Teaching disease ecology – in the time of COVID-19

In this year's update to his annual post, Krisztian Magori reflects on his experience teaching his disease ecology class at EWU under a stay-at-home order and celebrates the perseverance and dedication of his students in successfully completing this class and five awesome disease ecology research projects from home despite the circumstances. Hopefully a very unique blog post for history!

I never imagined that I will be teaching Disease Ecology in the middle of a pandemic. Granted, we often have pandemics, but rarely one where millions get infected and hundreds of thousands die. I’ll be honest, I was in denial up until Trevor Bedford realized that there have been community transmission in Washington State undetected for at least 6 weeks. I deluded myself that COVID-19 would not get to the US until the CDC announced that we will have to focus on mitigation and not containment. Since then, everything has been a blur.

The Stay-at-Home order announced by Washington Governor Jay Inslee has radically changed how I taught my disease ecology class at Eastern Washington University in multiple ways. First, I had to make sure to provide instruction from home, to the students, also at home, without ever meeting them face-to-face for the entire quarter, and make sure they learn the material. That meant that I had to make a video lecture for each chapter of my textbook (18 total), and then create reading quizzes for each to make sure to not leave any student behind. I processed two chapters of the book each week, reading the chapter myself, creating quiz questions, typing those into Canvas, and then creating the video lectures. Luckily, I had previous slides that I was able to use as starting points, some of them made by students in previous years. Being a disease ecology class, I obviously had to talk about COVID-19; however, I quickly decided that I will not shift the focus of the class entirely to that. In the first week, the students developed a COVID-19 Knowledge Base, asking questions about the pandemic from each other, and providing well researched answers, under my supervision. Early in the quarter, I also conducted a Knowledge, Attitudes and Practices survey on COVID-19 with them, and shared the results with the students, e.g. that while most of them took the pandemic seriously, many of them regardless kept visiting friends and family. Throughout the quarter, I shared with them presentations that graduate students and myself and colleagues gave on the pandemic in our Department, and whenever I could, I connected the material of the textbook of the pandemic. However, I stayed focused on concepts of the class, namely how ecosystems affect diseases and how diseases affect ecosystems, which is much broader than this pandemic itself.

My disease ecology class is a Senior Capstone class. As part of General Education at EWU, it provides an opportunity for students to synthesize and apply what they learned over their years at EWU and in our Biology program. In order to do that, students usually conduct group projects related to the content, in this case disease ecology, with my guidance. It was very important for me to preserve this aspect of the class, and not let it slip away, turning the class into just another upper-level elective. However, how can we do that with students stuck at home, isolated from each other? First, I solicited ideas from the students on projects that they would be interested in doing through an online discussion. Looking through their ideas, I selected common themes that several students highlighted, such as conducting a study on bats or on ticks or COVID-19. Students then had to vote which of these selected themes of their ideas would they be willing to work on, and the five themes with the most votes went ahead as group project topics. One concession I had to make, given the circumstances, was that I allowed some groups to work on systematic literature reviews instead of experimental or observational studies, which would not be sufficient for a project in any other quarter. I also made sure that the topics they chose were feasible to do at home without any of the equipment housed at EWU (such as PCRs and microscopes). Students were allowed to pick the group and project that they wanted to participate in.

