H&V Syllabus 2017 Ver 9-25-2017 With Honor Code

HUMANS AND VIRUSES M&I 155 A,B,C,D
Robert Siegel HumBio 155 H,V,C,D

Autumn 2017
Humans and Viruses

COURSE SYLLABUS
COURSE ORIENTATION
The class will discuss the interaction of humans and viruses from a number of
biological perspectives: molecular, ultrastructural, cellular, organismal, and clinical as well
as approaching human virology from the broader perspectives of history, culture, politics,
socioeconomics, and demography. The course will focus on a number of key areas:
the nature of human viruses including their classification

human and viral interactions
clinical aspects of viral disease
molecular pathogenesis
epidemiology and risk factors
public and global health aspects of virology including emerging viruses and
biological weapons
case studies involving particular viruses
retroviruses
oncogenic viruses
vaccination and disease eradication, and
chronic and persistent infections
Emphasis will be placed on general principles of biology and on matters of

decision-making and policy. The instructor will interject his perspectives on the nature of
science and society.
COURSE DIRECTOR
Robert Siegel chickenpox@gmail.com
(650) 678-8728
Dr. Siegel is a Professor at Stanford with appointments in the Department of

Microbiology and Immunology, The Program in Human Biology, the Center for African
Studies, and the Woods Institute for the Environment. For more than 20 years, he served
as Course Director of the Infectious Disease component of the required preclinical
curriculum. His courses focus on virology and infectious disease, on genetics and
molecular biology, on global health and development, biogeography and ecology, Darwin
and evolution, and photography. He has led BOSP overseas seminars to Tanzania
(twice), England, Madagascar (twice), The Pantanal, and Tasmania. He was also served
as Faculty-in-Residence at the Stanford Overseas campuses in Oxford, Santiago, and
Cape Town. Dr. Siegel has taught the following Sophomore College courses: The
Stanford Safari (2009 and 2013), Smallpox: Lethal Legacy, Forbidding Future (2010) and
2013), The Coming Influenza Pandemic (2011), and Measles Sneezes, Things That Go
Mumps in the Night (2012), and Viruses in the News (2014 and 2016). He has led
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Autumn 2017
Stanford Travel Study trips to Tanzania, Papua New Guinea, and the Galpagos. Dr.
Siegel has won numerous teaching awards including the Walter Gores Award, The Henry
Kaiser Award, and the ASSU Teaching Award. And his courses have been profiled in the
book InGenius and in the Huffington Post. Dr. Siegel has served in an advisory capacity
for numerous international NGOs, and other projects including Wonderfest, FACE AIDS,
Support for International Change, Ocean Medicine Foundation, Free the Children, Sage
Bionet, Teach AIDS, and the Discovery Channel. He is also a docent at Jasper Ridge
Biological Preserve and at Ao Nuevo State Park. He is an avid photographer, dish
walker, and traveler (to seven continents).
Additional information can be found on his web site:

http://web.stanford.edu/~siegelr/
Numerous samples of his photographic work can be found at
http://web.stanford.edu/~siegelr/photo.html
A short travel blurb can be found at
http://web.stanford.edu/~siegelr/travelblurb.html
TEACHING PHILOSOPHY
The course is intended to be interesting, educational, useful, challenging, and fun.
This will work best if each student contributes to the structure of the course and tries to
function as a self-motivated scholar. It is hoped that each student will surprise himself or
herself with what they are able to accomplish. It is also hoped that the students in the
class will form a community of scholars and friends that will persist through their college
career and beyond.
VENUE
Most class sessions will meet in LKSC 120. You will be notified of any room
changes both in-class and by email.
PREREQUISITES
Consent of instructor, enthusiasm about the topic, and willingness to work very hard.
FORMAT
The class will meet during a three-hour time slot on Tuesday and Thursday
afternoons during both quarters of the 4 course sequence. In general, the lecture time will
be divided into two lectures given by the instructor, separated by a break. Lectures will
make extensive use of PowerPoint presentations and other visual aids. Lecture will
include a Socratic interactive component with ample opportunity to ask questions.
Students will complete a number of projects aimed at applying viral concepts and
information. These include model building, viral website construction, viral pathogen card
creation, PowerPoint presentations, and viral study question development. Additional
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optional sessions will be devoted to demonstrations, review, and discussions. Each of

these is described in greater detail below
A number of scientific seminars on campus related to virology will be recommended
during the course sequence.
Assignments and grading will be explained below.
GRADING PHILOSOPHY
This class is NOT graded on a curve. That is to say, if everyone in the class
produces work of sufficiently high quality, you can all earn As. Students are expected to
be self-motivated and produce high quality work with emphasis on academic scholarship.
A great deal of credit will be given to those students who show independent initiative.
Rare A+s may be given to students who complete each course will both high total
point totals and exemplary performance on the final exam.
COURSE REQUIREMENTS
Assignments are described in more detail below.
AUTUMN COURSE REQUIREMENTS

1) Attendance at the Model Marathon 0% of grade - required!
2) Viral model 6% of grade
3) Pathogen cards (x3) 3% of grade
4) Class participation 2% of grade
5) New and hot blog (1 per week) 4% of grade
6) Observations / Twitter (4-5 per week) 4% of grade
7) Medium article 1% of grade
8) Viral diary 2% of grade
9) Wikipedia entry 2% of grade
10) Weekly problem sets (1 per week) 36% of grade (4% each)
11) Final examination 40% of grade
WINTER COURSE REQUIREMENTS
1) Viral web page 6% of grade

