Ecology of Infectious Diseases
Fall 2013
Course: BIOL490
Professor: Andrea Swei, PhD
Time: Tues and Thurs 2-3:30, HH 501
Lab: Wed 10-12, SCI 249
Office: HH 722
Office Hours: Wednesday 1-3
Email: aswei@sfsu.edu
Prerequisites: Biol 230 and 240
Text Materials:
Disease ecology: community structure and pathogen dynamics. Edited by Sharon K. Collinge and Chris
Ray. Oxford University Press 2006. New York. (ISBN: 0-19-856707-3)
Additional selected primary literature available on iLearn
Course description:
In this course, we will examine the ecological and evolutionary processes that govern the
transmission of pathogens in animal and plant systems. Topics that will be covered
include factors that lead to disease emergence, the impact of diseases on host populations,
and the role of community ecology and biodiversity on pathogen transmission. The course
will cover the theoretical underpinnings of disease ecology, case studies and examination
of research methodology, as well as laboratory exercise on executing
quantitative/modeling methods in disease ecology.
Student Learning Objectives:
Knowledge and understanding
1. Able to describe the basic principles that determine the invasibility, persistence, and transmission
of pathogens in a variety of systems
2. Understand the parameters involved in estimating disease transmission and persistence
3. Critically read scientific papers on patterns and processes that shape disease transmission and
spread
4. Be able to comprehend and explain methods and principles from primary literature
5. Describe how habitat change, climate change, and other disturbances influence the spread of
pathogens
6. Understand and be able to describe key examples of human, wildlife, domestic animal, and plant
disease systems and the factors that regulate their transmission and prevalence
Skills
1. Give an oral presentation on the ecology of an infectious disease
2. Group presentation
3. Be able to execute and parameterize basic epidemiological models in R
Course work: 600 Total Points
Exams: Two midterm exams, 100 points. Final exam, 100 points. All exams will be in class. Questions
will consist of multiple choice and short essay. (total 300 points)
Oral Presentation: Details TBA, 100 points.
Pop Quizzes: 4 closed-note in-class quizzes, 5 points each (total 20 points)
Lab: Write up of lab problems sets, 20 points each (total 160 points)
Participation: Participation in lecture and discussions, 20 points
Extra Credit: Extra credit may be given to students who participate in additional departmental seminars
at SFSU, UCSF, UC Berkeley or Stanford and write short reviews of the lectures. You must see the
instructor for approval of extra credit ideas.
Missed Test: If a student misses a midterm without either a certified medical excuse or prior instructor
approval, the student may take a makeup test at a designated time at the end of the semester. Only one
makeup test/quiz will be given. It will be fair but challenging! Tests missed with certified medical
excuses or prior instructor approval will be dealt with individually. If a student misses the final exam
without a valid excuse, a zero will be averaged into the grade. Missed labs cannot be retaken.
Grading:
Final grades are computed as a letter grade, plus or minus where appropriate: A (93.00-100%), A- (90.0092.99%), B+ (87.00-89.99%), B (83.00-86.99%), B- (80.00-82.99%), C+ (77.00-79.99%), C (73.0076.99%), C- (70.00-72.99%), D+ (67.00-69.99%), D (63.00-66.99%), D- (60.00-62.99%) and F (59.99%
or below). Work that is turned in late will lose 10% of total points per day past due.
At the end of the semester, if a student is borderline between 2 grades (for example, between an A- and a
B+), discretionary criteria will be used to determine which of the two grades, the student receives. These
criteria will include class participation, class attendance, and the student’s willingness to seek help.
Attendance: Attendance and punctuality are required for the class. All quiz questions are derived from
class material.
General Classroom Policy: Mobile phones must be switched off.
Honor Code: By your signature on the attendance sheet, you are agreeing to abide by a class honor code.
This means that you agree not to cheat or participate in any type of academic misconduct (plagiarism etc).
In addition, if you become aware that a classmate has cheated or engaged in academic misconduct, it is
your responsibility to bring it to the instructor’s attention. In this way, you and your classmates are
responsible for each other’s academic behavior. Any student caught
Disabilities: Students with disabilities who need reasonable accommodations are encouraged to contact
the instructor early in the semester. The Disability Programs and Resource Center is available to facilitate
the reasonable accommodations process. The DPRC, located in SSB 110, can be reached by telephone at
338-2472 (voice/TTY) or by e-mail at dprc@sfsu.edu.