The development of group projects proceeded in incremental small steps. First, students had to come up with a specific question or objective related to their topic. Once I provided feedback on those, each student had to find a published scientific article relevant to their group project, and dissect it to determine the methods and protocol of that study. They then used the information obtained to develop their own protocol and write a draft proposal for their group project. This proposal went through a series of reviews, both by the students in other groups, by myself, as well as Katie Johnson, the TA in the class. We were able to hold a Zoom meeting where Katie and I discussed the proposals with the students, answered any questions and provided feedback on their methods and ideas. It was awesome to see some of the students finally in the class, even if through Zoom, and we were able to record the session and post it for students who could not attend in person. The students had to submit a revised version of their proposal, and they were off with their projects (see lightly edited summaries of their projects below). Around the same time, EWU was holding a Virtual Student Research Symposium, and the students in the class were able to participate by submitting posters (with one group doing an oral presentation), mostly on their proposals at that point (see those in the links below). I was very happy that my students still had the chance to present their projects, even if not in person as in other years. In the remaining weeks of the quarter, I closely followed the progress of the students in their projects. In normal times, I would have asked them how they are doing in their projects in class in person. Under these circumstances, I had to do the same through Canvas discussions, which did require more effort. As we got to the end of the quarter, I brought them together again, first helping them analyze the data they collected, and produce results. They then used those results to reach a conclusion, which became the focus of an outline of a report describing their project as a group. We held a Zoom class meeting again to discuss the draft outlines they submitted and provide feedback. They then used their outlines to write scientific articles following the format of PLOS One, and submitted a revised version of their posters and presentation with their results and conclusions.

First of all, I’m very proud of the amount and quality of work that the students have completed during this class. They have all completed all the assignments, and I was able to give an A or an A- for every single student in the class. None of the students dropped the class, despite 2/3 of them losing their jobs, working from home with kids running around, and having all kinds of personal troubles. I very much admire and appreciate their resolve and determination, and will be willing to attest to that for them forever. In addition, they were able to complete meaningful and professional group research projects, not any lesser in quality than students in previous years. I have to admit, I was apprehensive about how we will be able to devise and complete research projects from home, without ever meeting in person or use the equipment at school! The students made it clear that it is more than possible to this, however crazy! Granted, this would not have been possible without the help and support of Katie, my TA and many people at EWU, who helped me order and ship supplies to the students. I grew very fond of the idea of sending do-it-yourself home science kits to the students through the mail. First, I sent out a batch of packages containing a tick collection kit, including a 1-by-1 m corduroy sheet, forceps, a couple centrifuge tubes with ethanol, a Sharpie and a 1 m long piece of twine (see featured image). Myself and my graduate student, Ben Thompson, created videos to show them how to use the kits to drag for ticks. I had them use these kits to try to collect ticks wherever they live, and send me the GPS coordinates where they tried to collect, pictures of the area, and of any ticks that they collected, basically involving them as student scientists in tick surveillance. One of the groups then were able to use the ticks collected to test the efficacy of different tick repellents, which I also sent them in a separate package. I also sent separate packages to another group with Petri dishes containing potato dextrose agar laced with antibiotic so they can grow the spur blight fungi parasitizing their raspberry canes, and test different fungicides (and I forgot to send them the disks which they solved with coffee filters). The mailing service from EWU was also critical for getting these packages to students, and I very much appreciate that.

So, what did I learn from this experience? First of all, I learned that it is possible to teach a quality disease ecology Senior Capstone class online with both instructors and students at home, without any university facilities, and conduct quality research group projects. I also learned that it takes heck of a lot more effort and intentional coordination to do that, both on the part of the instructors, staff and the students, than otherwise. I’m as exhausted as I was when I was teaching for the first time five years ago, and I really hope that I don’t have to do this again in Spring 2021! Regardless if I do, I will have all my video lectures already made, which will allow me to focus on enhancing the class with more active learning activities and discussions during class time. If we’re still at home, I plan on holding more live synchronous Zoom meetings, using PollEverywhere to quiz the attending students on the spot to gauge their understanding and uncover where more discussion is needed. This will also improve the overall dynamic and cohesion of the class. Despite not being able to meet any of my students throughout the quarter face-to-face, I do feel I developed a relationship with them as an instructor, and got to know them through their inputs and submission. However, it’s still not the same as being in the same classroom for ten weeks! If I do this again, I will try to shorten the development period of the group projects, as this time we got lucky that they were able to finish before the end of this quarter. All in all, I do consider this class a success, and based on some limited feedback, I believe that students learned a lot and enjoyed it as much as possible, given the circumstances. This will certainly be a memorable year, and a testament to what is possible if we have enough resolve and determination!

What makes bats special so that they are reservoirs for so many different pathogens?