2) Pathogen cards (x2) 2% of grade
3) Virus questions 5% of grade
4) Class participation 2% of grade
5) New and hot blog (1 per week) 4% of grade
6) Observations / Twitter (4-5 per week) 4% of grade
7) Wikipedia entry 1% of grade
8) Weekly problem sets (1 per week) 36% of grade (4% each)
9) Comprehensive final examination 40% of grade
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ASSIGNMENT CHECKLIST
This set of courses has a lot of assignments. In order to help you keep track of the
assignments and the due dates, you will receive a checklist. This list will also be available
on Canvas. The list is primarily for your person use and will not be used in grading. It is
important for you to keep track of your progress in the class.
CANVAS
The course web page on Canvas provides updated course information as well as a
variety of useful virus-related web resources.
The course syllabus, the course schedule, lecture handouts, problem sets, and
additional course materials will be posted on the course Canvas site. This is includes
some of the suggested supplement readings.
The site will also be used for posting course announcements, and for tracking
grades.
Some of the other functionalities of the site such as discussion fora may be used
throughout the quarter.
GOOGLE DRIVE
Students in the course will be invited to share in the course google drive folder.
Importantly, this includes a spreadsheet with all student virus assignments, as well as
student, faculty, and staff contact information.
Please make sure your personal information on this site is up-to-date, even after
the course is over.
BOBS COURSE WEB PAGE

Additional information may be found on my personal course web page:
http://www.stanford.edu/~siegelr/virus/humvir.html
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COURSE READER
The course reader consists of a compilation of individual lecture handouts. These
will be distributed in class throughout the quarter. You are expected to purchase a very
large three ring binder to hold the reader. It is advised that you get dividers to separate
each lecture and/or virus family.
Additional reading materials may be distributed in class and/or posted on the web.
Students will be responsible for all materials that are handed out in class. Handouts will
also include:
- course announcements
- changes in the lecture or reading schedule
- updated lecture information.
You may need to substitute revised or corrected handouts and intercalate
additional materials as appropriate.
*** Please bring reader and additional handouts to every class.
READINGS
The COURSE READER represents the main required reading for the course.
However, you will need to do a fair quantity of outside reading in order to enhance your
understanding and appreciation of each topic in the course. Because of the large amount
of reading, you should use your discretion as to which of the readings you should pursue.
Students are strongly encouraged to purchase ONE popular book on virology
and/or one textbook of virology. Students should direct their attention to the parts of these
books that are relevant to a particular day's lecture.
Following are several authoritative books on virology.
Fields Virology sixth edition by Knipe and Howley Generally considered the bible of
virology, this will tend to provide a wealth of information. There is a significantly
updated 2013 edition. Beware, however, of the price.
Virology: Principles and Applications by Carter and Saunders
Sherris Microbiology sixth edition by Ryan et al., ( 2014 McGraw-Hill)
Human Virology second edition by Collier, Oxford, and Keller ( 2011 Oxford Press)
Viruses: A Very Short Introduction by Dorothy H. Crawford (Sep 1, 2011)
How Pathogenic Viruses Work by Lauren Sompayrac ( 2002 Jones and Bartlett)
Principles of Molecular Virology fifth edition by Alan Cann ( 2011 Academic Press)
Fundamentals of Molecular Virology by Nicholas H. Acheson (2011)
Desk Encyclopedia of Human and Medical Virology by Brian W.J. Mahy and Marc H.V. van
Regenmortel (2009)
Understanding Viruses by Teri Shors (2011)
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Popular books on virology include.
A Dancing Matrix by Robin Marantz Henig

A Planet of Viruses by Carl Zimmer
Autism's False Prophets: Bad Science, Risky Medicine, and the Search for a Cure by Paul
A. Offit
Biohazard by Ken Alibek with Ken Handelman
Deadly Choices: How the Anti-Vaccine Movement Threatens Us All by Paul A. Offit M.D.
Deadly Feasts: Tracking The Secrets Of A Terrifying New Plague by Richard Rhodes
Demon in the Freezer by Richard Preston
Ebola by David Quammen
Flu by Gina Kolata
Hepatitis B: The Hunt for a Killer Virus, by Baruch Blumberg, 2002.
Invisible Invaders by Peter Radetsky
My Own Country by Abraham Verghese
Panic in Level 4 by Richard Preston
Plague Time by Paul Ewald
Polio: An American Story by David M. Oshinsky
Rabid A Cultural History of the World's Most Diabolical Virus by Bill Wasik and Monica
Murphy
Scourge: The Once and Future Threat of Smallpox, by Jonathan B Tucker, 2001.
Secret Agents by Madeline Drexler
Spillover: Animal Infections and the Next Human Pandemic by David Quammen
Splendid Solution by Jeffrey Kluger
The Cobra Event by Richard Preston
The Coming Plague by Laurie Garret
The Cutter Incident: How Americas First Polio Vaccine Led to the Growing Vaccine Crisis
by Paul A. Offit
The Devils Flu by Pete Davies
The Family That Couldn't Sleep by D.T. Max
The Great Influenza by John M Barry
The Hot Zone by Richard Preston
The Panic Virus: The True Story Behind the Vaccine-Autism Controversy by Seth Mnookin
The Viral Storm: The Dawn of a New Pandemic Age by Nathan Wolfe
Vaccinated: One Man's Quest to Defeat the World's Deadliest Diseases by Paul Offit
Virus Hunt: The Search for the Origin of HIV by Dorothy H. Crawford
Virus Hunter by C.J. Peters
Viruses, Plagues, and History by Michael Oldstone
Virus X by Frank Ryan
There are a number of excellent older Scientific American articles, particularly some of the
older articles. Students are encouraged to read these. Students are also encouraged to
make use of other resources available to you on campus. I have provided optional
readings and supplementary texts for students who want to get additional perspective or
go into a subject in more depth. I have additional topical bibliographies as well for anyone
who wants them.
PODCASTS
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Mark Crislips Persiflagers Puscast

