Global Change and Infectious Disease—Biology 173
Spring 2016
Professor Fred Cohan
Date / Subject1 / Jan 21 / The age of humans, as seen by pathogens(Cohan 2016), Ch. 1*.
Introduction to the breadth of human impacts upon the biotic world; the physics of global climate change; abiotic and biotic evidence for global warming; tour of the multifarious ways that humans have altered the environment with impact on pathogens
2 / Jan 26 / Primer on ecology and evolution of infectious diseases.
Diversity of pathogens(Sherman 2006), Ch. 1*, (Wolfe 2011), Ch. 1*; proteins and DNA(Klug 2006), pp. 5-7†; natural selection(Futuyma 2005), pp. 247-252†; evolutionary trees(Sadava et al. 2014)†.
3 / Jan 28 / Human ecology and the origins of infectious disease in our history (Part 1) (Cohan 2016) Ch. 2*.
The dangers of hunting in our prehistory (Wolfe 2011), Ch. 2*, and now (Quammen 2012), Part VIII*; digression on phylogeny and molecular clocks and application to HIV (Mindell 2006), Ch. 3*, (Worobey et al. 2008), Figs. 1-2†.
4 / Feb 2 / Human ecology and the origins of infectious disease in our history (Part 2) (Cohan 2016), Ch. 2*.
Microbial cleansing of early humans (Wolfe 2011), Ch. 3*; the chronic and latent diseases of hunter-gatherers; agriculture and the origins of acute, “childhood” diseases; domestic animals as sources of our acute diseases(Diamond 1997), Ch. 11*.
5 / Feb 4 / Natural holocausts—globalization of infectious diseases in human history (Part 1) (Cohan 2016), Ch. 3*.
Trade among ancient civilizations and the spread of diseases; the Plague of Athens(Thucydides 1972), p. 151-156* (actually much earlier than 1972, of course); effects of ancient diseases on social development (Morris 2010), Chs. 3, 6*; increasing trade and spread of disease and the demise of the Roman Empire; in particular, malaria (Sherman 2006), Ch. 3*, the Antonine and Cyprian plagues (Harper 2015)†, and Justianian’s Plague (Sherman 2006), Ch. 3.
6 / Feb 9 / Natural holocausts—globalization of infectious diseases in human history (Part 2) (Cohan 2016), Ch. 3*.
The Black Death, its geographic origins and the ecological changes underlying its return to Europe(Morelli et al. 2010), Figs. 1-2†; smallpox, its geographic origin and the timing of its entry into humanity(Shchelkunov 2009), Fig. 1†; the spread of European childhood diseases into the New World and the resulting holocaust of Native American peoples(Mann 2005), Ch. 4; why Native Americans were susceptible to these diseases.
7 / Feb 11 / Globalization today—local spillovers go viral with unnerving frequency (Part 1) (Cohan 2016), Ch. 4*.
The Homogenocene (Mann 2011), Ch. 1; spread of human diseases through transport of non-human animals; transport of (non-human) animal and plant plagues; emerging threats of human pandemics, including SARS and Ebola (Quammen 2012), Ch. 37-40.
8 / Feb 16 / Globalization today—local spillovers go viral with unnerving frequency (Part 2) (Cohan 2016), Ch. 4*.
Emerging threats of human pandemics, including HIV(Quammen 2012), Part VIII*,(Faria et al. 2014), Figs. 1-3†, and MERS; worldwide spread of locally established pathogens, including West Nile Virus (Kilpatrick 2011)†, Chikungunya (PAHO 2015)†, and Zika (WHO 2015)†; predicting where a pathogen will next spread (Feldacker et al. 2011)†, (Talbot 2014)†.
