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Code: 101002 ECTS Credits: 6
Degree Type Year Semester
2500502 Microbiology 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.


Neus Ferrer Miralles

Use of Languages

Principal working language:
english (eng)
Some groups entirely in English:
Some groups entirely in Catalan:
Some groups entirely in Spanish:

Other comments on languages

Classes are given in English


Antonio Villaverde Corrales
Esther Vazquez Gomez


Is essential to have a good level of spoken and written English and a general background in Biochemistry, Molecular Biology, Cell Biology, Microbiology and Immunology.

*All teaching activities and assessments will be carried out in English in any context (face-to-face, semipresential or online).

Objectives and Contextualisation

The teaching objectives of the course are the acquisition by students of basic knowledge about the biology, structure, genetics and evolution of viruses within the framework of its pathogenesis and pharmacological possibilities and research opportunities 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.


  • Apply microorganisms or their components to the development of products of interest in health, industry and technology.
  • Apply suitable methodologies to isolate, analyse, observe, cultivate, identify and conserve microorganisms.
  • Characterise the causal agents of microbial diseases in humans, animals and plants in order to diagnose and control them, perform epidemiological studies and be aware of present-day problems with these diseases and strategies to combat them.
  • Identify the molecular mechanisms of pathogenesis and relate them to the response to infection in order to design and develop strategies for diagnosing and combating diseases caused by microorganisms.
  • Obtain, select and manage information.
  • Use bibliography or internet tools, specific to microbiology or other related disciplines, both in English and in the first language.
  • Work individually or in groups, in multidisciplinary teams and in an international context.

Learning Outcomes

  1. Identify and describe the microorganisms used in bioterrorism.
  2. Identify the techniques used in the conservation and storage of microorganisms.
  3. Identify the techniques used in the multiplication, detection and identification of viruses.
  4. Identify viral elements that are useful for the design of antigens, immunogens and vaccines.
  5. Identify viral elements that are useful for the design of diagnostic reagents.
  6. Know and identify the biotechnological and nanomedical applications of viruses in microelectronics, as biosensors and for controlled drug delivery.
  7. Know the molecular bases of viral invasiveness and virulence and recognise the value of attenuated viral variants in vaccine design.
  8. Know the molecular processes of the viral cycle and identify the potential targets of antiviral drugs.
  9. Know the most important groups of pathogenic microorganisms.
  10. Obtain, select and manage information.
  11. Understand the microbiological bases that are used to develop products of interest in healthcare.
  12. Use bibliography or internet tools, specific to microbiology or other related disciplines, both in English and in the first language.
  13. Use omics techniques for identifying target genes and proteins related to pathogenicity and virulence, and usable in the design of vaccines and antimicrobial compounds.
  14. Work individually or in groups, in multidisciplinary teams and in an international context.


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.”


The course will comprise classroom lectures and active learning activities with scientific problems and cases by which students will acquire skills necessary to perform literature research, propose experimental approaches and design problem solving strategies. Oral presentations of active learning activities will encourage teamwork, coordination of activities and rational presentation of work plans and results. Active learning activities will be focused on methodological aspects and biomedical, biotechnology, pharmaceutical and nanotechnological applications of virus as well as derived viral structures. Personal tutorial guidance sessions will be available by email appointment and will be held in the office C3/331. In those sessions, students will have the opportunity to receive individual guidance according to their needs.

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


Title Hours ECTS Learning Outcomes
Type: Directed      
Active learning activities 15 0.6 10, 14, 12
Lectures 30 1.2 11, 9, 8, 6, 7, 4, 5, 1, 2, 3, 13
Type: Supervised      
Personal tutorial guidance sessions 2 0.08 11, 9, 8, 6, 7, 4, 5, 1, 2, 3, 10, 14, 12, 13
Type: Autonomous      
Group work: preparation of written reports 2 0.08 10, 14, 12
Literature search 28 1.12 10, 12
Personal study 44 1.76 11, 9, 8, 6, 7, 4, 5, 1, 2, 3, 13
Preparation of oral and written presentation of reports 1 0.04 10, 14, 12
Reading 23 0.92 10, 14


The evaluation will be done through one midterm exam (20 %) and one final exam (50 %). The sum of the marks obtained in the evaluation of all written exams will represent 70 % of the final grade. Remedial exam will not be scheduled for the midterm exam (20 %). Remedial exam will be scheduled for the final exam (50 %). The mark obtained in the final exam (or remedial exam) must be higher than 4.0 to be used in the final mark calculation. In the case of obtaining a lower mark than 4.0 in the final exam (or remedial exam), provided the weighted average of all the activities is below 4.5, the maximum mark would be 4.530 % of the grade will be obtained by oral and written presentations of assignments and classroom problem-solving activities, remediial exams will not be scheduled for any these activities.  
Evaluation of classroom lecture competencies (70 % of final grade)
-During the course two written tests will be scheduled for this evaluation form. The first test will have a weight of 20 % and the second (final exam) a weight of 50 %. To be eligible for the retake process (final exam), the student should have been previously evaluated in a set of activities equaling at least two thirds of the final score of the course or module.Thus, the student will be graded as "Not Evaluable" if the weighting of all conducted evaluation activities is less than 67 % of the final score.
Evaluation of oral and written presentations (30 % of the final grade)
-Students will present the reports of the assigned active learning exercises in classroom sessions. Oral presentations will be evaluated on content, organization and communicative skills. Additional written reports will be evaluated on content and organization.
Delay in the delivery of activity assignments will represent a 100 % reduction in the mark obtained in the evaluated activity.

EXAM TO GET A HIGHER GRADE: All those students who have passed both theory exams may retake the final exam to improve the grade of the subject. The student who wants to raise the mark (only theory) may re-examine the final exam (50 %) as long as he or she has expressed in writing (email) his/her willingness to take the exam tothe coordinator of thesubject at least ten days before the final exam. By taking the exam in order to get a higher grade, the student implicitly renounces the grade he or she had obtained in the final exam. The grade that will be taken into account will be that of the last exam the student has taken. There is no option to improve the other grades.


 “*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
Evaluation of group assignements: written report 20 % 0 0 10, 14, 12
Final exam: multiple choice 50 % 3 0.12 11, 9, 8, 6, 7, 4, 5, 1, 2, 3, 13
First midterm exam: multiple choice 20 % 2 0.08 9, 7, 1, 2, 3
Oral and/or written presentation of reports 10 % 0 0 10, 14, 12


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-A.J. Cann. 2015. Principles of molecular virology. 6th Ed. Elsevier Academic Press, Amsterdam.
-A. J. Cann. 2012. Principles of molecular virology. 5th Ed. Academic Press, Waltham, MA. https://www.sciencedirect.com/science/book/9780123849397
-A.J. Cann (traducción de Javier Buesa Gómez). 2009. Principios de virología molecular. Acribia DL, Zaragoza, .
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-S.J. Flint, G.F. Rall, V.R. Racaniello, A.M. Skalka, L.W. Enquist. 2015. Principles of virology, V.1, ASM Press, Washington DC. https://ebookcentral.proquest.com/lib/uab/reader.action?docID=6037145
-S.J. Flint, G.F. Rall, V.R. Racaniello, A.M. Skalka, L.W. Enquist. 2015. Principles of virology, V.2, ASM Press, Washington, DC. https://ebookcentral.proquest.com/lib/uab/reader.action?docID=6029122
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