Vincent Racanellos This Week in Virology
Radiolab specific episodes
TED specific episodes
WEBSITES
To look for information:
Center for Disease Control and Prevention - http:/www.cdc.gov/

World Health Organization - http://www.who.int/en/
Medscape - http://www.medscape.com/infectiousdiseases
International Committee on the Taxonomy of Viruses -
http://ictvonline.org/index.asp?bhcp=1
ViralZone - http://viralzone.expasy.org/
Wikipedia:
eg virus: http://en.wikipedia.org/wiki/Virus
For potential New and Hots (see later section):
ProMed (Program for Monitoring Emerging Disease) web site and listserv
http://www.promedmail.org/
Google Alerts email alerts on particular topics
http://www.google.com/alerts
LIBRARY RESOURCES
Some readings may be placed on reserve at Lane Medical Library. Of particular
interest for problem sets and other reference information is the book, Fields Virology Sixth
edition, Knipe and Howley, editors-in-chief, Raven Press, New York, 2013. This two-
volume set is the best comprehensive text, around 3000 pages worth. Get to know it. It is
invaluable. (Unfortunately it costs megabucks.) In the course, we will simply refer to
these books as Fields. There should be copies on reserve. The newest version is also
available as an ebook for Stanford students through Lane Medical Library Portal at:
http://lane.stanford.edu/online/eb.html. Please do not use an edition prior to the sixth as a
pertinent reference.
Another highly authoritative source on clinical matters is another massive two-
volume tome: Mandel, Douglas, and Bennetts Principles and Practice of Infectious
Diseases Eighth edition (2014) - usually referred to as Mandel. Mandel is also available
through the Lane Portal.
HUMAN BIOLOGY VIRAL LIBRARY
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The Instructor has a large collection of books and articles on viral topics. These
will be available for use in the Human Biology office, at select times including nights and
weekends. They may not be removed. In the past, students have enjoyed working
together using the library. (Misery loves company?) Please be courteous in sharing and
protecting these resources.
Students are welcome to use the conference rooms when they are not being used
for classes and meetings. Classes and sections always have priority. Rooms are
available at night and or weekends and occasionally during weekdays by arrangement.
TEACHING ASSISTANTS (TAs)

The Teaching Assistants (TAs) are one of your most valuable resources in this
class. The TA can provide assistance with conceptual material and strategies for
completing the class assignments including the problem sets. The TAs will also teach
sections and will also be available for consultation on an individual basis. The TAs will
also grade the problem sets and the final exam. See below for a separate section
describing TAs sessions.
Michelle Bach mspark19@stanford.edu (972) 922-1594

Devon Zander dnzander@stanford.edu (406) 871-9660
Michelle: I am a junior and recent alum of Human and Viruses Class of 2017. I was
first welcomed into the World of Virology as a student in Dr. Bobs Sophomore
College Seminar Viruses in the News and have also taken another course taught by
Dr. Bob called The Viral Inquiry Project. I am an Emergency Medical Technician
(EMT) and a Certified Nursing Assistant (CNA), and I am passionate about topics in
Global Health and Infectious Disease. I am from Dallas, Texas and took the motto
Everythings Bigger in Texas a little too seriously during last years Humans and
Viruses Model Marathon. When Im not in class/working on psets/biking ferociously
from East Campus to Med Campus, you can catch me hiking the Dish, trying out
new ramen places, or standing in line for the midnight premier of the next Marvel
movie. I am so incredibly excited to be your TA this year and cant wait to meet
everyone!
Devon: I am a senior majoring in Human Biology with a concentration in Infectious

Disease. I took Humans and Viruses last year along with Dr. Bobs Viruses in the
News and Virology Inquiry Project courses and fell in love with the world of virology,
especially measles. Outside of class, Im an HIV*PACT counselor, EMT, and was
an RA in Trancos last year. When not extolling the benefits of vaccination or
pondering what will happen on the next episode of the Amazing Race, I can easily
be found reading, baking bread, or researching a new trail to hike for when I return
to my home state of Montana.
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TA SECTIONS
Your Teaching Assistants (TAs) will conduct sections at times to be arranged. We
will try to find times that will be convenient to as many of you as possible. As much as
possible, we will try to accommodate everyone.
Sections may vary in their format depending on interest and need. Formats may
include review sessions, backgrounder sessions, discussion sections, and topics of
supplemental interest. In the past, students have found these sessions to be extremely
valuable. You may attend to as few or as many as you wish.
Review sections will allow students to ask questions, to review material, to obtain
help with problem sets, to have course demonstrations or model building sessions, to view
supplementary movies or slides, and to bring up new material of interest. You are strongly
encouraged to attend. Review session may also include optional self-assessment quizzes
that will review material to be covered on the final. Backgrounder sessions will include
reviews of molecular biology and immunology, and tutorials on web design, and
PowerPoint. Discussion sections will focus on policy issues.
COURSE ASSISTANTS (TAs)

Additional Course Assistants may intermittently help with the grading or running the
optional weekly sections.
EMAIL
Communication with students and course announcements will often be delivered by
email. Students are expected to check their Stanford accounts every day. You are
expected to reply to ALL group emails sent by the instructor.
EMAILING FILES
All emailed files should follow the following naming convention:

course-yourname-document title or subject key words-draft version-date
For example:
humans and viruses yourname adenovirus model write-up December 1,
2017.doc
Although this is longer and annoying, it is extremely helpful and descriptive.
Do not name your file something like siegel paper or final draft or presentation.
ALL FILES NAMES MUST INCLUDE YOUR NAME. REALLY! REALLY!