Review session for Exam 1: Wed., Feb. 17, 8-10 PM, Exley 150
Feb 18 / Exam 1 on Lectures 1-8, ThursdayFeb. 18, in class
9 / Feb 23 / The ecology of spillovers—how humans and other creatures become exposed to novel diseases (Part 1)
Disease gateways into humanity: bushmeat hunting and butchering (Wolfe 2011), Ch. 8-9*; primates, rodents, bats, and domestic and commensal (Firth et al. 2014)† animals as sources of novel diseases in the past and future; what is it about bats (Quammen 2012), Part VII*; the role of unsavory medical (Pépin 2011)† and agricultural practices (Wolfe 2011), Ch. 8, (Mann 2011), p. 220-231*.
10 / Feb 25 / The ecology of spillovers—how humans and other creatures become exposed to novel diseases (Part 2).
Recurrent spillovers of a disease from one reservoir and the efficacy of treating the reservoir population (MERS, Ebola, and Fasciolosis); super-spreaders and tipping points (Gladwell 2000), Ch. 1*; how to identify the animal source of a novel human species (phylogenetics and beyond) (Yip et al. 2009), Figs. 1-3†, (Haydon et al. 2002)*, (Liu et al. 2010), Figs. 1-2†.
11 / Mar 1 / The ecology of spillovers—how humans and other creatures become exposed to novel diseases (Part 3)
Predicting where and from whom the next spillover will emerge (Menachery et al. 2015), Fig. 1†, (Jones et al. 2008), Fig. 1, 3, Table 1†, (Wolfe 2011), Ch. 10*; a phylogenetic perspective on identifying the viruses most likely to mump species(Jackson and Charleston 2004)†; biogeography and the disease eco-regions of the world (Just et al. 2014)†; anthroponosis (zoonosis in reverse) (Mayr 1989)†, (Quammen 2012), Ch. 10†,(Solomon 2013)†.
12 / Mar 3 / The evolution of spillovers—how a wild-animal pathogen refocuses on humans.
Evolutionary stages toward becoming a human pathogen (Woolhouse and Gaunt 2007)*, (Woolhouse et al. 2005)*; how infection in alternative “bridge” hosts can foster evolution toward a new host (Allison et al. 2012)†; how immunosuppressed humans may act as a bridge (LeBreton et al. 2007)†, (Anonymous 2012)†; role of changes in existing genes (Streicker et al. 2012)† versus horizontal acquisition of novel genes (Veyrier et al. 2009)†.
Essay 1 is due in class—March 24
13 / Mar 22 / Evolutionary fine-tuning of a pathogen’s symptoms and transmission—tracking the host’s ecology.
How the mode of transmission determines the optimal level of virulence (Ewald 1993)*,(Sherman 2006), Ch. 1*; evolution of increased and decreased virulence in HIV (Ariën et al. 2007)*,(Ariën et al. 2005)†; evolution of lower virulence in syphilis in its first century in Europe (Knell 2004)*; recent increases in virulence in West Nile (Kilpatrick 2011)†; increased virulence in Chikungunya(Powers and Logue 2007)† and Zika(ECDC 2015)†.
14 / Mar 24 / Global warming and infectious disease (Part 1)(Luber et al. 2014), Section on “Disease carried by vectors”*.
Poleward and upward spread of various vector-borne diseases, including malaria (Siraj et al. 2014)†, Blue Tongue Virus (Purse et al. 2005)†, Chikungunya, Rift Valley Fever (Gould and Higgs 2009)†, Tick-Borne Encephalitis Virus (Lindgren and Gustafson 2001)†.
15 / Mar 29 / Global warming and infectious disease (Part 2).
Ecological Niche Modeling (Peterson et al. 2002)† and predicting the future spread of vector-borne (Peterson 2009)† and reservoir-based (Daszak et al. 2013)† diseases; challenges of predicting a pathogen’s future range when vectors can evolve to tolerate warmer climates (Egizi et al. 2015)†;predictions of greater food poisoning in a warmed world (Kovats et al. 2004)†, but perhaps less influenza (Lowen et al. 2007)†; novel diseases in Arctic animals due to global warming (Burek et al. 2008)†.