By Deion Anderson, Eleanor Gorkovchenko, Nicole Hamada, Carolina Martinez, Lupe Martinez

As we speak, there is an ongoing global pandemic that is consuming the lives of thousands of individuals. Starting in Wuhan China, presumably in December 2020, COVID-19 is believed to have spread from infected bats. Our focus was studying bats as hosts to zoonotic pathogens. We conducted a systematic literature review in order to analyze why bats serve as reservoirs for so many different diseases in an attempt to find a solution. We found that bats have immune systems that are primed and ready to combat infection by walling the virus out of cells. In addition, bats have a relatively high metabolic rate, in part due to flying, which results in an overall increased body temperature. This characteristic is hypothesized to lead to more virulent pathogens as they adapt to these febrile conditions. Thus, when a virus participates in a spillover event to humans, the resulting virus is highly adapted to extreme conditions and therefore will be more likely to persist in humans. This hypothesis is known as the “flight-as-fever” hypothesis, and although it has not been proven, it does provide a plausible explanation for the metabolic adaptation of the virus, as well as the selectivity for virulence. Similarly, their flight patterns and their lightweight bodies make viruses hard to stay contained within individual bats for a long period of time. Such a high immune response helps the bats, but also encourages a swift spread; it’s highly transmissible yet not destructive to them individually. Animals with more sluggish immune systems are more likely to be overwhelmed by the virus. Bats that live in temperate regions have to deal with winters by either hibernating or migrating. They cluster in groups as a way to conserve energy when hibernating. These groups can range from a couple hundred to hundreds of thousands of individual bats.This pattern can rapidly spread disease throughout the group infecting all viable hosts.  Some cave ecosystems my be maintained by bats by bringing in an outside energy source (their guano, or droppings) to caves that lack any other source of energy. Their guano serves as a source of food to other cave creatures. However, their infected guano can then infect other organisms further spreading the disease. By understanding bats’ immune response, flight and roosting patterns we were able to find some reasons why bats serve as special reservoirs for so many different diseases. The future of disease ecology relies on the importance of exposing future medical professionals to disease ecology early in their education, and we are grateful to be taught in such a chaotic time.

Pregnant Mothers, Fetuses, and the Placenta Against HIV

By Kristine Colglazier, Drea Flores, Maksim Kalpakchi, Emma Oaks, Jenna Ryan

Human Immunodeficiency Virus (HIV) originated in West Africa from a type of chimpanzee that was discovered to have SIV (simian immunodeficiency virus). SIV mutated into HIV when humans presumably consumed the meat of infected animals and the virus was able to infect and replicate. The first known case of HIV-1 (the predominant strain in the developed world) was recorded in 1959 but the transmission mechanism and date of infection was unknown. However, researchers now know that the virus is transmitted through the bodily fluids of an infected individual as an STI (sexually transmitted infection) and from mother to fetus during pregnancy, after birth, and through breastfeeding. Within years of infection, HIV is known to cause AIDS (acquired immunodeficiency syndrome), a potentially life threatening condition that weakens the immune system and can be fatal due to other infections persisting in the body. Our research was focused on specifically how the HIV virus affects pregnant mothers and their fetuses. Our questions in this project involved understanding HIV transmission from mother to fetus, how the placenta plays a role in fetal protection, and how prevention and treatment occurs during pregnancy. To answer the questions of these processes, we conducted a meta-analysis of about 20 different scientific articles relating to our topic. We did a keyword search in Web of Science using “placenta, HIV, transmission, and placenta” subsequently reducing the number of articles by selecting only reviews. All the group members read the articles and filtered them based on inclusion criteria. Articles were included if they discussed the topics of placental transmission of HIV, detrimental effects to mother and child, as well as treatment methods. Data was collected from the chosen articles on the topics of adverse effects found in mothers and babies, as well as the mode of transmission between mother and babies focusing on mechanism of placental transmission, possible birth defects, and differences in infection between pregnant mothers versus non-pregnant mothers. We learned that the placenta acts as a physical barrier to protect the fetus from infection and toxic materials. It is possible for HIV to cross the placenta and infect the fetus but at a much lower incidence than from breastmilk or exposure during birth. Antiretroviral medicines are very important and effective for treatment of HIV in pregnant women. Antiretrovirals taken during pregnancy or just before the birth of the fetus lower mother to child transmission from 20% to less than 2%. Additionally, antivirals taken by the mother can diffuse through the placenta to provide the fetus with improved defenses in the instance
that the fetus were to contract HIV from the mother.