This includes pictures, PowerPoint, dossiers, PDFs, EVERYTHING.
If you are sending me a draft that is close in content to a previous draft, please
indicate the alterations with the track changes command or comparable color annotation.
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COURSE SCHEDULE
The course schedule will be distributed as a separate handout and posted on the course
calendar. The schedule represents my best understanding of the content and timing of
the course events. Given the number of different components of the seminar, things may
change even after the course has begun. These changes will be posted in real time and
announcement will be made by email or in class. Students are expected to be flexible in
embracing these schedule changes.
ATTENDANCE
Students are expected to attend all class sessions. Exceptions will be made for issues of
personal or family health. Please notify the instructor as soon as possible regarding any
sessions that you need to miss.
CLASS ACCOUNT
The class account is humansandviruses@gmail.com. This will be the location for the
course calendar, additional course information, and the course blog, as well as a
repository for course assignments, and supplemental reading materials. For certain
issues and additional readings, the canvas site will also be used.
COURSE REQUIREMENTS
GRADE SHEETS
Students are required to turn in a grade sheet if they wish to receive credit for the
course. Grade sheets should be filled out and handed in by the end of the second day of
class, September 28th, 2017.
ASSIGNMENT OF VIRAL FAMILIES (Autumn quarter)
For several assignments including the viral model, virus web page, virus pathogen
cards, and viral questions, students will be assigned a specific human virus family.
Students must work on a different virus family for each of these assignments; and every
family must be covered by at least one member of the class. Student preferences will be
taken into account when possible.
N.B. For the web pages, some reassignments will be made because of changes in
the class enrollment. In particular, each family will have no more than one student
assigned to it.
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VIRAL MODEL (Autumn quarter)
Students are required to build a model of a specific human virus or viral family.
This is intended to illustrate some of the properties of viral structure, viral symmetry, viral
assembly, or viral gene expression. Models should be accompanied by an explanation of
the properties that your model illustrates as well as any problems that were encountered
in the construction of the model. In doing your write-up, you should address the following
issues:
a) Describe your model
If pertinent, discuss the use of colors and/or other visual effects.
b) What specific principles does your model clarify?
Include any insights you derived from building your model.
c) What substantive questions does you model raise?
d) What are the shortcomings of your particular model?
e) Why did you select the particular materials used?
f ) In general, what functions do models serve?
g) What are the advantages of static versus dynamic models?
Use a separate paragraph and section heading for each issue.
Every model should have a title and a bibliography.
Please put your name on all submitted work.
Students are encouraged to work together although each student must turn in a
separate model and model write-up.
Students will each present their models and explain the significance of its
construction and design at the model marathon (see below). Every presentation must
include visual aids.
In summary, there are three parts to the model assignment:
a) the model
b) the write up
c) the presentation.
Please begin your presentation by introducing yourself and your model. Be sure to
project and enunciate.
The instructor will assign pathogens although requests will be accepted. The
instructor must sanction any trades.
Models will be judged on their creativity, clarity, and utility.
The model constitutes 6% of your grade.
MODEL MARATHON (Autumn quarter)

Models will be presented the last week of autumn quarter. Attendance is
mandatory. Assistance will be provided in running the projector and computer equipment.
The presentation will be videotaped and the models will be photographed.
Pictures, write-ups, and videotapes from previous years are available for review. They
may be helpful in coming up with creative ideas.
A prize will be given to the student with the best model and model presentation. A
student vote will select the winner. Previous winners include Angel Fabian, Cameron
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Barr (2003), Aaron Platt-Ross (2004), Ben Fohner (2005), Thomas Lew (2008),
Nguyen Phan (2012), and Alex Lindqwister (2014), and Michelle Bach (2016).
The model marathon will be held Monday, November 27 6:00 pm 2:00 am
Attendance of the entire marathon is absolutely mandatory!
MEDIUM ARTICLE (AUTUMN QUARTER)
Students are expected to write one article to be posted on Medium or another

approved online publishing platform. Articles should be around 800 words with some
flexibility based on the content. More than the typical blog entries, your Medium article
should be more about your personal story or your opinion about some topic that is directly
pertinent to human virology. Additional credit is given for additional medium articles. See
Standing Extra Credit.
OBSERVATIONS (Autumn and Winter)
Observations are 1-2 sentence reflections on course material. Students are

expected to make at least 4-5 observations per week. Observations may be based upon
the reading, web explorations, class trips, student presentations, etc. Observations may
be quite directed or highly reflective. Observations are to be posted on Twitter.
TWITTER (Autumn and Winter)
Students are expected to set up individual Twitter accounts and post their
observations with the class hash tag.
To set up an account, go to http://twitter.com/
To post to the class twitter, begin your twitter with @humansandviruses.
You can see the class posts at http://twitter.com/#!/humanandviruses
WIKIPEDIA (AUTUMN AND WINTER)

Each student is expected to create at least one substantive Wikipedia entry related
to the subject material of the class. Topics should be approved by the professor. We will
provide assistance for those who have not previously created a Wikipedia entry.
Additional credit is given for additional substantive Wikipedia entries. See Standing Extra
Credit.
PATHOGEN CARDS (AUTUMN AND WINTER)