16 / Mar 31 / Changes in precipitation and infectious disease: fluctuations in Central Asian precipitation and Plague in Europe (Stenseth et al. 2006)†, (Schmid et al. 2015); El Niño and Sin Nombre Virus (Dearing and Dizney 2010)†; climate-change-induced extreme flooding and water-borne infectious disease and rat-borne diseases (Firth et al. 2014)†; climate-change-induced drought(Chase and Knight 2003)† and mosquito-borne diseases(Brown et al. 2014)†, (Rocha 2015)† and meningitis (Cuevas et al. 2007)†.
Review session for Exam 2, Monday, April 4, 8-10 PM, in Exley 150
Exam 2 on Lectures 9-16, Tuesday April 5, in class
17 / Apr 7 / Infectious diseases caused by poverty, neglect, greed, and war in modern times. Public health works inspired by “socialism of the microbe” (Tomes 1998), Ch. 5*, and demise of public health works with ascendant conservativism;(McGuire 2010), Ch. 11*;diseases spread by rats (Firth et al. 2014)†; the inability of poor countries to deal with emergent diseases such as Ebola and to treat chronic diseases such as AIDS and tuberculosis (Mendelson et al. 2015)†; the problem of war and collapsed infrastructure on infectious disease, especially with a novel spillover (Gayer et al. 2007)*.
18 / Apr 12 / The miracle and decline of antibiotics.
The miracle (Levy 1992), Chs. 1-2*; evolution of antibiotic resistance (Groopman 2012)*; abuse of antibiotics in agriculture (Harrison et al. 2013)†; ubiquity of antibiotic resistance genes in the environment and in our gut bacteria (Dantas and Sommer 2014)†; little progress in developing new antibiotics (Butler et al. 2013)† but a new breakthrough with previously uncultivable bacteria (Zimmer 2015)†; support to preserve efficacy of antibiotics from the White House.
19 / Apr 14 / Phage therapy—an alternative to antibiotics (Zimmer 2011) (“The Enemy of our Enemy: Bacteriophages”)*.
The advantages and disadvantages of phage therapy (Bull et al. 2002)†; how to isolate phage to kill a particular bacterium (Synnott et al. 2009)†; steps toward industrialization of phage therapy (Mattey and Spencer 2008)†.
20 / Apr 19 / Global change and the human microbiome.
The various ways that modern living has altered our microbiomes, especially antibiotics (Blaser 2014), Ch. 8*,(Specter 2012)†,(Gordon 2012)†,(Anonymous 2013); a healthy microbiome as defense against gut infection (Grady 2013)†, (Kelly 2013)†; fecal transplants as treatment for a denuded microbiome (Buffie and Pamer 2013)†; antibiotics and weight gain, in both farm animals and humans (Kennedy 2014)†; a healthy microbiome and mental health (Collen 2015)*; various modern plagues caused by antibiotic assault on the human gut microbiome (Blaser 2014), Ch. 9†, 10†, 13*; avoiding antibiotic abuse is not just altruism—it is self-help.
21 / Apr 21 / Forest fragmentation, change in land use, and infectious disease.
The extent of forest fragmentation; forest fragmentation and Lyme Disease (Walters 2003), Ch.4*; forest fragmentation and other diseases (Keesing et al. 2008)*; hemorrhagic fever viruses and changes in land use; Valley Fever and irrigation in the American West (Goodyear 2014)†.
22 / Apr 26 / Infectious disease, extinction, and ecosystem functioning.
Extinctions and near extinctions (Chestnut Blight, Chytrid, Batrachochytrium, White Nose Syndrome); ecosystem effects of infectious disease (Fisher et al. 2012)*; effects of pathogens on keystone species (Collinge et al. 2008)*; why fungal pathogens cause extinctions; some very nasty pathogens that have not caused extinctions; pathogens with wide agricultural implications.
