: 10/16/2015] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND It is a common medical practice to characterise an infection based on the causative agent and to adopt therapeutic and prevention strategies targeting the agent itself. However, from an epidemiological perspective, exposure to a microbe can be harmless to a host as a result of low-level exposure or due to host immune response, with opportunistic infection only occurring as a result of changes in the host, pathogen, or surrounding environment. METHODS We have attempted to review systematically the key host, pathogen, and environmental factors that may significantly impact clinical outcomes of exposure to a pathogen, using Pseudomonas aeruginosa eye infection as a case study. RESULTS AND DISCUSSION Extended contact lens wearing and compromised hygiene may predispose users to microbial keratitis, which can be a severe and vision-threatening infection. P. aeruginosa has a wide array of virulence-associated genes and sensing systems to initiate and maintain cell populations at the corneal surface and beyond. We have adapted the well-known concept of the epidemiological triangle in combination with the classic risk assessment framework (hazard identification, characterisation, and exposure) to develop a conceptual pathway-based model that demonstrates the overlapping relationships between the host, the pathogen, and the environment; and to illustrate the key events in P. aeruginosa eye infection. CONCLUSION This strategy differs from traditional approaches that consider potential risk factors in isolation, and hopefully will aid the identification of data and models to inform preventive and therapeutic measures in addition to risk assessment. Furthermore, this may facilitate the identification of knowledge gaps to direct research in areas of greatest impact to avert or mitigate adverse outcomes of infection.
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Affiliation(s)
- Ilias Soumpasis
- Safety and Environmental Assurance Centre, Unilever, Sharnbrook, UK;
| | - Laura Knapp
- Safety and Environmental Assurance Centre, Unilever, Sharnbrook, UK
| | - Tyrone Pitt
- Clinical Bacteriology Consultant, London, UK
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