Every student will be required to create five pathogen cards (three fall quarter, two
winter quarter) for the class card game Pathogenesis. Each card must include the
following information:
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Virus name
Description of virus (taxonomy)
Sketch of the virus
Power
Offenses
Attacks
Outcome
Speed
Defenses
Vaccines
Behavioral
Treatment
Game action (be creative)
One Liner regarding virus
As much as possible, card information should be as accurate as possible in terms

of biomedical information.
Grading of the cards will not be based on artistic ability. (See contest section
below.)
More details on the cards will be posted on the web during the quarter. This will
include descriptions of each information category and sample cards.
The instructor will assign pathogens although requests will be accepted. The
instructor must sanction any trades. Pathogen cards are due (November 16, 2017) and
(February 12, 2018)
Final versions of the cards will be part of the web pages. See above.
Pathogen cards constitute 3% (autumn) / 2% (winter) of your grade.
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VIRAL WEB PAGES (Winter)
Students are required to create a web page (or series of linked web pages)
pertaining to a specific human viral family. These pages are intended are references for
your fellow students and for other students of virology. They are expected to build upon
the web pages created by previous Humans and Viruses students
(http://virus.stanford.edu/viruslist.html). Student web pages will ultimately be
incorporated into the Stanford Virus Group web page: http://virus.stanford.edu.
Each student virus page is expected to include information pertinent to your family:
The names of the page authors and the date of creation of the page
Update 2017 with
10 things to remember about your family

10 timeline dates and events
Molecular biology special features
At least 5 new findings from 2017 or 2018
At least 5 primary references from 2017 or 2018 (These may correspond to
the findings.)
Links to pages from all previous students with the same family
Links to important virus pages even if previously cited
5 additional new links
At least 3 updated web links outside Stanford
Additions and corrections to prior students pages

Bibliography
Web pages should also include:

5 pathogen cards (scanned or otherwise)
1 drug profile
The course web page (http://web.stanford.edu/~siegelr/virus/humvir.html)

contains detailed information on how to create and modify a web page
(http://www.stanford.edu/~siegelr/webnotes.html). It also provides a template page
(http://www.stanford.edu/~siegelr/virustemplate2004.html) that may be used as a
stating point for creating your page.
Students are welcome to use material from the course reader or from the course
web page. Other sources must be properly cited.
Depending on the number of students in the class, students will be expected to
work individually or in groups. The instructor will assign viral families and drug profiles
although requests will be accepted. The instructor must sanction any trades.
It is critically important that you save an electronic copy of your work.
Web assignment should be completed Friday March 16 th, 2018 at midnight.
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The timeline content is due February 16, 2018.

For students who are interested, additional extra credit web assignments are listed
in the standing extra credit portion of the homework.
The web page constitutes 6% of your grade.
PROBLEM SETS (Autumn and Winter)

There will be a problem set pertinent to each week of material: ten total in autumn
quarter, ten in winter. They will be distributed the week the material is presented and due
the following week at 1:29 p.m. on Tuesday (that is, before the next class starts). In total,
the problem sets will comprise 36% of the course grade. Each problem set will be
weighted equally.
Problem sets are open book assignments. You may consult any source, including
your fellow classmates or other people.
For each answer you must:

- Cite at least one relevant reference, unless otherwise noted. That reference
canNOT be another person.
- Be concise. If a correct answer includes superfluous information that is
erroneous, points will be deducted from that answer. Don't meander!
- Write legibly. Typing is highly recommended.
- Use a separate page for each question.
- Use human viruses unless otherwise noted.
Consult the course bibliography and Canvas for possible leads as to where to look
for answers and relevant references. Use bibliographic databases such as PubMed. The
online journals and resources at Lane Library (http://lane.stanford.edu/index.html) are of
particular note. Google Scholar is another excellent resource for finding authoritative
references.
Use your ingenuity. Discretionary extra credit will also be given for particular
resourcefulness in digging up references for your answers.
Web references may only be used if they are from authoritative sources (e.g. WHO
or CDC sites). All web references need to be cited in full. Web references may not be
used as primary references unless they are from electronic journals.
An example of the general NIH reference format for journal articles:

Freedman SB, Adler M, Seshadri R, Powell EC. Oral ondansetron for gastroenteritis in a
pediatric emergency department. N Engl J Med. 2006 Apr 20;354(16):1698-705. PubMed
PMID: 16625009.
Problem Set Due Dates

AUTUMN QUARTER SCHEDULE
Problem set 1 October 3, 2017 at 1:29 p.m.
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Problem set 6 November 7, 2017 at 1:29 p.m.
Problem set 9 December 5, 2017 at 1:29 p.m.
Problem set 10 December 12, 2017 at 1:29 p.m.
WINTER QUARTER SCHEDULE

Problem set 1 January 16, 2018 at 1:29 p.m.
Problem set 4 February 6, 2018 at 1:29 p.m.
Problem set 8 March 6, 2018 at 1:29 p.m.
**All problem sets are to be turned in before class.
Additional Credit
Extra credit problems and other extra credit assignments will be included on each
of the weekly problem sets.
If there are topics of particular interest, I will also accept short answer type
questions proposed by students for possible use as extra credit problems.
All extra credit assignments will be graded more strictly than the regular
assignments. Extra credit assignments must be completed without assistance from your
fellow students.
STANDING EXTRA CREDIT
In addition to the weekly problem sets, students may do an unlimited amount

of standing extra credit (SEC) to boost their point total in the class. See
separate handout for details. These must be submitted before the end of dead
week.
BOOK REVIEWS (STANDING EXTRA CREDIT)
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Autumn 2017
Students may post a book review on Amazon or an equivalent web site. Books to review
should be one of the popular books on virology listed in the syllabus or another approved
book. Additional credit is given for additional book reviews. See Standing Extra Credit.
SUBMITTING PROBLEM SETS