Add/Drop/Withdrawal:
For complete schedule see: http://www.sfsu.edu/~admisrec/reg/regsched134.html
Class start:
August 27, 2013
Drop deadline:
Monday, September 9
Add deadline:
Monday, September 9 (last date to add with permit numbers).
Withdrawal:
September 10-November 22. After that, no withdrawal unless seriously ill, in
case of accident, or circumstances beyond the student’s control.
Final exam:
Thursday December 19th 1:30-4pm in HH501
Lecture Schedule
Week
1
Date
Aug 27
Topic
Tues: Introduction to disease ecology and evolution
Reading
2
Aug 29
Sep 3
Sep 5
Thurs: Community ecology and host-pathogen systems
Tues: Foundations of disease ecology: SIR models and R0
Thurs: Macroparasite systems
3
Sep 10
Tues: Host population regulation by parasite
Collinge Ch 2
Anderson and May 1991
King et al. 2006, Collinge Ch
10
Hudson et al. 1998
Sep 12
Thurs: Parasite induced behavioral modification
Moore 1983
Sep 17
Tues: Guest lecture on amphibian declines (Dr. Vance
Vredenburg, SFSU)
Wake and Vredenburg 2008
Sep 19
Thurs: Wildlife disease and seasonality
5
Sep 24
Sep 26
Tues: Spatial-temporal dynamics and networks: rabies
Thurs: Midterm
Collinge. Ch 3, Dobson and
Meagher 1996
Collinge Ch 12
6
Oct 1
Oct 3
Oct 8
Tues: Evolution of virulence
Thurs: Student presentations
Tues: Heterogeneity and transmission: superspreaders and
AIDS
Thurs: Biodiversity and the dilution effect
Galvani 2003, Ewald 1993
Oct 15
Tues: Vector-borne diseases: Lyme disease, malaria, West
Nile Virus
Collinge Ch 3, Druilhe et al.
2005
Oct 17
Thurs: Student presentations
9
Oct 22
Bennett 2010, Ch 9
10
Oct 24
Oct 29
Oct 31
Tues: Guest lecture on Dengue virus (Dr. Shannon Bennett,
CAS)
Thurs: Seasonality and Conservation
Tues: Student presentations
Thurs: Midterm
11
Nov 5
Tues: Disease control: herd immunity and culling
vaccinations
Nov 7
Thurs: Novel pathogens, prions and infectious cancers
Lloyd-Smith et al. 2005
TREE,
Mackinnon et al. 2008
McCallum and Dobson 2002
Nov 12
Tues: Coevolution and antibiotic resistance: tuberculosis
Levy and Marshall 2004
Nov 14
Thurs: Guest lecture on avian malaria (Dr. Ravinder
Sehgal, SFSU)
Tues: Guest lecture on viral discovery (Dr. Samia
Nacacche, UCSF)
Thurs: Guest lecture on physiology and disease (Dr. Rudolf
von May, UC Berkeley)
Thanksgiving break
Collinge Ch 13
Guest lecture on white nose bat syndrome (Tina Cheng,
UCSC)
TBD
Guest lecture on African frog declines (Dr. David
Blackburn, CAS)
Guest lecture on Sudden Oak Death (Dr. Margaret Metz,
UC Davis)
Collinge Ch 11
4
7
Oct 10
8
12
13
Nov 19
Nov 21
14
15
Nov 2628
Dec 3
Dec 5
16
Dec 10
Dec 12
Final Exam
Lloyd-Smith et al. 2005
Nature
Keesing et al. 2010
Altizer et al. 2006
TBD
TBD
TBD
TA-led Review
Thursday December 19th 1:30-4pm
Location: HH 501
Lab Schedule
Week
Week 1
Week 2
Week 3
Week 4
Week 5
Week 6
Week 7
Week 8
Week 9
Week 10
Week 11
Week 12
Week 13
Week 14
Week 15
Week 16
Schedule
No lab
Lab 1: Introduction to R part I
Lab 2: Data analysis and plotting
Discussion
Midterm review
Lab 3: Difference equation model
Lab 4: Chain binomial lab
Lab 5: SI lab
Discussion
Midterm review
Lab 6: SIR Lab
Lab 7: R0 lab
Lab 8: GLMM analysis
Discussion
Open Lab
No lab
Instructor
GA led
GA led
GA led
GA led
GA led
GA led