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2020/2021

Virology

Code: 100873 ECTS Credits: 6
Degree Type Year Semester
2500252 Biochemistry OB 2 2
The proposed teaching and assessment methodology that appear in the guide may be subject to changes as a result of the restrictions to face-to-face class attendance imposed by the health authorities.

Contact

Name:
Antonio Villaverde Corrales
Email:
Antonio.Villaverde@uab.cat

Use of Languages

Principal working language:
catalan (cat)
Some groups entirely in English:
No
Some groups entirely in Catalan:
No
Some groups entirely in Spanish:
No

Other comments on languages

Lectures and evaluations will be done in catalan and spanish, exclusively, at the discretion of the teaching staff. Teaching materials will be offered in English. The VIROLOGY from the Microbiology degree (101002) is offered in English.

Teachers

Neus Ferrer Miralles
Esther Vazquez Gomez

Prerequisites

A good knowledge of Microbiology, Biochemistry and Cell Biology and interest in Virology.

Objectives and Contextualisation

The teaching objectives of the course are the acquisition by the students of basic knowledge about biology, structure, genetics and evolution of viruses. This will be done within the framework of their pathogenesis and considering the pharmacological possibilities and research opportunities that Virology can offer in those fields. It will be also focused on emerging applications of the viruses in biotechnology and nanotechnology, and the need for constant updating of information through bibliographic databases.

 

 

Competences

  • Apply general laboratory security and operational standards and specific regulations for the manipulation of different biological systems.
  • Collaborate with other work colleagues.
  • Describe the structural, physiological and biochemical characteristics of the different types of cells and explain how their properties fit in with their biological function.
  • Integrate scientific and technological knowledge.
  • Manage bibliographies and interpret the information in the main biological databases, and also know how to use basic ICT tools.
  • Read specialised texts both in English and one’s own language.
  • Stay abreast of new knowledge of the structure, organisation, expression, regulation and evolution of genes in living beings.
  • Think in an integrated manner and approach problems from different perspectives.

Learning Outcomes

  1. Collaborate with other work colleagues.
  2. Define rules for the safe handling of microorganisms.
  3. Identify the genetic properties of microorganisms.
  4. Identify the genetic, physiological and metabolic properties of microorganisms that can potentially be used in biotechnological processes.
  5. Identify the physiological and metabolic characteristics of microorganisms.
  6. Master the nomenclature of microorganisms.
  7. Read specialised texts both in English and one’s own language.
  8. Think in an integrated manner and approach problems from different perspectives.

Content

1. An introduction to viruses and Virology

 

The world of viruses. Strict parasitism, multiplication and transmission. The viral disease and the concept of "iceberg". Viral diversity. The viral particle: size, chemical composition, morphology and nomenclature. Functions of the capsid, stability and recognition. Chemical composition, structure and organization of the viral genome: structural and non-structural genes. The polarity of the nucleic acid. The viral cycle: extracellular and intracellular phases. Virus multiplication:

productive and non-productive infection. Sequential expression of viral genes. Viruses, mobile genetic elements and living beings.

 

 

2. Historical overview of Virology

 

Hypotheses about the maintenance of life and spontaneous generation. The work of Pasteur. Microscopic infectious agents and Koch's postulates. The nineteenth century: the discovery of viruses. The tobacco mosaic virus: the concept of "filtrable infectious agent". Discovery of animal viruses. The twentieth century: characterization, chemical and genetic structure of viruses. Significant events in the history of virology. The eradication of smallpox and the risk of re-emergence. Clinical aspects of virology and biotechnology. Bioterrorism.

 

 

3. Viral multiplication

 

Cell recognition. Nature and function of receptors. Internalization. Uncoating. The cellular shutdown. Stimulation of cellular functions: papovavirus and adenovirus. Synthesis of RNA, DNA and viral proteins: temporal sequences. Cytopathic effects. Exit of viral particles with and without lysis. Apoptosis. Cellular transformationin RNA virus: cellular oncogenes,activation and transduction. Cellular transformation in DNA virus: viral oncogenes and oncoproteins. Processing of viral proteins. Targets for antiviral drugs. RNA interference.