Students are expected to submit two copies of each problem set an electronic
copy and a hard copy.
For the hard copy, each problem should be printed on a separate piece of paper.
At the beginning of class on Tuesday, each problem will be placed in a separate pile for
grading. Graded hard copies may be used in the final dossier.
The electronic copy will be submitted on the assignment bin on Canvas.
For the first time, students will be expected to submit their problems in electronic form
only. In order to facilitate grading, each question should be submitted as a single file and
placed in the appropriate canvas assignment folder. This binning system will allow the
graders to grade the problem sets one question at a time rather than one student at a
time.
Do NOT cut and paste from published texts. All work must be in your own words
and show evidence of personal understanding.
NEW AND HOT
Students are required to post at least one entry on the New and Hot blog every
week. These will be selectively discussed in class. These items should be related
directly or indirectly to the field of virology. Items may fall within any of the following
areas.
New resources
New discoveries
New experimental research
New events and their impact on culture
New personal experiences related to the course topic
Court cases
Relevant outbreaks, aspects of eradication, other related infectious disease topics
New and Hots can be found in many places, but one excellent source is
http://www.google.com/alerts .
Another is http://www.promedmail.org/.
CLASS BLOG: HUMANSANDVIRUSES.BLOGSPOT.COM

Students are expected to post at least one item per week on the class blog:
http://humansandviruses.blogspot.com
The password will be announced in class.
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Autumn 2017
The material posted to the blog should correspond to your New and Hot findings.
Do not use stories that have already been posted. Make sure to keep up with the blog to
avoid such redundant posts.
Post early to avoid being scooped.
VIRUS QUESTIONS (Winter)

Each student will generate test questions regarding a particular virus family each
quarter (two sets total). Each set should include 5 multiple-choice questions, 5 short
answer questions, and two policy or analytical questions. Depending on the number of
students in the class, students will be expected to work individually or in groups. The
instructor will assign viral families although requests will be accepted. The instructor must
sanction any trades.
It is critically important that you save an electronic copy of your work.
Questions should be followed (on a separate page) by answers to each of the
questions.
Viral questions should be completed Friday, March 2, 2018 at midnight.
Virus questions cards constitute 5% of your grade.
VIRAL DIARY (Autumn quarter)

Keep a viral disease diary for the entire quarter. For each suspected viral disease
that you get list 1) a putative diagnosis, 2) daily record of signs and symptoms, 3)
medications (by ingredient and brand name) or other treatments taken including any
apparent relief that you obtained. Try to be as inclusive as possible. If you are truly viral
free, that must be indicated on your diary. (You may omit diseases and/or entries that you
find compromising or embarrassing for one reason or another.)
You must have a TA or the instructor initial your updated diary every week.
This is an important exercise to discover the ubiquity of viral disease - more than
half of you will get some viral infection this quarter.
The viral diary is due on the last day of class.
The diary constitutes 2% of your grade.
FINAL EXAMINATION (Autumn and Winter)

Both final exams will be cumulative to date and will be worth 40% of your total
grade. The time and location are listed in the schedule. Questions will be based on the
lectures, reader, handouts, and problem sets including some of the extra credit problems.
Any topics on the lecture notes or handouts may also be tested even if they are not
mentioned in lecture. "Optional" readings and lectures will not be tested. Questions from
the virus question assignment may be included on the exam. Students are encouraged to
submit additional questions for possible inclusion as well.
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Autumn 2017
Every student must take and pass the final exam regardless of your point total
going into the exam.
The weekly problem sets (described above) will be used in lieu of midterm
examinations.
Final Examination Review Sessions

The last week of the course there will be a series of optional, intensive review
sessions for the final. Sessions begin by addressing questions posed by the students.
This is followed by a systematic Socratic approach in which students are quizzed. New
material may be presented but it will not be on the final. Students have found these
sessions invaluable in consolidating the course material. Students are encouraged to
attend as many sessions as possible.
Practice Tests
There are over 100 pages of practice final exams from previous years. They will be
posted on the course web site. These exams make excellent study materials and will be
reviewed in some of the TA sessions (in response to demand by the students). This year's
exam is likely to include many of the same topics or possibly even the same questions as
in prior years. Therefore, it is wise to use these exams as a study guide.
CLASS PARTICIPATION (Autumn and Winter)
Students are expected to play an active role in the class. This includes raising
pertinent questions in class, or after class. For each class, students should be prepared
to discuss at least one new and hot and one observation. Participation may also include
involvement in the weekly sections and in the optional sessions.
Class participation constitutes 2% of your grade.
Also see section on MI115C.
DOSSIER (Autumn and Winter)
At the end of each quarter, all students are required to turn in a dossier of all their
assignments and other work in the class. This should include copies of all your
assignments and other work completed in conjunction with the course as well as
photographs of all physical projects.
***You must turn in an electronic and a hard copy version of your dossier.
The electronic copy needs to be submitted on Canvas.
Please contact Professor Siegel or the TAs if you are having difficulty because the file size
is too large.
The dossier should include:
Binder or folder
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Autumn 2017
A cover page with your name, the date, the course, and a picture from the course
A list of all work / table of contents (by page or section)
Blog postings
Twitter / observations
Viral diary
Problem sets
Assignment write-ups (model, web page, questions, etc.)
A list of topics of particular interest in the course
A list of notable course events
How will you build upon this course - plan for the future
List of any additional evidence of initiative and/or scholarship including
articles or books you read
Numbered pages or tabulated sections
In order to receive credit for the class, you must turn in a COMPLETE dossier as
specified above.
Incomplete or slipshod dossiers will not be accepted.
You must turn in hard copy AND electronic copy versions:
Autumn quarter final deadline: Friday December 15, 2017.
Winter quarter final deadline: Friday, March 23, 2018.
Electronic copies can be uploaded to the course google drive account. They can
also be mailed to chickenpox@gmail.com
(Please do not send them to siegelr@stanford.edu.)
Dossiers posted on Drive will be accessible as references to all the students in the
course.
You should also keep a permanent copy of your dossier for reference.
The dossier is extremely useful in terms of potential letters of recommendation.
Take pride in your work!

