Epidemics - the Dynamics of Infectious Diseases

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Course Date: 29 September 2014 to 24 November 2014 (8 weeks)

Price: free

Course Summary

Malaria, HIV/AIDS, Influenza, Measles - we’re in a constant battle against infectious diseases. This is a course about the dynamics of such diseases - how they emerge, how they spread around the globe, and how they can best be controlled.

Estimated Workload: 1-2 hours/week

Course Instructors

Ottar Bjornstad

Ottar Bjornstad, PhD is a theoretical ecologist working as a professor in the Departments of Entomology and Biology. His main interests are population ecology and population dynamics with particular emphasis on mathematical and computational aspects. He is also an adjunct professor in the Department of Statistics, and carries out research in statistical ecology and in methods for analyzing spatiotemporal data.

Ottar is involved in many collaborative studies on the outbreak and persistence of infectious disease.

His work has five interrelated themes:

  • Ecological statistics: how can we test theories about spatiotemporal variation using abundance data?
  • Population dynamics: how do the interactions between individuals and between individuals and the environment determine fluctuations in abundance? What are the effects of heterogeneity in the environment?
  • Interactions between species: how do competition, predation and parasitism affect disease dynamics?
  • Spatial dynamics: what causes regional synchrony or asynchrony in fluctuations?
  • Ecology of infectious disease: how do host and pathogen characteristics affect incidence of disease?
He combines mathematical modelling with analysis of empirical data sets to generate and test hypotheses.

Rachel Smith

Rachel A. Smith, PhD is an Associate Professor of Communication Arts & Sciences and Human Development & Family Studies, and an Investigator in the Center for Infectious Disease Dynamics and the Methodology Center at the Pennsylvania State University. Smith studies social influences in health.

Her research program focuses on how social identities, social interactions, and social memberships shape and are shaped by communication. She uses a variety of quantitative methods, including dyadic analysis and social network analysis, to study patterns of relationships as well as interpersonal or intergroup influences in persuasion and compliance. She tends to focus on social health conditions, such as infectious diseases and genomics. Her current research centers on building and testing theories focusing on the relationships and dynamics among stigmas, communication, and health.

She has expertise in health message design and evaluation, and extensive experience with the evaluation of funded programs nationally and internationally. For example, she led the community-characteristics research arm of PEPFAR program evaluations with JHUCCP for Namibia (2004-2007), including network mapping and analysis, completed formative research to inform the development of two innovations for malaria and food security in Mozambique (2009-2011), and contributed to a working team focused on scale up for impact for the Gates Foundation (2012). She has made numerous presentations in scientific, technical, policy, and advocacy fora, and authored over 50 scientific, technical, and public health articles and chapters, the majority in peer-reviewed journals.

Her specific CIDD-related interests include:

  • Identifying critical message features and critical people within social networks that facilitate and inhibit the diffusion of beliefs, attitudes, or behaviors related to managing health and well-being
  • Identifying impacts of social influence (e.g., social networks, support, norms, and stigma) on communicators' susceptibility to health aliments and immunity
  • Developing and extending theoretical models of stigma communication and label management
  • Optimizing network-based interventions (e.g., opinion leader designs), entertainment-education interventions, and the diffusion and adaptation of evidence-based interventions to new target audiences and communities.

Mary Poss

Mary Poss, PhD is a professor of biology and of veterinary and biomedical sciences and a member of the Center for Infectious Disease Dynamics and the Center for Comparative Genomics and Bioinformatics. She researches the molecular mechanisms of virus adaptation to changing host environments spanning cellular to population scales.

Among her research interests are:

  • Viruses as Rapidly Evolving Markers of Host Population Dynamics which uses rapidly evolving virus genes as markers to study recent changes in host population demographics. This approach has application to species conservation and to the ecology of infections in natural host populations.

  • Emerging Virus Infections: Newly recognized diseases in humans and animals often arise from infections with viruses that naturally reside in a different host species. She uses experimental systems and computational methods to determine how viruses respond to new host environments.

  • Viruses and Innate Immunity: Mary uses an in vitro system to examine the spatial and temporal dynamics of cell-specific innate responses to primary infection by acute respiratory viruses and consequences to establishment and spread of a secondary virus. She uses an in vivo system to integrate temporal changes in host innate responses and virus genomes in systemic lentivirus infections.