 

 

4. Viral structure

 

Morphology of viral particles. Architectonic study of viral particles: electron microscopy and three-dimensional reconstructions. The X-ray diffraction: requirements and level of crystallographic resolution. Molecular architecture of helical and icosaedrical symmetry. Trans-membrane proteins in viral envelopes. Receptor binding sites. The viral antigens and epitopes B and T. The neutralization and evasion of antibody neutralization. Genetic and epitopic variability.

 

 

5. Viral genomes and genetics

 

Principles of economy and complexity of the viral genome, overlapping genes. Segmented and multipartite genomes. Sequencing of viral genomes and function prediction. Recombination, rearrangement and phenotypic mixing. Types of viral mutants. Defective viruses: integrated rearrangement and phenotypic mixing. Types of viral mutants. Defective viruses: integrated genomes, satellite virus and defective interfering particles. Complementation. The infectious clone. Gene expression in different types of viruses, temporary regulation strategies. Principles of reverse genetics. Tools for viral gene transfer and gene therapy. Presentation of antigen and peptides in recombinant viruses. Gene cloning and expression vectors of viral origin.

 

 

 

6. Origin and evolution of viruses

 

Origin of viruses and regressive theories for a cellular origin. Mechanisms of generation of diversity. Mutation frequencies and relative abundance of mutants. Fixation of mutations. Viral replicases and copying fidelity. Variability and evolution in RNA viruses and retroviruses. The viral quasispecies. Evolutionand evolutionary potential. Darwinian selection and Darwinian mutations. Founding effects and bottlenecks. Genetic and antigenic divergence, the influenza virus. Analysis of the viral phylogeny.

 

 

7. Emerging viruses and viral diseases

 

Emergence of new viral diseases. Host jump and viral reservoirs. Viral emergence and viral re-emergence. Environmental factors, social and technological factors. Importance of arthropod vectors. The human species as a terminal host. New emerging viruses and human viruses. Hemorrhagic fevers. The Ebola virus and human immunodeficiency virus. The new hepatic viruses. The continuing re-emergence of influenza virus and others.

 

 

8. Methods in Virology

 

Obtaining viral particles. The cell culture. Small and medium scale cell culture. Purification. Quantitative analysis of viral particles. Detection of viral components and applications in the diagnostic methodology. The virology laboratory: areas and distribution. The biological safety levels of containment: P1 to P4. Air treatment. Tributary treatment. Vaccine factories: industrial-scale up production of viral particles.

 

 

9. Viral taxonomy

 

Early classifications of viruses: Baltimore classification of animal viruses. The International Committee on Taxonomy of Viruses and the classification system. Properties used in viral taxonomy. Families of animal viruses and viruses not classified. The major human pathogens and their diseases.

 

 

10. Prions and viroids

 

Infectious proteins: the prion. Development of the prion concept. The amyloid. Synthesis and processing of PrPc. PrPsc formation and propagation of prions. Spongiform encephalopathies: inheritance and contagion. Phenotypic diversity of prions; strains. The "scrapie" and bovine spongiform encephalopaty. Interspecific barriers. The human spongiform encephalopathies: Kuru, Creutzfeldt-Jakob disease and hereditary diseases. Prions in yeast. Viroids: structure and consistency of domains. Possible pathogenetic mechanisms. The hepatitis delta.

 

 

11. Bacteriophages

 

Use of bacteriophages in molecular genetics and biotechnology. The "Phage Display". The generation of antibodies without immunization and the search for new ligands. Directed molecular evolution. Systems of selection of antiviral drugs: the case of protease inhibitors.

 

 

12. Viral pathogenesis

 

Characteristics of viral infections. Entry routes. Localized and systemic infections. Invasiveness. Viremia. Nerve transmission. Target tissues: tropism. Virulence. Role of organic response in the pathogenesis. Infection: transmission routes. Vectors and reservoirs. Persistent viral infections, mechanisms of persistence. The measles virus. The Epstein-Barr virus.Viral hepatitis. HIV infection; dynamic aspects of persistence. The movement of plant viruses.