Make it look pretty.
Sample dossiers are available for your perusal.
PERMISSIONS
The dossier is for evaluation (and possible recommendations). However, as you
know, I sometimes use student presentations as demonstrations or as parts of my
presentations - with attribution. As you saw, I try to maintain the students formatting so it
is obvious that it is not my work.
If you have any preferences regarding the possible use of your work, please let me
know (especially emphatic nos or emphatic yess). I will not use any work that you prefer
not to share.
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Autumn 2017
MI 115C VIROLOGY INQUIRY PROJECT (VIP)

VIP is an additional 1 unit P/NC course taught in conjunction with Humans and
Viruses. Completion of the class requires
1) attendance at 10 TA-led sections or other instructor approved activities such as
infectious disease grand rounds, department of medicine grand rounds, academic
seminars related to virology, fellows teaching rounds, or special guest sessions.
2) 1 page write up for each session attended
3) submission of dossier with write-ups
OTHER IMPORTANT INFORMATION

OFFICE HOURS
Your instructor and the teaching assistants will also be available by appointment.
Please see section on Walking the Dish.
COOPERATION BETWEEN STUDENTS/ WORKING TOGETHER

Students are encouraged to work together on most phases of the course (except
extra credit assignments and the final examination). Even on cooperative
assignments, students are required to compose assignments entirely in their own
words. Again, this does not mean merely shifting a few words around. This will be strictly
enforced.
(Although I should not have to say this, it is imperative that you be courteous to
your fellow students. Any student found stealing or hiding references will be brought to
the attention of the university administration for full disciplinary action.)
BACK UP
I have received far too many emails from students who have lost files (notes,
presentations, photos) due to stolen computers and failed hard drives. Do not join this
club. In particular, beware of iPhone notes.
PLAGARISM
By now, all of you should know the difference between putting information in "your
own words" and merely changing a few words around. The latter does NOT demonstrate
understanding and will be marked down. Direct quotes may be used judiciously when
appropriate. They should be placed in quotation marks and correctly referenced.
REGRADE REQUESTS
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Autumn 2017
All regrade requests must be submitted in writing to the instructor. Changes may
be made up or down. The judgment of the instructor is final.
COURSE EVALUATIONS
Rather than wait until the end of the class, when changes may no longer be
implemented, students are encouraged to provide feedback to the instructor throughout
the course. This may be done anonymously, through the TAs, or during office hours.
Reasonable suggestions will be promptly instituted. Please let me know of any additional
topics that you wish to have covered.
DEMONSTRATION LABS AND ENRICHMENT SECTIONS
There will be a series of optional demonstrations, review sessions, and

discussions. These demonstrations will include some or all of the following:
- diagnostic virology lab
- electron microscopy suite
- tour of a molecular virology laboratory, and
- pathology of cytopathic effect.
Additional optional sessions not directly related to virology will also be arranged.
These may include:
- an evening in public health (probably in winter)
- tips on applying to medical school by a Stanford admissions officer.
OPTIONAL LECTURES
Every quarter on campus, there are a number of special lecture series and research
seminars that are directly pertinent to the course materials in Humans and Viruses. These
lectures, particularly those given by famous researchers, will be called to the attention of the
students as their dates approach. Students are strongly encouraged to attend but will NOT be
responsible for the material presented.
Fellows Rounds are held Tuesday mornings in CCSR 4205 at 8:00 a.m. These are
teaching sessions on a variety of infectious disease topics. There is usually food. The level is
somewhat advanced but the content is usually excellent. Frequently, these are followed by
Remington Rounds in which infectious disease fellows go over clinical cases with a master
clinician.
Students are invited to attend Infectious Disease Grand Rounds, held the first three
Thursdays of each month from 4:30 to 6:00 PM. These are formal teaching events usually
focusing on recently hospitalized patients. Unfortunately, many of these sessions conflict with
the end of class. However, grand rounds are held year-round. (See also Optional Lectures
regarding Fellows Rounds.)
Department of Medicine Grand Rounds are at 8:00 am on Wednesday mornings in
LKSC Berg Hall. These talks periodically pertain to virology. Relevant talks will be
announced in class.
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Autumn 2017
CLINICAL EXPERIENCES
For motivated students, there may be opportunities to shadow the infectious disease
consulting team for daily working rounds. Please contact Dr. Siegel for additional details.
.
RESEARCH AND HONORS
Many of the students who have taken this class have pursued their interest in viruses
by working in a research laboratory focusing on infectious disease or immunology. Please
contact Dr. Siegel if you would like help in locating possible labs of interest. Alternatively,
some Human Biology students have completed honors projects that focused on viruses but
did not involve laboratory work. Many creative avenues of research are possible.
CONTESTS
T-shirt
Depending on demand, we will make course T-shirts. If we actually make the
shirts, a free T-shirt will be given to the student with the best T-shirt design. Selection
will be based on student and instructor preference.
Model
A prize will be given to the student with the best model and model presentation.
Selection will be based on a vote by the students.
Pathogen card design

Extra credit will be given to the student with the best design for the pathogen deck.
Selection will be based on instructor preference.
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Autumn 2017
EATS
All students are invited to bring contributions to our biweekly food fest.
Please bring your own reusable cups and utensils.
NAME TAGS
You will be asked to make a two-sided name tag. Please use your name tag
throughout the quarter, particularly if we have guest speakers.
LOGISTICS AND SET-UP
Your help in setting up and cleaning up the equipment in the room is greatly
appreciated along with help transporting materials to class.
Please note that Dr. Siegel may need time prior to class for set-up. Questions about
logistical matters can be raised after class or during the break. Matters that pertain to the
whole class can be brought up during class.
Thanks for your consideration regarding these matters.
CLEAN-UP AND RECYCLING

The instructor takes great pride in the Stanford environment. Please help make this
the best possible learning environment by keeping things tidy. As much as possible, please,
help by recycling paper, plastic, and metal (but not viruses).
COFFEE ABOUT NOTHING/BROWN BAG LUNCHES