  • Pathogen Interactions: Simultaneous infection with multiple parasites is a common phenomenon; however, the effect of coinfecting species on the course of infection for either parasite is often not investigated. Mary studies the molecular mechanisms of disease attenuation that occur during coinfection with virulent and apathogenic distantly related feline lentiviruses.

David Hughes

David Hughes, PhD an assistant professor of Entomology and Biology at the Center for Infectious Disease Dynamics where he studies the role of behavior in driving disease in insect societies and agroecosystems. His interests lie in parasites and behavior; especially in situations where the host is social as in the case of ants and humans.

Role of behavior in disease transmission is of particular interest. At one extreme we have parasites that have evolved strategies to control host behavior and at the other there is the ability on the part of hosts to completely avoid infection through behavioral defense. To approach the former he uses ants and other insects that are manipulated by diverse parasites. Most of David's recent work has been on fungi that control ant behavior- the zombie ant phenomenon which is one of the most dramatic examples of behavioral manipulation we know about.  To approach the latter example (of behavioral defense) David and his group study ant societies in both the rainforest and the lab to ask how to the recognize and avoid disease.  David takes his understanding of disease in rain forests and works in tropical farms that have come to replace forests to ask how the ecological disruption affects the spread of plant diseases. 

Humans are also social of course so studying disease in ants leads one to think of disease in humans.  David has recently become very interested in human behavior and in particular the expression of altruistic care by certain individuals during epidemics. David is working on the thesis that belief systems shape the expression of this behavior. 

David is very interested in biodiversity and life histories and how extreme our lack of knowledge is in this regard. A lot of his work is in tropical rain forests on understudied taxa which drives home the apparent ignorance we have.  Such simple things as the behavior of infected individuals and vectors; or the diversity of parasites in apparently well known groups remain unknown.  This lack of knowledge extends to agroecosystems where he works. To remedy this he came up with the idea of linking farmers around the world to share knowledge and together with Marcel Salathe developed  PlantVillage

He is also very much interested in the concept of the extended phenotypes. Finally, he likes architecture and how the cultural evolution of cities shapes the evolution of diseases. 

Peter Hudson

Peter Hudson, PhD is the Willaman Professor of Biology and the Director of Huck Institutes of the Life Sciences, where he focuses on the ecology of wildlife diseases, including zoonoses. His group uses a mixture of fieldwork, laboratory studies and mathematical modeling to explore disease dynamics in three main study areas.

Epidemiology and population dynamics

  • How disease flows through wild animal populations
  • Mechanisms that lead to disease persistence within populations
  • The consequences of individual infections on host population dynamics. For instance, how the sub-lethal effects of infection destabilize host population dynamics by influencing the fecundity of individuals.

  • Identifying variation in transmission between infected individuals — and the role of "superspreaders" in disease dynamics.

Parasite interactions
  • How infection by one disease agent alters host susceptibility to other parasites and pathogens.
  • The consequences of these interactions for host population dynamics.

Much of Peter's work has implications for the control of wildlife diseases, and of emerging zoonotic disease.

Matthew Ferrari

Matthew Ferrari, PhD an assistant professor of biology and statistics at the Center for Infectious Disease Dynamics where he studies the transmission and distribution of infectious diseases and develops mathematical models to explain the impact of vaccination and global change on the incidence of infectious disease. The use of these mathematical and statistical tools assists in his understanding of patterns of disease incidence, and the effects of heterogeneity, in time and space.

Matthew's specific areas of research include:

Measles dynamics in developing countries 
Measles still kills hundreds of thousands of children each year in developing countries. Attempts to eradicate the disease through mass vaccination are hampered by both logistical and epidemiological challenges; for instance, high birth rates can make it difficult to maintain the necessary 95% vaccine coverage.

