Interdisciplinary Explorations in Virology

Syllabus, Fall 2014

Course Description 

In this course, we will use a case-study approach to investigate the biology of human pathogenic viruses, focusing in particular on factors that impact the outbreak and spread of human viral diseases. CC- Interdisciplinary

Student Learning Goals

As a result of taking this course, students will be able to:

1) Describe the basic structures and replication strategies of the major classes of human viral pathogens;

2) Explore and analyze the political, social, economic and biological factors that impact the outbreak and spread of viral diseases;

3) Demonstrate familiarity with the specialized vocabularies and fundamental concepts of the various disciplines involved in the epidimiological analysis of viral disease outbreaks;

4) Show an appreciation of how different academic disciplines can supplement and reinforce one another in the study of viral disease outbreaks and their causes;

5) Articulate an understanding of the complexities and ambiguities inherent in explaining epidemiological issues from with in the frameworks of a variety of disciplines, including biology, sociology, political science and economics.

6) Deliberately use the disciplines under study for advanced analysis of viral disease outbreaks in a way that is not normally available to each discipline alone.

Important Course Information

Professor:  Dr. Tammy Tobin
Course Questions? Email me!

 

TIMES, PLACES AND MANNERS IN WHICH TO GET IN TOUCH WITH ME:

Office Location: 234F New Science Building
Office Phone: 4067
Office hours by appointment: M,W, F 8:30-9:45 am, M 3-4. Other hours gladly set up by appointment, too. Walk-ins are always welcome!

Tweeting Hours: @Tobintc #SUMicrobz: M 2-4.

Texting Hours: Nope, sorry. My minimal cell phone plan will not support them :-)

Email Policy (tobinjan@susqu.edu): Monday-Friday: I always respond to emails as quickly as I can (generally within a few hours during the work day). However, I am an early riser (5:00 am), so emails that are sent after 8:00 pm M-F will probably NOT receive a response until the next morning. Weekends/Holidays: Unless I am completely out of email contact (this is possible, as I am an avid hiker/camper) I will check my email daily during weekends and holidays and respond within 24 hours.

Required Text

Virology: Principles and Applications by Carter and Saunders, 2nd edition (Wiley, paperback ISBN 978-1-119-99142-7, etext ISBN 978-1-118-62976-5)

Grade Standards 

Your final grade will be based on three exams (30%), Peer-Evaluated Teamwork (10%), in-class assignments and mini case study worksheets (30%), and a written report of your semester "Outbreak" project (30%).  Grades will be based on the table below.  There is no curve.
 

Percent Grade Letter Grade
93 A
90 A-
87 B+
84 B
80 B-
77 C+
74 C
70 C-
67 D+
64 D
60 D-
<60 F

 

Attendance 

If you are not in class, you will receive a zero for that day's work, and for that day's participation.  If you think you have a really good reason for missing class, you must let me know about it in advance, and I will decide if a make-up assignment is warranted.

Late Work

Since the reason I assign work for class is to help you learn, I will always accept late work, and it will always receive more points than work that is simply not turned in (as long as you get something right, that is). Late (unexcused) work will be assessed a 10% per day late penalty, and that penalty starts the minute that I start class - so please do NOT come to class late because you are printing out that day's assignment. It won't change your grade a bit.

Accommodations

I am committed to working with students with disabilities by providing reasonable and adequate accommodations. If you have a documented learning disability, please bring the paperwork from Disability Services to my office. I will be happy to work with you to help you get the most out of this course.

Printer-Friendly Version of the Syllabus

Fun Stuff:

Ebola Pages

Centers for Disease Control

World Health Organization

Epidemiology and Prevention of Vaccine-Preventable Diseases: The CDC "Pink Book"

International Committee on the Taxonomy of Viruses (ICTV) Website

MMWR's photos, reports and quiz widget


MMWR's photos, reports and quiz widget. Flash Player 9 or above is required.
MMWR's photos, reports and quiz widget.
Flash Player 9 or above is required.
 

Schedule of Events for Fall 2014
 
 

Date
Topic
Assignment (Due at or before Beginning of Class)
8/25

Syllabus and Introduction

Handout: Ebola Worksheet

 

8/29

Introduction to Viruses and Epidemiology

Handout: Virology Class 1 Notes

1) Read Carter, Chapter 1

2) Read Where do emerging pathogens come from?

9/1

Emerging Infectious Diseases: Who, What, Where, When and Why?

