VIRO3001/3901 Unit of Study Handout!

24th Jan 2012

School of Molecular Bioscience

Virology VIRO3001/ Virology (Advanced) VIRO3901
Semester 1, 2012

Unit of Study Summary

This Unit of Study is an introduction to the field of virology and serves as a basis, and is
a strongly recommended prerequisite, Medical and Applied Virology VIRO3002 offered in
Semester 2.
Virology VIRO3001/VIRO3901 encompasses 4 themes: Virus Classification, Structure
and Replication; Animal, Plant and Bacterial Viruses; Concepts of Host/Pathogen
Interactions; and Methods and Techniques in Virology.
Virus Classification, Structure and Replication: defines what viruses are and
how they are classified and introduces common characteristics of various types
of viruses, from their taxonomy and structure, to their genome and how their
type impacts on replication and viral gene expression.
Animal, Plant and Bacterial Viruses: examines viruses from the perspective
of host-range, with particular emphasis on how host biology shapes viral
replication and poses unique challenges to productive virus infection.
Concepts of Host/Pathogen Interactions: this theme illustrates fundamental
concepts in viral/host interactions, highlighting viruses associated with human
diseases. The immune response to viral infection will be introduced as well as
concepts such as viral latency, recombination, cell transformation, methods to
control virus infection and the emergence/re-emergence of novel viruses. Prions
and unusual infective agents will also be discussed.
Methods and Techniques in Virology: this final theme covers currently used
techniques in virology research as well as recent advances in the field. Lectures
in this theme will provide a background and theoretical basis for practical
sessions that run concurrently with core lecture delivery.
The hands-on practical component is designed to enhance students practical laboratory
skills and to complement the lecture series by giving students practical experience in
important laboratory techniques. Tutorials will involve student research presentations on
selected topics.

Teaching Objectives

Teaching in this Unit of Study is aimed at introducing students to the principles of virology
including:
1. The structure and replication mechanisms of various viruses
2. Viruses of bacteria, plants and animals
3. Techniques used in virology research
4. Viruses relevant to humans and their control

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VIRO3001/3901 Unit of Study Handout! 24th Jan 2012

Learning Outcomes
After completion of this VIRO3001, students should be able to:
define the key characteristics of viruses that distinguish them from other agents
of disease such as bacteria, sub-viral particles and prions
explain how different classes of viruses replicate, and the impact of genome
type on replication and virus structure
explain how the immune system is able to combat viral infections and confer
immunity, and the various ways viruses have evolved to circumvent this control
mechanism
perform basic cell culture, fluorescence microscopy, diagnostic and molecular
techniques used in a modern virology laboratory, and understand the scientific
principles behind these techniques
explain how anti-viral drugs and vaccination act to limit virus replication
explain how viral diseases emerge and the threat posed to public health
Students who complete VIRO3901, should additionally be able to:
critically evaluate primary scientific literature
explain how different scientific approaches are used to support a hypothesis,
using illustrative examples

Quality of Teaching in this Unit of Study

Principles
To enhance and facilitate learning in VIRO3001/VIRO3901, students will experience a
Unit of Study that:
1. has been designed by experienced educators based on pedagogical principles
2. is enriched with a range of formal and informal learning experiences, face-to-
face and online
3. provides up-to-date information, strategies and technologies that are relevant to
the current scientific community
4. encourages a research-based approach to the study of viruses
5. strives to provide the best possible learning environment
Evaluation
This Unit of Study will be evaluated annually using either the standard Institute for
Teaching and Learning Unit of Study Evaluation Surveys or a discipline-based request
for feedback and comment. The outcomes of this Evaluation/feedback will be acted upon
and implemented in a timely fashion as appropriate.