In collaboration with Medecins Sans Frontières Matthew and his team are investigating local and regional dynamics of annual measles epidemics in West African countries (Niger, Tchad, Democratic Republic of Congo), in order to recommend vaccination strategies to minimize mortality and morbidity due to measles. They are using time series analysis and epidemic models to investigate:

  • The nature of the strong annual seasonality in incidence at the regional scale
  • Local variation in the scale of measles outbreaks

Vector behavior and spatial transmission
Scaling within-host immune dynamics to populations
Dynamics of directly transmitted pathogens on host networks
Statistical methods for estimating transmission rates
  • Discrete time, stochastic models to develop statistical methods to estimate transmission rates for incidence data
  • Computational methods (e.g. Markov chain Monte Carlo) to account for the uncertainty due to imperfect measurement

Scaling within-host immune dynamics to populations
The rapid clearance or long-term persistence of parasites within hosts is determined by the interaction of both parasite life-history characteristics and the immune response of the host to infection. Variation along this axis has implications for the rate of parasite shedding, the accumulation of transmissible stages in the environment, and the encounter rate and transmission rate in naive hosts. Thus, the host immune system is a critical regulator of the cycle of infection and transmission that determines large-scale patterns of parasite distribution and burden at the population scale.

Matthew works with Dr. Isabella Cattadori to study the impact of interactions between worm life-history characteristics and host immune response on population-level transmission processes.  They combine lab-scale experiments in a rabbit/worm model with long-term temporal observations of worm burden and distribution in wild populations of rabbit to quantify the role of within host processes in determining population scale processes.

Dynamics of directly transmitted pathogens on host networks
Matthew uses simulation and analytical techniques to investigate how the spread of disease in social networks of hosts is affected by heterogeneities in contacts and local restrictions on transmission. These have important implications for the scaling of transmission across networks of different size and geometries — and can even lead to structural evolution of the network itself (as hosts are removed by mortality or acquired immunity).

Statistical methods for estimating transmission rates
Disease incidence data are often gathered at spatial and temporal scales that are coarse relative to scales considered by quantitative epidemiological models of host-pathogen systems (e.g. case counts are generally reported over discrete time intervals, while many classic epidemic models employ differential calculus, which makes predictions in continuous time). Furthermore, observed data often suffer from incomplete reporting, imperfect diagnosis, measurement error and other biases. One of the great challenges in quantitative epidemiology is to develop statistical models that provide a coherent link between theory and data. He is developing:
  • Discrete time, stochastic models to develop statistical methods to estimate transmission rates for incidence data
  • Computational methods (e.g. Markov chain Monte Carlo) to account for the uncertainty due to imperfect measurement

Andrew Read

Andrew Read, PhD is an Alumni Professor in the Biological Sciences, professor of entomology and director of Penn State's Center for Infectious Disease Dynamics. He studies the evolution of pathogens, driven by modern medicine and farming.

His research focuses on the ecology and evolutionary genetics of infectious disease, including:

Evolution and virulence

  • How do public and animal health programs affect pathogen evolution (particularly the evolution of virulence)? Having developed a theoretical framework, we are now testing its predictions in laboratory experimental systems.
  • To what extent are parasite virulence and host resistance environmentally determined?
  • How does natural selection resolve the trade-off pathogens face between replication within a host and transmission from it?
  • How does host resistance affect pathogen evolution?
  • Why is malaria not a more serious disease?

Interactions between pathogens
  • When and how do malaria clones coinfecting a host compete? What determines the outcome of competition? How does competition affect clone fitness? How does competition affect the evolution of virulence and other traits?
  • Is within-host competition seen in mixed Trypanosome clone infections?

Phylodynamics and the evolution of immunity
  • How does host immunity shape parasite life history strategies?
  • Do genetically diverse infections make hosts sicker or more infectious?
  • When and how does pathogen-imposed selection favour increased host resistance?
  • How do immune systems evolve?

Control strategies
  • Will vaccination and chemotherapy prompt the evolution of more virulent pathogens?
  • Can entomopathogenic fungi be used to produce a cheap organic pesticide for sustainable malaria control?
  • Can we make evolution-proof drugs, vaccines and insecticides?
  • Much disease is immunopathology. Why does natural selection allow self-harm?

Marcel Salathé

Marcel Salathé, PhD is an assistant professor of biology at the Center for Infectious Disease Dynamics. A Branco Weiss Society in Science fellow, he studies how social networks affect the spread and control of infectious diseases. 

