Advanced General Virology


Date: Wednesday, March 25, 2020.

Dear future colleagues,

For every cellular organism on this earth, there is a virus. Viruses impact our health, economy, and environment. Many viruses are looked upon as dangerous threats because numerous viruses cause devastating human, animal, and plant diseases; SARS-CoV-2 is a clear and present danger that demonstrates this perfectly. However, viruses are, in fact, one of the guardians of the planet's ecosystems. How this is done is indirect. For example, microorganisms constitute more than 90% of the biomass in the sea. It is estimated that viruses kill approximately 20% of this biomass each day and they are the main agents responsible for the rapid destruction of harmful algal blooms, which often kill other marine life. The effects of marine viruses are far-reaching; by increasing the amount of photosynthesis in the oceans, viruses are indirectly responsible for reducing the amount of carbon dioxide in the atmosphere by approximately 3 gigatons of carbon per year . In addition, endogenous viral elements (EVE) are responsible for tuning the host immune responses and for enhanced responses to poorly immunogenic antigens, such as T cell-independent type 2 antigens or tumors .

The study of viruses has given man insights into a myriad of sciences and applications. Major developments in immunology, molecular biology, vaccinology, mutation, evolution, and even material sciences and nanotechnology, were only possible by the study of virus models. It is for this reason that we will focus our study on the basic concepts of virology without venturing too far into diseases caused by viruses (other courses will be more appropriate for that).

I will try to integrate applied information into every concept discussed. I will also make sure that the practical aspects of the science (e.g. in-vitro cultivation, and molecular diagnosis) are discussed alongside the theoretical subjects. However, because of time limitations, some important topics related to the science will be left for future courses (e.g. principals of vaccine design).

As you shall soon discover, there is a lot to be gained by our study of viruses on the personal and national levels. Virology is an integral part of many of today’s problems and biotechnological solutions; therefore, it is an integral part of our program at the Faculty of Veterinary Medicine, Cairo University. I wish you all the best of luck in your endeavor for knowledge and understanding.

Course objectives

1. To help students understand the impact of viruses on the earth and all its inhabitants.
2. To explain the basics of virus structure.
3. To allow students to understand the bases of virus classification.
4. To discuss select models of viral replication strategies.
5. To help students understand select models of pathogenesis of viral infections.
6. To outline the immune response to viral infections and select models of viral evasion of the immune response.
7. To give students an in-depth view of the mutation and evolution of segmented viruses using the influenza model.
8. To discuss the bases of viral zoonoses.
9. To discuss the basic concepts of virus identification and characterization.
10. To allow students to practice virus cultivation and purification (however, this will be subject to relief of control measures implemented to slow the spread of SARS-CoV-2 the cause of COVID-19).
11. To overview strategies for control of viral infections in human and animal models.

Course Requirements and Policy
1. Because of the current pandemic, we will have to communicate primarily via emails. However, every week we will join an online conference to discuss the concepts that may be hard for you to grasp on your own; that includes some of the reading assignments that you will be given. Teaching, exams, and reports will be in English.
2. The course format is based on discussion of key papers reporting one or more aspects of basic virology.
3. You will be given guidance how to get the course material (see below) early in the course. You are required to read it. Several exam questions will involve concepts discussed in the journal articles assigned to you.
4. You are required to make a short scientific review* (3 pages, single spaced, 12 pts, Times New Roman) on a topic related to the molecular basis for epidemiology or zoonosis.
5. You are required to suggest a one-page experimental design* to attempt solving one of the problems you see relevant to the topic you have reviewed. I imagine that you will find ample questions to ask in the age of COVID-19. Your experimental design could be a solution to
6. There will be two pop exams* to access what you really absorbed during our contact and to determine what needs to be done to improve the outcome of your learning activities. The exams are not mandatory; however, your scores in these exams will be added to your total sum in the form of extra-credit points. Please, take them seriously.
7. Practical parts related to vaccine development and testing will be given by our colleague Dr. Basem Abdel-Hamid. It is likely that this semester we will use online material due to the pandemic.
8. Plagiarism is prohibited and will not be tolerated. The simplest description of plagiarism is defined by “claiming that something is yours while it is the work and thought of someone else”. You MUST think, write using your own style, and reference people that have helped you create your own ideas and style. YOU WILL FAIL IF YOU COMMIT PLAGIARISM.

Course material
Reading assignments (required):
1. Generation of Synthetic Severe Acute Respiratory Syndrome Coronavirus Pseudoparticles: Implications for Assembly and Vaccine Production. J Virol. 2004 Nov; 78(22): 12557–12565. doi: 10.1128/JVI.78.22.12557-12565.2004.
2. Replication of not-known-vector flaviviruses in mosquito cells is restricted by intracellular host factors rather than by the viral envelope proteins. Journal of General Virology (2010), 91, 1693–1697 DOI 10.1099/vir.0.019851-0.
3. SARS-Coronavirus Replication Is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum. 2008.
4. The proximal origin of SARS-CoV-2. Nature Medicine (2020). Published: 17 March 2020.

Recommended course material:
5. Fenner's Veterinary Virology - 4th Edition. N. James Maclachlan and Edward J. Dubov. Academic Press 2011. ISBN: 9780123751584.
6. Principles of Molecular Virology. 4th Edition. Alan J. Cann. Elsevier Academic Press. 2005. ISBN (Standard Edition): 0-12-088787-8.

*Activities and % of final grade:

% of grade Objective Activity
10% Practice scientific communication skills. Encourage creative thinking. Practice reporting and organization. Short Report.
10% Encourage creative thinking. Practice reporting and organization. Experimental Design (written).
10% Measure student progress. Measure course progress. Discussion of assigned journal articles (#=4).
20% Measure ability to apply practical knowledge. Laboratory Exam
50% Measure student outcome, and rank students. Final Exam
Extra Credit 2.5% Encourage regular study, creative thinking. Pop test 1
Extra Credit 2.5% Encourage regular study, creative thinking. Pop test 2

Contact information:
Please, use the e-mail to schedule an online appointment.

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