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VIRO3001/3901 Unit of Study Handout! 24th Jan 2012

Reaction to student feedback

VIRO3001/VIRO3901 strives to become a dynamic unit of study and continual feedback
will be sought and suggestions to improve effectiveness of teaching and learning will be
implemented.
Suggestions obtained from previous student feedback from other units of study in the
Discipline of Microbiology that have been adopted for VIRO3001/VIRO3901 include:
the unit is web-based for greater flexibility and accessibility of unit support
material, and recordings of lectures and lecture summaries
the lecture and practical content has been designed into theme areas and
includes scientifically up-to-date and interesting material relevant to the fields of
general and some medical virology, delivered by active researchers
tutorials have been designed to encourage active student involvement
emphasis of assessment will be on understanding the presented material rather
than on regurgitation of the information
implementation of online formative self-assessment
constructive feedback on progress will be provided to all students in a timely
fashion
Statement by Unit of Study Coordinator
I am committed to effective University teaching of the highest standard and have an
open-door policy for student consultation. I am striving to improve the quality of teaching
and learning in this Unit of Study in order to encourage students to learn effectively. All
staff teaching in this Unit supports this process.
I trust that students will be challenged in VIRO3001/VIRO3901 to reach their full
potential and enjoy themselves in the process.
Dr Tim Newsome, Unit of Study Co-ordinator.

Contact

Web Pages: eLearning

Unit of Study Co-Ordinator:
Dr Tim Newsome
Rm 562, Biochemistry/Microbiology Building G08
Email: tim.newsome@sydney.edu.au, phone: 9351-2907
Teaching Assistant:
Dr Deborah Blanckenberg
Room 535, Biochemistry/Microbiology Building G08
Email: deborah.blanckenberg@sydney.edu.au, phone: 9351-2540
Administrative Assistant (Student Service):
Room 435, Biochemistry/Microbiology Building G08
Phone: 9036-5417; FAX: 9351-4726
Additional lecturers:
A/Prof Allison Abendroth A/Prof Barry Slobedman
Dr Russell Diefenbach Prof Peter Waterhouse
Dr Jacquelyn Horsington A/Prof Kevin Downard
Dr Gary Muscatello Prof Peter Reeves

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VIRO3001/3901 Unit of Study Handout! 24th Jan 2012

Lectures

VIRO3001/3901: Lectures will be held at 10AM on Thursdays and Fridays at 10AM in

Carslaw Lecture Theatre 373.
VIRO3901 only: Lectures in the advanced lecture series will be held on Monday at
10:00am in New Law School Annexe SR 340 in teaching weeks 3 and 913 only.
See the schedule at the end of this document for exact dates of lectures. Attendance is
strongly recommended for a full understanding and engagement of the material
delivered.

Practical Classes and Tutorials

Students are required to bring their own lab coat to the practical classes and
tutorials. Failure to do so will result in exclusion from the session in compliance
with the Australian Standards for Safety in Microbiological Laboratories AS/NZS
2243.3: 2003.
Practical Classes start in Week 2 and will be held on Thursday OR Friday from 1:00
5:00 pm in Lab 542 (level 5) or 300 (level 3) in the Biochemistry and Microbiology
Building GO8. Students will be centrally allocated to one of these sessions. The practical
classes are designed to complement and enhance the theoretical background provided
in the lectures and give the opportunity of hands-on experience in some of the current
and cutting-edge virology techniques.
The six practical classes will cover:
sterile techniques of eukaryotic cell culture including passaging adherent cell
lines, counting cells using a haemocytometer with phase contrast microscopy
and assessing cell viability using Trypan Blue exclusion
observing various cytopathic effects on host cells caused by viruses and
determining PFU using a plaque assay
understanding and performing of serological techniques such as the
haemagglutinin assay and ELISA test to determine the presence of viral
agents
enhanced knowledge of currently used molecular biology techniques in
virology including PCR, fluorescence microscopy and immunoblotting with one
detailed hands-on example for each application.
Attendance at practical classes will require electronic submission of a small number of
pre-class questions addressing safety and the background to the practical class. These
also form part of the assessment for this unit of study. Practical classes 13 will include a
short piece of continuous assessment based on the practical class to be handed in by
the end of the class. Assessment for practical classes 46 will comprise a written project
report covering material from these classes.
Tutorials form part of the practical course and will be held on 3 specified days (see
practical schedule at the end of this hand-out). These will be held from 1:003:00pm (in
your usual practical allocated time) on Thursdays OR Fridays in weeks 1012. Students
will be assigned into small groups of 3-4. Each group will select from a list of supplied
topics, that will be available during the first practical class, an area on which they will
research and then present a short (15 minute) Powerpoint presentation to the rest of the
demonstrator group. Presenting research results orally is an important way of
communicating data and ideas, and students in this Unit will have the opportunity to
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VIRO3001/3901 Unit of Study Handout! 24th Jan 2012

learn how to effectively communicate these. The presentation will be assessed and will
contribute to the practical component. Attendance by all students at the tutorials is
expected and forms part of the continuous assessment.