Apr 28 / Essay 2 is due in class
23 / Apr 28 / How we can prevent future plagues (Part 1)
24 / May 3 / How we can prevent future plagues (Part 2).
Review session-Tuesday, May 10, 8-10 PM, in 150 Exley Science Center
Final exam—Wednesday, May 11, 2-5 PM, in 150 Exley Science Center (our classroom).
* Required reading
† Recommended reading
Office hours
In our office hours, you are welcome to ask questions about lectures, class discussions, readings, and other issues relating to the course material.
Fred Cohan (Professor)
Office hours: Fridays 1:15-2:00 in my office (Shanklin 207), and by appointment
Weekly review sessions: Fridays, 2:15-3:15, in Exley 113 (except Exley 137 on Jan. 29)
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Andrew Dingzhong Sun (Graduate teaching assistant)
Office hour: Mondays 1:30-2:30, Shanklin 208
Melissa Bernardo (Graduate teaching assistant)
Office hour: Thursdays, 2:30-3:30, HA 261
Lars Berg (Undergraduate course assistant)
Office hour: Tuesdays,2:30-3:30, Shanklin 312
Will Sawyer (Undergraduate course assistant)
Office hour: Wednesdays, 7:00-8:00 PM, Exley 443.
Hannah Steinberg (Undergraduate course assistant)
Office hour: Tuesdays, 7:30-8:30 PM, Shanklin 208 (in Cohan lab)
Course requirements
We will have two exams during our lecture period, on February 18 and April 5. These exams will be principally short answer, multiple-choice, and fill-in-blank questions. The exams will be based on lecture material, class discussions, and required readings.
Our comprehensive final exam (covering material from the whole semester) will be on the registrar-assigned date. This exam will include questions in the format of our three in-class exams, plus essay questions.
Two short essays will be due on March 24 and April 28. Each essay will answer a question dealing with lecture material, class discussions, or assigned readings. The essays must be typed and submitted as a paper copy. Detailed instructions for each essay are provided on the class web site under “Essay assignments.”
You will be required to participate in class. This will include answering questions in class with your clickers. (These are hand-held radio transmitters that allow you to answer multiple-choice questions in class. You will be responsible for keeping your clicker in good repair and equipped with charged batteries.) Also, you are encouraged to participate in class discussions.
Reading assignments will be posted on our class’s WesFiles web site. Access to the site will be provided in an upcoming email.
Here are the credits for each assignment:
Exam 1 / 150 pointsEssay 1 / 150 points
Exam 2 / 150 points
Essay 2 / 150 points
Final exam / 250 points
Participation (through discussion contributions and clickers) / 50 points
Policy on accommodations for disabilities
It is the policy of Wesleyan University to provide reasonable accommodations to students with
documented disabilities. Students, however, are responsible for registering with Disabilities Services, in addition to making requests known to me in a timely manner. If you require accommodations in this class, please make an appointment with me as soon as possible, so that appropriate arrangements can be made. The procedures for registering with
Disabilities Services can be found at .
Readings
Allison, A. B., C. E. Harbison, I. Pagan, K. M. Stucker, J. T. Kaelber, J. D. Brown, M. G. Ruder, M. K. Keel, E. J. Dubovi, E. C. Holmes, and C. R. Parrish. 2012. Role of multiple hosts in the cross-species transmission and emergence of a pandemic parvovirus. J Virol 86:865-872.
Anonymous. 2012. City health officials investigating deadly bacterial meningitis outbreak among HIV-positive men. CBS New York. CBS Local Media.
Anonymous. 2013. Your microbes, your health. Science 342:1440-1441.
Ariën, K. K., R. M. Troyer, Y. Gali, R. L. Colebunders, E. J. Arts, and G. Vanham. 2005. Replicative fitness of historical and recent HIV-1 isolates suggests HIV-1 attenuation over time. AIDS 19:1555-1564.