There will be a series of optional, informal coffees / brown bag lunches providing
students with ample opportunity to meet with the professor outside of the formal class setting.
Topics of conversation may be far ranging and not limited to virology or even science. These
will be announced by email.
DISH WALKS
Several times per week, usually in the afternoon, I walk the Stanford Dish loop. You
are invited to join me on these walks for conversation, photography, advising, a bit of exercise,
or just getting out into nature.
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Autumn 2017
FUTURE TAs
I would be delighted to have students who are currently taking this course to be TAs
when the class is offered in the future. Please let the instructor know of your interest by email.
Selection of students will be based partly, but not exclusively upon your performance in the
class. Class participation and enthusiasm will also be strongly considered.
RECOMMENDATIONS
Students planning to seek letters of recommendation from the instructor must score
within the top 20% of the class. Also refer to the section describing the dossier.
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Autumn 2017
HONOR CODE
In this course, the students, professor, and teaching team will be expected to adhere to
the Stanford Honor Code.
1. The Honor Code is an undertaking of the students, individually and collectively:

1.That they will not give or receive aid in examinations; that they will not give or
receive unpermitted aid in class work, in the preparation of reports, or in any
other work that is to be used by the instructor as the basis of grading;
2.That they will do their share and take an active part in seeing to it that others
as well as themselves uphold the spirit and letter of the Honor Code.
2. The faculty on its part manifests its confidence in the honor of its students by
refraining from proctoring examinations and from taking unusual and unreasonable
precautions to prevent the forms of dishonesty mentioned above. The faculty will
also avoid, as far as practicable, academic procedures that create temptations to
violate the Honor Code.
3. While the faculty alone has the right and obligation to set academic requirements,
the students and faculty will work together to establish optimal conditions for
honorable academic work.
STUDENTS WITH DOCUMENTED DISABILITIES

Students who may need an academic accommodation based on the impact of a disability
must initiate the request with the Office of Accessible Education (OAE). Professional staff
will evaluate the request with required documentation, recommend reasonable
accommodations, and prepare an Accommodation Letter for faculty dated in the current
quarter in which the request is made. Students should contact the OAE as soon as
possible since timely notice is needed to coordinate accommodations.
The OAE is located at 563 Salvatierra Walk

Phone: 723-1066 URL: http://studentaffairs.stanford.edu/oae
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HUMANS AND VIRUSES M&I 155 A,B,C,D

Robert Siegel HumBio 155 H,V,C,D

Humans and Viruses

the nature of human viruses including their classification

Emphasis will be placed on general principles of biology and on matters of

Dr. Siegel is a Professor at Stanford with appointments in the Department of

ver26 9-25-2017 Syllabus for Humans and Viruses

Additional information can be found on his web site:

ver26 9-25-2017 Syllabus for Humans and Viruses

optional sessions will be devoted to demonstrations, review, and discussions. Each of

Assignments are described in more detail below.

AUTUMN COURSE REQUIREMENTS

WINTER COURSE REQUIREMENTS

1) Viral web page 6% of grade

ver26 9-25-2017 Syllabus for Humans and Viruses

BOBS COURSE WEB PAGE

ver26 9-25-2017 Syllabus for Humans and Viruses

*** Please bring reader and additional handouts to every class.

Following are several authoritative books on virology.

ver26 9-25-2017 Syllabus for Humans and Viruses

Popular books on virology include.

A Dancing Matrix by Robin Marantz Henig

ver26 9-25-2017 Syllabus for Humans and Viruses

Mark Crislips Persiflagers Puscast

To look for information:

Center for Disease Control and Prevention - http:/www.cdc.gov/

For potential New and Hots (see later section):

HUMAN BIOLOGY VIRAL LIBRARY

ver26 9-25-2017 Syllabus for Humans and Viruses

TEACHING ASSISTANTS (TAs)

Michelle Bach mspark19@stanford.edu (972) 922-1594

Devon: I am a senior majoring in Human Biology with a concentration in Infectious

ver26 9-25-2017 Syllabus for Humans and Viruses

COURSE ASSISTANTS (TAs)

All emailed files should follow the following naming convention:

Although this is longer and annoying, it is extremely helpful and descriptive.

ALL FILES NAMES MUST INCLUDE YOUR NAME. REALLY! REALLY!

ver26 9-25-2017 Syllabus for Humans and Viruses

ASSIGNMENT OF VIRAL FAMILIES (Autumn quarter)

ver26 9-25-2017 Syllabus for Humans and Viruses

VIRAL MODEL (Autumn quarter)

MODEL MARATHON (Autumn quarter)

ver26 9-25-2017 Syllabus for Humans and Viruses

MEDIUM ARTICLE (AUTUMN QUARTER)

Students are expected to write one article to be posted on Medium or another

OBSERVATIONS (Autumn and Winter)

Observations are 1-2 sentence reflections on course material. Students are

TWITTER (Autumn and Winter)

To set up an account, go to http://twitter.com/

To post to the class twitter, begin your twitter with @humansandviruses.

You can see the class posts at http://twitter.com/#!/humanandviruses

WIKIPEDIA (AUTUMN AND WINTER)

PATHOGEN CARDS (AUTUMN AND WINTER)

ver26 9-25-2017 Syllabus for Humans and Viruses

As much as possible, card information should be as accurate as possible in terms

ver26 9-25-2017 Syllabus for Humans and Viruses

VIRAL WEB PAGES (Winter)

10 things to remember about your family

Additions and corrections to prior students pages

Web pages should also include:

The course web page (http://web.stanford.edu/~siegelr/virus/humvir.html)

ver26 9-25-2017 Syllabus for Humans and Viruses

The timeline content is due February 16, 2018.