Practical Manual

A printed practical manual will be provided free-of-charge in the first practical session. An
online version of the practical manual will also be available via the online PebblePad
portal (a link will be provided on the VIRO3X01 eLearning site).

Textbooks

Recommended Textbook:
Introduction to MODERN VIROLOGY by N.J. Dimmock, A.J. Eaton & K.N. Leppard; 6th
ed 2007, Blackwell publishing. Approximately $65 from Co-op Bookshop.
We have recently integrated this textbook due to a significant escalation in price of the
new edition of the previous textbook, nonetheless Flint (see below) is an excellent
textbook and students planning on taking VIRO3001 and 3002 might find the purchase
of a new or second-had copy worthwhile as Flint is an extremely comprehensive text that
deals with many topics more thoroughly than Dimmock. Copies of Dimmock and both
editions of Flint are available in the Medical and SciTech libraries.
Reference Books:
Principles of Virology - Molecular Biology, Pathogenesis, and Control of Animal Viruses
by Flint, S. J.; Enquist, L.W.; Racaniello, V. R., and Skalka, A. M.; 2nd ed., 2004, ASM
Press. 3rd edition available 2009.
Basic Virology by Wagner, E.K. et al; 3rd ed., 2008, Blackwell.
Virus Taxonomy by Fauquet C. et al; 2005, Elsevier.
Several copies of all the above books are available in Medical and SciTech libraries.

Deadlines

Assignments and Reports must be handed in by certain deadlines. Failing to meet these
deadlines will incur mark deductions of 10% of the total mark available for every day past
the due date. Deadlines are the absolute latest time points by which such assignments
need to be submitted without being penalised, but early submissions will be gladly
accepted. Refer to policies on the VIRO3001 eLearning website.
Pre-class assessments for practical classes 1-5 must be completed and submitted
electronically at 5pm the day before the relevant class.

Special Consideration

Any student who believes that their performance has been or may be adversely affected
by illness or other misadventure may request special consideration to the circumstances
from the Faculty. Such a request must be made following the guidelines below within
seven (7) days of the assessment task for which you are seeking consideration (ie
7 days from the assignment due date or date of examination) and must be accompanied
by appropriate documentary evidence (eg medical certificate, police report, or other)
For detailed guideline refer to:
University of Sydney guidelines for Special Consideration

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VIRO3001/3901 Unit of Study Handout! 24th Jan 2012

School of Molecular Bioscience guidelines for Special Consideration

Attendance Requirements

All students are expected to attend all lectures, practical classes, tutorials, and case
studies. A variety of notes, handouts, data sheets, and information provided throughout
the Unit of Study are intended to supplement the lectures not to substitute for them.
Absences from all scheduled practical sessions, tutorials and case studies must be
explained and supported by appropriate documentation.
Even if special consideration has been granted, it is the students responsibility to know
and understand the material covered in the missed session.
Please note that the Faculty of Science has a minimum 80% attendance requirement for
a student to pass any unit of study (Faculty of Science Handbook 2012).