Ariën, K. K., G. Vanham, and E. J. Arts. 2007. Is HIV-1 evolving to a less virulent form in humans? Nat Rev Microbiol 5:141-151.
Blaser, M. J. 2014. Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues. Henry Holt and Co., New York.
Brown, L., J. Medlock, and V. Murray. 2014. Impact of drought on vector-borne diseases – how does one manage the risk? Public Health 128:29-37.
Buffie, C. G., and E. G. Pamer. 2013. Microbiota-mediated colonization resistance against intestinal pathogens. Nat Rev Immunol 13:790-801.
Bull, J. J., B. R. Levin, T. DeRouin, N. Walker, and C. A. Bloch. 2002. Dynamics of success and failure in phage and antibiotic therapy in experimental infections. BMC Microbiol 2:35.
Burek, K. A., F. M. Gulland, and T. M. O'Hara. 2008. Effects of climate change on Arctic marine mammal health. Ecol Appl 18:S126-134.
Butler, M. S., M. A. Blaskovich, and M. A. Cooper. 2013. Antibiotics in the clinical pipeline in 2013. J Antibiot (Tokyo) 66:571-591.
Chase, J. M., and T. M. Knight. 2003. Drought-induced mosquito outbreaks in wetlands. Ecol Lett 6:1017-1024.
Cohan, F. M. 2016. Global Change and Infectious Disease.
Collen, A. 2015. 10% Human: How Your Body's Microbes Hold the Key to Health and Happiness. HarperCollins, New York.
Collinge, S. K., C. Ray, and J. F. Cully, Jr. 2008. Effects of disease on keystone species, dominant species, and their communities. Pages 129-144 in R. S. Ostfeld, F. Keesing, and V. T. Eviner, editors. Infectious Disease Ecology: The Effects of Ecosystems on Disease and of Disease on Ecosystems. Princeton University Press, Princeton.
Cuevas, L. E., I. Jeanne, A. Molesworth, M. Bell, E. C. Savory, S. J. Connor, and M. C. Thomson. 2007. Risk mapping and early warning systems for the control of meningitis in Africa. Vaccine 25 Suppl 1:A12-17.
Dantas, G., and M. O. A. Sommer. 2014. How to fight back against antibiotic resistance. American Scientist 42:44-51.
Daszak, P., C. Zambrana-Torrelio, T. L. Bogich, M. Fernandez, J. H. Epstein, K. A. Murray, and H. Hamilton. 2013. Interdisciplinary approaches to understanding disease emergence: The past, present, and future drivers of Nipah virus emergence. Proceedings of the National Academy of Sciences of the United States of America 110:3681-3688.
Dearing, M. D., and L. Dizney. 2010. Ecology of hantavirus in a changing world. Ann N Y Acad Sci 1195:99-112.
Diamond, J. 1997. Guns, Germs, and Steel: The Fates of Human Societies. Norton, New York.
ECDC. 2015. Zika virus epidemic in the Americas: potential association with microcephaly and Guillain-Barré syndrome. Rapid Risk Assessment, Stockholm.
Egizi, A., N. H. Fefferman, and D. M. Fonseca. 2015. Evidence that implicit assumptions of 'no evolution' of disease vectors in changing environments can be violated on a rapid timescale. Philos Trans R Soc Lond B Biol Sci 370.
Ewald, P. W. 1993. The evolution of virulence. Sci Am 268:86-93.
Faria, N. R., A. Rambaut, M. A. Suchard, G. Baele, T. Bedford, M. J. Ward, A. J. Tatem, J. D. Sousa, N. Arinaminpathy, J. Pepin, D. Posada, M. Peeters, O. G. Pybus, and P. Lemey. 2014. HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations. Science 346:56-61.