 

 

13. Responses to viral infection

 

Non-specific antiviral mechanisms. Induction and activity of interferons. Induction and evolution of the immune response. Role of antibodies and T cells. Prophylaxis of viral infections: vaccination. Types of vaccines: attenuated and inactivated. Polio vaccines. Molecular basis of attenuation. New generation vaccines. Antigens and immunogens. Recombinant proteins and peptides. Pseudo-capsid vaccine. The vaccine against hepatitis B and papilloma viruses.

Vaccination with DNA.

 

 

14. Artificial viruses

 

Viral gene therapy; important features and biological risks. Artificial viruses as alternatives to viral gene therapy. Types of artificial viruses and used biomolecules. Modular strategies. Selection of functional domains. Examples and applications of artificial viruses.

 

“*Unless the requirements enforced by the health authorities demand a prioritization or reduction of these contents.”

 

Methodology

Classes will be distributed over 3 hours per week, of which 2 will correspond to master classes and 1 to the resolution of problems, group work in the classroom and presentation of oral works.

 

“*The proposed teaching methodology may experience some modifications depending on the restrictions to face-to-face activities enforced by health authorities.”

Activities

Title Hours ECTS Learning Outcomes
Type: Directed      
Preparation and public presentation of works and projects 45 1.8 2, 6, 5, 3, 4
Room or remote lectures 48 1.92 1, 7, 8
Type: Supervised      
Text reading 50 2 1, 7, 8

Assessment

The assessment will be done through 3 exams, two non-eliminatory partials and one final exam which will include the third part and a synthesis exam. Exams will be distributed during the course, with a total weight on the final mark of 70% (15%, 15% and 35 + 5% respectively). In addition, 30% of the mark will be obtained by the oral presentation of works and solving classroom problems or presenting written works. For these activities (30%) recovery will not be programmed. 

The recovery exam will be a test type and can only be accessed by students who have failed the overall grade for the course, but have at least 3.5 on the overall grade. In compliance with article 112 ter point 2 of the UAB Academic Regulations in force, to participate in the recovery, students must have previously been evaluated in a group of activities the weight of which equals a minimum of two thirds of the total grade for the course or module. Therefore, the students will obtain the grade of "No Evaluable "when the evaluation activities carried out have a weight lower than 67% in the final grade.

 

“*Student’s assessment may experience some modifications depending on the restrictions to face-to-face activities enforced by health authorities.”

Assessment Activities

Title Weighting Hours ECTS Learning Outcomes
Final exam: 3 partial + syntesis test. Test exams 40 % 2 0.08 2, 6, 5, 3, 4
Oral and/or written presentation 30 % 3 0.12 1, 7, 8
Partial exams. Multiple choice 30 % 2 0.08 1, 6, 5, 3, 7, 8

Bibliography

A. Granoff and R.G. Webster. (Constantment actualitzada i ampliada). Encyclopedia of virology (on-line Ed.) Academic Press. London.

(http://www.sciencedirect.com/science/referenceworks/9780123744104)

A. J. Cann. 2015. Principles of molecular virology. (6th Ed). Academic Press. London. (http://www.sciencedirect.com/science/book/9780123849397)

S. J. Flint i altres. 2015. 4th Edition. Principles of virology: Molecular biology (volume I), pathogenesis and control (volume II). ASM Press. Washington.

E. Domingo, Virus as Populations: Composition, Complexity, Dynamics, and Biological Implications, Academic Press, 2015.

I.W. Fong, Emerging Zoonoses: A Worldwide Perspective, Springer, 2017. https://mirades.uab.cat/ebs/items/show/164887 

G. Rezza, G. Ippolito, Emerging and Re-emerging Viral Infections: Advances in Microbiology, Infectious Diseases and Public Health Volume 6, Springer, 2017.

P. Tennant, G. Fermin, J.E. Foster, Viruses; molecular biology, host interactions, and applications to biotechnology, Academic Press, 2018

S. Howley, D. Knipe, S. Whelan, Fields VIROLOGY - Vol.1. Emerging Viruses. 7th Edition. Wolters Kluver, 2021.

G. Fermin, G. 2018. Viruses. Elsevier. https://mirades.uab.cat/ebs/items/show/155194