Unit of Study Standards

The grade descriptors for this unit are in line with the University of Sydney Academic
Board Resolutions for Assessment.
The following Grade Descriptors are to be read in conjunction with the specific criteria
and learning outcomes being assessed for each assessment task. Taken together,
these will indicate to you how we have gone about assessing your work in this unit.
Grade Descriptors Explanation / Interpretation
High distinction Work of exceptional standard Complete mastery of topics showing extensive assimilation; treatment of tasks
(85-100) show an advanced synthesis of ideas; demonstration of initiative, complex
understanding and analysis; work is well presented; all criteria addressed and
learning outcomes achieved to a high level
Distinction Work of superior standard Excellent achievement, consistent evidence of deep understanding and
(75-84) application of knowledge; treatment of tasks show advanced understanding of
topics; demonstration of initiative, complex understanding and analysis; work
is well-presented; all criteria addressed and learning outcomes achieved
strongly
Credit Highly competent work Confident in explaining microbial processes, with evidence of solid
(65-74) demonstrating potential for higher understanding and achievement; occasional lapses indicative of unresolved
study issues; treatment of tasks show a good understanding of topic; work is well-
presented with a minimum of errors; all criteria addressed and learning
outcomes achieved clearly
Pass Work of acceptable standard Satisfactory level of engagement with and understanding of topic; some
(50-64) inconsistencies in understanding and knowledge of microbes in infection; work
is adequately presented, with some errors or omissions, most criteria
addressed and learning outcomes achieved adequately
Fail Work not of acceptable standard Unsatisfactory achievement and engagement with the discipline; inadequate
(<50) or fundamental misunderstanding of topics; most criteria and learning
outcomes not clearly or adequately addressed or achieved; lack of effort/
involvement in the unit

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VIRO3001/3901 Unit of Study Handout! 24th Jan 2012

Assessment

Task Purpose Due Date Weight

Practical: 40% total
Pre-class Preceding Practical classes 1-5 students are required to 5pm the day 5 x 1%
assessment complete a brief very short answer/MCQ assessment covering before Prac
safety aspects of the upcoming class and familiarity with the
procedural and theoretical aspects experiments to be
undertaken. Completion of the pre-class assessment is a
requirement for attendance and students will receive feedback
based upon their performance.
Continuous This assessment tests the students comprehension of the End of Pracs 3 x 2%
assessment background material, the results obtained and their interpretation 1-3
and assimilation of the results. There is a continuous
assessment for Practical classes 1-3 and they must be handed
in by the end of class and students will receive feedback on their
performance.
Project This assessment replaces the continuous assessment for 5pm, 21st May 7%
Practical classes 4-6, which are thematically linked and involves
the characterisation of a recombinant virus through classical and
modern virological techniques.
Presentations This is a group activity (3-4 students) and concerns the Submitted 5pm, 7%
presentation of a primary piece of literature including the 14th May.
analysis experimental techniques used in current virological Delivered
research, linking the theory covered in the core lecture stream Weeks 10-12
with the techniques studied in the Practical classes.
Theory of Qualitatively assess achievement of unit learning outcomes of Formal exam 15%
Prac exam your: period
Understand and apply the scientific principles behind basic
cell culture, fluorescence microscopy, diagnostic and
molecular techniques used in a modern virology laboratory.
Identify and apply the concepts of positive and negative
controls to experiments conducted in virological research
This assessment comprises 20 multiple choice questions (no
negative marking). A more detailed description of learning
outcomes is found in summaries in the Practical class manual.
eLearning This assessment will provide formative assessment in the style Available Week Formative
quiz of the Theory of Prac exam and cover the learning outcomes 10
(see above) of this part of the course. The quiz is optional and
can be attempted an unlimited number of times and online
feedback is provided.

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VIRO3001/3901 Unit of Study Handout! 24th Jan 2012

