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MCB 532 Human Pathogenic Viruses: Lectures and Discussion Papers

Course description: Students will learn basic and advanced concepts in virology by focusing on major groups of human pathogenic viruses. The major emphasis will be on virus replication, evolution, and pathogenesis. Offered Autumn Quarter of odd years.


This class will next be offered Autumn quarter 2023. The material on this website refers to the curriculum from the Autumn quarter 2021 class. 

Class size is limited to 32 students in the MCB, Microbiology,  Pathobiology, or Immunolgy Ph.D programs. Other programs by permission of instructor.  Add codes are available from Mauro Do <>.

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 a both a lecture and discussion of a paper.

Class is offered autumn quarter of odd years. 

Michael Emerman <>


Time & Location

Autumn Quarter 2021

Tuesdays and Thursdays
1:30-3:00 p.m.
Fred Hutch, Room B1-072/B1-074

(Note: The class will be virtual to start the quarter, but may move to a hybrid format later. There will  be virtual options for attending class regardless. )


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.

Schedule for 2021

Lecture schedule for 2021

How to...

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.


Lecture 1

Thursday 9/30/21: Introduction to Concepts in Virology

Michael Emerman

Read "The Tree-Thinking Challenge" found 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.

Lecture 2


Tuesday 10/5/21: Viral Genetics and Evolution

Michael Emerman

Nature Medicine ,volume 27, pages 434–439 (2021), DOI: 10.1038/s41591-020-01228-y
(you don't need to read the supplemental figures, but extended Figure 5 and extended Figure 8 might help you)

Lecture 3

Thursday 10/721: Paramyxoviruses (Measles)

Michael Emerman


PLoS Biol. 2018 Jun 28;16(6):e2006459


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

Lecture 4

Lecture 5


Thursday10/14/21: Orthomyxoviruses (Influenza II)

Michael Emerman

Science: Vol. 310. no. 5745, pp. 77 - 80 (2005)

Lecture 6

Tuesday 10/19/21: Filoviruses (Ebola)

Michael Emerman


A Highly Pathogenic Avian H7N9 Influenza Virus Isolated from A Human Is Lethal in Some Ferrets Infected via Respiratory Droplets

Cell Host Microbe, Volume 22, Issue 5, 8 November 2017, Pages 615-626.e8


Lecture 7

Thursday 10/21/21: Picornaviruses (Polio)

Michael Emerman

Ebola Virus Glycoprotein with Increased Infectivity Dominated the 2013–2016 Epidemic 

Cell, Vol 167, issue 4, 3 November 2016, Pages 1088-1098.e6

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?

Lecture 8

Thursday 10/26/21: Coronaviruses

Michael Emerman

No paper discussion today.  Please answer the two practice quiz questions and upload them to the Canvas site. 

Lecture 9

Thursday 10/28/21: Genomic Epidemiology of SARS-CoV-2

Trevor Bedford

Lethal Respiratory Disease Associated with Human Rhinovirus C in Wild Chimpanzees, Uganda, 2013

Emerg Infect Dis. 2018 Feb; 24(2): 267–274.



Lecture 10

Tuesday 11/2/21: Alphaviruses

Michael Emerman
2021 Sep 5;2021.08.12.456173. doi: 10.1101/2021.08.12.456173. Preprint

Lecture 11

Thursday 11/4/21: Flaviviruses (West Nile and Zika)

Nisha Duggal

Chikungunya Virus Vaccine Candidates with Decreased Mutational Robustness Are Attenuated In Vivo and Have Compromised Transmissibility

J. Virol 2019 Aug 28;93(18):e00775-19. doi: 10.1128/JVI.00775-19

Lecture 12

Tuesday 11/9/21: Arenaviruses (Lassa Fever)

Vanessa Montoya

Next step in the ongoing arms race between myxoma virus and wild rabbits in Australia is a novel disease phenotype

Proc. Natl, Acad Sci.  2017 Aug 29;114(35):9397-9402. doi: 10.1073/pnas.1710336114.

You can also listen to the TWiV episode about this paper:   . The discussion about the paper starts at the 42 min marks and ends around the 1 hr 28 min mark.

 Take home problem set will be assigned this day, and will be due Thursday 11/18 by class time.  You should submit it to the Canvas site.  You may work in groups of up to 4.   Instructions on the Canvas site


Lecture 13

Tuesday 11/16/21: Retroviruses and HIV replication

Michael Emerman

No discussion paper today. 


Final Projects Assigned

Tuesday 11/16/21: 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.

Lecture 14

Thursday 11/18/21: HIV Pathogenesis and latency

Michael Emerman

No paper discussion today.  Problem set due by class time.

Lecture 15

Tuesday 11/23/21: Poxviruses (Smallpox)

Michael Emerman

 No paper. Use the time to work on your final projects.

Lecture 16

Tuesday 11/30/21: Papillomaviruses

Denise Galloway

 No paper. Use the time to work on your final projects.

Lecture 17

Thursday 12/2/21: Herpes Viruses

Michael Lagunoff

 No paper. Use the time to work on your final projects.

Lecture 18

Tuesday 12/7/21:  Paleovirology and Virus Origins

Michael Emerman

No paper. Use the time to work on your final project.

Last class presentations

Thursday 12/9/21: Last class presentations

Michael Emerman

90 second presentations from students on interesting aspects of your assigned viruses. 

Send me one slide by Wednesday afternoon so that I can assemble them in a random order for Thursday.

Final Projects Due

Due Tuesday Dec. 14 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.