After receiving his PhD from the ETH in Zürich, Switzerland, he spent two years as a postdoctoral research fellow at Stanford University where he studied the effect of human contact network structure on infectious disease spread. His research group currently uses complex systems models, wireless sensor network technology and large-scale data sets from online social media sites to analyze the spread of disease and health behaviors on social networks. 

His group's main goal is to measure and improve health outcomes  with basic research, mobile technology and social media. His research  program includes scholarly work, education, app development (such as crowdbreaks.com and plantvillage.com) and service to the community.

The way he develops his research program is rooted in four observations (in no particular order of priority).

  • Fundamentally, health and disease are biological phenomena, but ignoring the effect of human behaviors on health and disease outcomes would be ignoring the main drivers of health and disease dynamics in the 21st century.
  • The internet – in all its flavors, ranging from static websites, to communication tools such as email, to social media, to the mobile internet (smartphones, sensors, etc.) – has become a source of information about human behaviors at an unparalleled scale. This opens up completely new research fields.
  • The ability to collect, mine, filter, analyze and visualize enormously large data sets from this data source is one of the great practical and educational challenges of our times.
  • Programming is becoming the lingua franca of science.

Course Description

Not so long ago, it was almost guaranteed that you would die of an infectious disease. In fact, had you been born just 150 years ago, your chances of dying of an infectious disease before you've reached the tender age of 5 would have been extremely high. 
Since then, science has come a long way in understanding infectious diseases - what they are, how they spread, and how they can be prevented. But diseases like HIV/AIDS, Malaria, Tuberculosis, or the flu are still major killers worldwide, and novel emerging diseases are a constant threat to public health. In addition, the bugs are evolving. Antibiotics, our most potent weapon against bacterial infections, are losing their power because the bacteria are becoming resistant. In this course, we'll explore the major themes of infectious diseases dynamics.

After we’ve covered the basics, we'll be looking at the dynamics of the flu, and why we're worried about flu pandemics. We'll be looking at the dynamics of childhood diseases such as measles and whooping cough, which were once considered almost eradicated, but are now making a comeback. We'll explore Malaria, and use it as a case study of the evolution of drug resistance. We'll even be looking at social networks - how diseases can spread from you to your friends to your friends' friends, and so on. And of course we’ll be talking about vaccination too. We’ll also be talking about how mobile phones, social media and crowdsourcing are revolutionizing disease surveillance, giving rise to a new field of digital epidemiology. And yes, we will be talking about Zombies - not human zombies, but zombie ants whose brains are hijacked by an infectious fungus. 

We're looking forward to having you join us for an exciting course!


Will I get a Statement of Accomplishment after completing this class?
Yes. Students who successfully complete the class will receive a statement of accomplishment signed by the instructors.

What resources will I need for this class?
For this course, all you need is an Internet connection and the time to watch lectures.

What will I learn if I take this class?
You’ll learn how epidemics unfold - how they emerge, how they spread, and what we can do to stop them. Along the way, you'll learn some basic scientific concepts about infectious disease dynamics.


This course will cover key concepts that relate to the emergence, the spread, and the control of infectious disease epidemics.

We'll cover various broad topics, including:
  • The basics: history of infectious diseases, basic concepts of disease dynamics, parasite diversity, evolution & ecology of infectious diseases
  • Emergence of diseases: The basic reproductive number, critical community size, epidemic curve, zoonoses, spill over, human / wildlife interface, climate change, hot zones, pathology
  • Spread of diseases: transmission types (droplets, vectors, sex), superspreading, diffusion, social networks, nosomical transmission, manipulation of behavior
  • Control of diseases: drug resistance, vaccination, herd immunity, quarantines, antibiotics, antivirals, health communication, ethical challenges of disease control
  • The future of infectious diseases: Evolution of virulence, emergence of drug resistance, eradication of diseases, medicine & evolution, crop diseases & food security, digital epidemiology


This course will consist primarily of video lecture and animations for the majority of the instruction.  To enhance the learning experience there will be a massive virtual simulation of an epidemic unfolding during the course.

Suggested Reading

We will provide you with links to relevant scientific articles in the field that are freely available as open access articles. Examples:

Course Workload

1-2 hours/week

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