Theory: 60% total

Theory Qualitatively assess achievement of unit learning outcomes of Formal exam 60% total
examination your: period
define the key characteristics of viruses that distinguish
them from other agents of disease such as bacteria, sub-
viral particles and prions
explain how different classes of viruses replicate, and the
impact of genome type on replication and virus structure
explain how the immune system is able to combat viral
infections and confer immunity, and the various ways
viruses have evolved to circumvent this control mechanism
explain how anti-viral drugs and vaccination act to limit
virus replication
explain how viral diseases emerge and the threat posed to
public health
This assessment comprises 40 multiple choice questions (no
negative marking) and 8 short answer questions. A more detailed
description of learning outcomes is found in lecture summaries.
eLearning These assessments will provide formative assessment in the Available Formative
quiz style of the Theory examination and cover the learning outcomes Weeks 5, 10
(see above) of this part of the course. The quizzes is optional and 13
and can be attempted an unlimited number of times and online
feedback is provided.Three quizzes are provided that each cover
approximately a third of the core lecture series.
The Theory of Prac exam (30 minutes) and the Theory exam (120 minutes) will be held as
a single exam paper during the formal examination period.
To pass VIRO3001 students must pass the Practical assessment AND pass the Theory
assessment.
Additional Assessment task for VIRO3901students only:
In Week 13, VIRO3901 students will sit a short theory exam and be required to:
Answer 1 from 2 essay questions based on VIRO3901 advanced lecture series,
a
A mark in excess of 65% achieved in the essay will achieve a bonus of up 7
marks to be added to the total mark for the theory component of the
assessment. To pass VIRO3901 students must pass the essay question based
on the advanced lecture series, fail to do so will result in the student being
assessed as VIRO3001 students.
For all students:
At the end of semester all marks may be scaled in accordance with Faculty of Science
guidelines.
In the case of further assessment required due to illness or misadventure, these may take
the form of written and/or oral examinations and will be held in the week commencing 2nd
July,012.

Plagiarism Policy

A summary of examples of plagiarism and means to avoid them that are appropriate for
students enrolled in the Faculty of Science Handbook 2012.
With each item of assessment that you submit, you will be required to attach a signed
compliance statement agreeing that you have read, understood and have complied with
this plagiarism policy.

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VIRO3001/3901 Unit of Study Handout! 24th Jan 2012

Language

Students from non-English speaking backgrounds who experience difficulties with writing
skills, comprehension, communications or examinations are encouraged to seek help
from the Learning Centre.
Students born outside Australia, even if they do not experience difficulties in
understanding, writing or expressing themselves, may be particularly vulnerable in an
examination where the emphasis is on rapid and succinct expression.

4th Year Honours

Students interested in the Microbiology Honours Program should contact Dr Tim

Newsome or Dr Hannah Nicholas.

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 Week Date Lectures Practicals Tutorials 3901 Lectures
1-5PM Thursday/Friday 1-3PM Thursday/Friday 10AM Monday
10AM Thursday 10AM Friday Lab 300/542 G08 T.B.C. New Law School SR 340
Carslaw LT 373 Carslaw LT 373

Week 1 5-Mar 1 Course Intro 2 Intro to Viruses

Tim Newsome Tim Newsome

Week 2 12-Mar 3 Classification 4 Virus Structures Practical Intro

Tim Newsome Tim Newsome

Week 3 19-Mar 5 Cell Culture 6 DNA Viruses Practical 1: Cell Culture Intro to 3901
Tim Newsome Tim Newsome

Week 4 26-Mar 7 RNA viruses 8 Bacteriophage I Practical 2: Cytopathic

Tim Newsome Peter Reeves Effect

Week 5 2-Apr 9 Bacteriophage II

Good Friday
Peter Reeves

Easter

Week 6 16-Apr 10 Molecular Tech 11 Plant Viruses I Practical 3: Serology

Tim Newsome Peter Waterhouse

Week 7 23-Apr 12 Plant Viruses II 13 Viruses in Livestck Practical 4: PCR

Peter Waterhouse Jacq Horsington

Week 8 30-Apr 14 Animal Viruses 15 Immune Resp I Practical 5: Immunoblot

Tim Newsome Allison Abendroth

Week 9 7-May 16 Immune Resp II 17 Herpesviruses Practical 6: AL1 Hendra virus outbreak
Allison Abendroth Russell Diefenbach Immunofluorescence Gary Muscatello

Week 10 14-May 18 Retroviruses 19 Latency Student Presentations I AL2 Hendra virus outbreak
Barry Slobedman Barry Slobedman Gary Muscatello

Week 11 21-May 20 Influenza 21 Cell transformation Student Presentations II AL3 Virus Transport
Kevin Downard Tim Newsome Tim Newsome

Week 12 28-May 22 Prions 23 Control of Viruses Student Presentations III AL4 Virus Transport
Jacq Horsington Jacq Horsington Tim Newsome

Week 13 4-Jun 24 Emerging Viruses 25 Course Summary Exam

Tim Newsome Tim Newsome