Class size is limited to 32 students in the MCB, Microbiology, Pathobiology, or Immunolgy Ph.D programs. Other programs by permission of instructor.
email graduateeducation@fredhutch.org for add codes.
Grading: 40% of your grade is based on class participation, 30% on the problem sets, and 30% on the final project. Every class consists of both a lecture and discussion of a paper.
Michael Emerman <memerman@fredhutch.org>
Autumn Quarter 2023
Tuesdays and Thursdays
1:30-3:00 p.m.
Fred Hutch, Room B1-072/B1-074
Note: The class will be in person. I will record the sessions so that students can review lectures or watch ones they missed. However, it will not be a hybrid class. There may some sessions that are virtual under special circumstances.
If you're off-campus (either UW or FHCRC), click on the appropriate links in this box below before trying to access full text course readings.
Once you've logged in, use your "back" button to return to this page and click on the links to the readings.
FHCRC/MCB students (sign in with your HutchNetID and password). Or, more easily use VPN option that should be downloaded on your computer at the Fred Hutch to access all of the articles.
UW students (use the link to access the UW library and then sign in with your UW NetID login to access all articles)
Let me know if you are unable to access any of the discussion papers through the means listed above or through on campus access.
Lecture schedule for 2023
Download or print a Pdf copy of the lecture before class.
Click on the link for the Discussion papers and you will be routed to the article at the journal's website. You should be able to download a Pdf of the Discussion paper from there assuming that you are on the UW or Fred Hutch campus at the time. See the "Off-Campus?" box on your left for accessing papers when you are not on the UW or FHCRC campuses.
Thursday 9/28/23: Introduction to Concepts in Virology
Michael Emerman
Read "The Tree-Thinking Challenge" found here or here. When you finish, download the supplement at the end of the article and take both quizes on your own by Lecture 3. This short tutorial, How to Read a Phylogenetic Tree will also help you. We will use phylogenetic trees to understand virus evolution and origins in many lectures throughout the course.
Tuesday 10/10/23: Viral Genetics and Evolution
Michael Emerman
Thursday 10/12/23: Paramyxoviruses (Measles)
Michael Emerman
If you feel lost after Lecture 2, you might find some of the concepts easier to understand by reading this short review: Quasispecies Theory and the Behavior of RNA Viruses
Tuesday 10/17/23: Orthomyxoviruses (Influenza I)
Michael Emerman
PLoS Pathog 13(5): e1006371. 2017.
Thursday 10/19/23: Orthomyxoviruses (Influenza II)
Michael Emerman
Tuesday 10/24/23: Filoviruses (Ebola)
Michael Emerman
Thursday 10/26/23: Picornaviruses (Polio)
Michael Emerman
Cell, 2016 Nov 3;167(4):1079-1087.e5.doi: 10.1016/j.cell.2016.10.013.
Reading this preview by Harmit Malik and Trevor Bedford will also help with some of the concepts
Did a Single Amino Acid Change Make Ebola Virus More Virulent?
Tuesday 10/31/23: Coronaviruses
Michael Emerman
Thursday 11/2/23: Retroviruses and HIV replication
Michael Emerman
Tuesday 11/7/23: HIV Pathogenesis and latency
Michael Emerman
1970s and 'Patient 0' HIV-1 genomes illuminate early HIV/AIDS history in North America
Nature volume 539, pages 98–101 (2016).
Also look at Extended Data 2
Thursday 11/9/23: Hepadnaviruses
Jessie Kulsputrakul and Carley Gray
Lens epithelium-derived growth factor fusion proteins redirect HIV-1 DNA integration
P.N.A.S. 2010 Feb 16;107(7):3135-40.doi: 10.1073/pnas.0914142107
Thursday 11/9/23: Final project assignments
Before (or after) the lecture today you will pick a number corresponding to an envelope containing the name of a virus that we have not covered in class. Your project will be on this virus. See attached file for instructions.
Tuesday 11/14/21: Flaviviruses
Leslie Goo
Emerg Infect Dis. 2018 Feb;24(2):267-274. doi: 10.3201/eid2402.170778.
Thursday 11/16/23: Adenoviruses
Edward Arnold
J. Virol 2019 Aug 28;93(18):e00775-19. doi: 10.1128/JVI.00775-19
Tuesday 11/28/23: Poxviruses (Smallpox)
Michael Emerman
No paper. Use the time to work on your final projects.
Thursday 11/30/23: Paleovirology and Archeovirology
Daniel Blanco-Mello
No paper. Use the time to work on your final projects.
Tuesday 12/5/23: Virus Origins and conclusions
Michael Emerman
No paper. Use the time to work on your final project.
Thursday 12/7/23: Last class presentations
Michael Emerman
2 minute presentations from students on interesting aspects of your assigned viruses.
Send me one slide by Wednesday at 2PM so that I can assemble them in a random order for Thursday
Due Wednesday Dec. 13 by 3PM.
You should upload your Powerpoint file to the Canvas site by the deadline. Name your file like this: your last name_name of your virus. If there is a problem, then either email it to me or bring it by my office (C2-019 in the Hutchinson Building) on a flash drive and I will load it onto my computer.