Handout: Class 2 Worksheet

Everyone Must Read:

1) Carter, Chapter 21

2) Emerging infectious diseases; controversies, causes and control

3) Emergence of Zaire Ebola Virus Disease in Guinea — Preliminary Report

Then Read One of the Following Papers, As Assigned:

A) Conflict and Emerging Infectious Diseases

B) Global Aspects of Emerging and Potential Zoonoses: a WHO Perspective

C) Global Climate Change and Infectious Diseases

D) Urbanisation and infectious diseases in a globalised world

9/5

The Impact of Communication on Disease Outbreaks

Discussion: Fear, Tradition and Prejudice

Handout: Virology Class 3 Worksheet

1) Read Communicating the Threat of Emerging Infections to the Public

2) Read excerps from Ebola, Culture and Politics: The Anthropology of an Emerging Disease.

9/8

Virus Structure and Replication - An Overview

Handout: Virology Class 4 Notes

 

1) Read Carter, Chapters 3-4, 10 (Animal Viruses, Only)

9/12

Virus Structure and Replication, Continued

Handout: Ebola Replication and Pathogenicity

1) Read Infection Mechanism of Genus Ebolavirus

Additional readings (not assigned):

A new player in the puzzle of filovirus entry: Nature Reviews Immunology v. 7, 2007 p. 556-567

How Ebola and Marburg viruses battle the immune system: Nature Reviews Microbiology v. 10 2012 p.317-321

9/15
OUTBREAK!  
9/19

Mini Case Study #1: dsDNA Viruses

Handout: Virology Class 5 Notes

1) Read Carter, Chapter 11

This, and all subsequent sessions will be supplemented by material from chapters 4-9, as appropriate.

9/22
The Outbreak Continues  
9/26

Virus Vaccines and Antiviral Agents

Handout: Virology Class 6 Notes

1) Read Carter, Chapters 24-25

2) Read "What is Zmapp, the ebola syrum?" http://mashable.com/2014/08/17/ebola-serum-zmapp/


Bio-high-tech treatment for Ebola may have saved two US citizens http://arstechnica.com/science/2014/08/bio-high-tech-treatment-for-ebola-may-have-saved-two-us-citizens/

9/29

Exam 1

10/3

Pause in the Action...Outbreak will resume 10/7
 
10/6

Bonnie Bassler Discussion

 

Read:

1) Reviving the Pipeline of Life-Saving Antibiotics: Exploring Solutions to Spur Innovation

2) Platforms for Antibiotic Discovery

Web Sources of Information:

CDC Detect and Protect:  Information about antibiotic resistance
http://www.cdc.gov/drugresistance/detect-and-protect/

Information about the ADAPT legislation
http://www.pewtrusts.org/en/research-and-analysis/q-and-a/2014/01/29/adapt-a-regulatory-pathway-to-develop-antibiotics-and-fight-drug-resistant-infections

Information about the GAIN legislation
http://www.pewtrusts.org/en/research-and-analysis/issue-briefs/2013/11/07/gain-how-a-new-law-is-stimulating-the-development-of-antibiotics

Assignment: Complete these questions and bring to class on Monday.

10/10

The Outbreak Continues

 
10/13 Fall Break!  
10/17

Mini Case Study #2: dsRNA Viruses

Mini Case Study #2

Handout: Virology Class 8 Notes

1) Read Carter, Chapter 13

10/20
The Outbreak Continues
 
10/24

Mini Case Study #3: (+) strand RNA viruses

Mini Case Study #3

Handout: Virology Class 9 Notes

1) Read Carter, Chapter 14

10/27

Exam Two

Exam Two Review Questions
11/3
The Outbreak Continues
 
11/7

Mini Case Study #4:

Mini Case Study #4

Handout: Virology Class 10 Notes

Read Carter Chapter 16: Influenza Virus
11/10
The Outbreak Continues
 
11/14

Mini Case Study #5

Handout: Virology Class 11 Notes

Read Carter Chapter 19: Hepadnaviruses (and other Reverse-Transcribing DNA Viruses)
11/17
The Outbreak Continues
 
11/21
Final Work on the Outbreak
 
11/24
Exam Three

Exam Three Review Questions

12/1-12/5

Outbreak Presentations

 

Final Exam Period - Tuesday, December 9 3-5 pm

Final Outbreak Paper Due

Final Paper Instructions

Final Outbreak Paper Due no later than 5:00 pm, Tuesday, December 9 via email.