Feldacker, C., S. T. Ennett, and I. Speizer. 2011. It's not just who you are but where you live: an exploration of community influences on individual HIV status in rural Malawi. Soc Sci Med 72:717-725.
Firth, C., M. Bhat, M. A. Firth, S. H. Williams, M. J. Frye, P. Simmonds, J. M. Conte, J. Ng, J. Garcia, N. P. Bhuva, B. Lee, X. Che, P. L. Quan, and W. I. Lipkin. 2014. Detection of Zoonotic Pathogens and Characterization of Novel Viruses Carried by Commensal Rattus norvegicus in New York City. MBio 5.
Fisher, M. C., D. A. Henk, C. J. Briggs, J. S. Brownstein, L. C. Madoff, S. L. McCraw, and S. J. Gurr. 2012. Emerging fungal threats to animal, plant and ecosystem health. Nature 484:186-194.
Futuyma, D. J. 2005. Evolution. 2nd edition.
Gayer, M., D. Legros, P. Formenty, and M. A. Connolly. 2007. Conflict and emerging infectious diseases. Emerg Infect Dis 13:1625-1631.
Gladwell, M. 2000. The Tipping Point: How Little Things Can Make a Big Difference. Little, Brown, and Co.
Goodyear, D. 2014. Death dust: The valley-fever menace. Pages 52-61 The New Yorker. Advance Magazines Publishers Inc., New York.
Gordon, J. I. 2012. Honor thy gut symbionts redux. Science 336:1251-1253.
Gould, E. A., and S. Higgs. 2009. Impact of climate change and other factors on emerging arbovirus diseases. Trans R Soc Trop Med Hyg 103:109-121.
Grady, D. 2013. Disgusting, Maybe, but Treatment Works, Study Finds. New York Times. New York Times Company, New York.
Groopman, J. 2012. Sex and the superbug. Pages 26-30 The New Yorker, New York.
Harper, K. 2015. Rethinking the Plague of Cyprian: Pandemics and Passages to Late Antiquity. Journal of Roman Archaeology.
Harrison, E. M., G. K. Paterson, M. T. Holden, J. Larsen, M. Stegger, A. R. Larsen, A. Petersen, R. L. Skov, J. M. Christensen, A. Bak Zeuthen, O. Heltberg, S. R. Harris, R. N. Zadoks, J. Parkhill, S. J. Peacock, and M. A. Holmes. 2013. Whole genome sequencing identifies zoonotic transmission of MRSA isolates with the novel mecA homologue mecC. EMBO Mol Med 5:509-515.
Haydon, D. T., S. Cleaveland, L. H. Taylor, and M. K. Laurenson. 2002. Identifying reservoirs of infection: a conceptual and practical challenge. Emerg Infect Dis 8:1468-1473.
Jackson, A. P., and M. A. Charleston. 2004. A cophylogenetic perspective of RNA-virus evolution. Mol Biol Evol 21:45-57.
Jones, K. E., N. G. Patel, M. A. Levy, A. Storeygard, D. Balk, J. L. Gittleman, and P. Daszak. 2008. Global trends in emerging infectious diseases. Nature 451:990-993.
Just, M. G., J. F. Norton, A. L. Traud, T. Antonelli, A. S. Poteate, G. A. Backus, A. Snyder-Beattie, R. W. Sanders, and R. R. Dunn. 2014. Global biogeographic regions in a human-dominated world: the case of human diseases. Ecosphere 5:1-21.
Keesing, F., R. S. Ostfeld, and V. T. Eviner. 2008. Introduction.in R. S. Ostfeld, F. Keesing, and V. T. Eviner, editors. Infectious Disease Ecology: Effects of Ecosystems on Disease and of Disease on Ecosystems. Princeton University Press, Princeton.
Kelly, C. P. 2013. Fecal Microbiota Transplantation — An Old Therapy Comes of Age. New England Journal of Medicine.
Kennedy, P. 2014. The fat drug. New York Times. New York Times Company, New York.