Homemade Remedy Might Work Best Against Raspberry Spur Blight

By Courtney Graham, Ashley Kelley, Cole Sherwood

Petri dish with culture of Didymella applanate and antibiotic disks immersed in fungicide

Our group project was on testing 3 different fungicides on raspberry plants infected with Didymella applanate,  which causes spur blight. The group consisted of three students, who each had 4 plants. One person tested a systemic fungicide that contains synthesized mono- and di-potassium salts of phosphorous acid (phosphonic acid), which serve as the active ingredients. This was applied to three out of the four plants, the fourth plant was the control. This process was repeated with a second group member; however, they tested a contact copper fungicide. Finally, the third member treated the same number of plants with a home-made sodium bicarbonate mixture, which is just a quart of water with a tablespoon of baking soda and a few drops of dish soap. At the beginning we expected the systemic fungicide to be the most effective. We had about three weeks to do this project and after the first treatment, we swabbed the plants and did cultures of the fungus. Our results showed that the systemic fungicide had the greatest effect on the fungus, however also shows the most foliage damage. The copper didn’t really have an effect, and the sodium bicarbonate worked a little, but had a positive effect on plant growth. All in all, this was a fun experiment, and it turns out that maybe using a homemade remedy might be a better option when trying to treat fungus without killing the plant.

Lemon Eucalyptus proves to be just as effective in repelling ticks as DEET, and both are more effective than Picaridin

By Katherine Bunakov, Caleigh Carlson, Marianna Denully, Doug Gourley, Kyle Keenan, Jordan Rupley

Dermacentor tick in circle trying to climb up
Master handling of tick with forceps and vial at the same time 🙂

Ticks are a species of arthropod that have been known to cause illness in unsuspecting hosts upon being bitten. With this information in mind, determining the most effective solutions to preventing a tick bite is important to consider from both a disease ecology and public health standpoint. Individuals are capable of protecting themselves through wearing protective clothing, avoiding tick prone areas, and by using tick repellent. As our capstone research project, we set out a goal to figure out the most effective tick repellent of the following three found in grocery stores: Off! Deep Woods Insect Repellent VII, Repel Plant-Based Insect Repellent Lemon Eucalyptus Insect Repellent, and Sawyer Picaridin Insect Repellent. These options contain two chemical based repellents (DEET and Picaridin) and one homeopathic repellent (Lemon Eucalyptus). In order to test these repellents, we each individually collected ticks in Washington State and Idaho. It is important to note that Dermacentor variabilis and Dermacentor andersoni are the most common tick species found in Washington and have been found to spread disease. The method of study we used to conduct our research was to simply collect the ticks from various locations within the Eastern portion of Washington state and Northern Idaho. The corduroy blanket that was supplied from Dr. Magori was then cut into four 18 x 24 inch pieces and each piece was treated with a specific repellent, including tap water as a control variable and the blankets were hung in vertical position. The ticks were then placed in the center of the blankets within a 5 cm diameter circle, and their activity was observed for two minutes. The movement of the ticks was the factor that was used to determine if the repellent was effective or not. Within two minutes if the ticks dropped from the blanket we considered it a positive result (repellent worked) and if the ticks climbed upward (at least 5cm) we considered it to be negative (repellent did not work), while no movement from the ticks was considered an inconclusive trial. As a result, we found that the data between the Off! Deep Woods Insect Repellent VII and Repel Plant-Based Insect Repellent Lemon Eucalyptus Insect Repellent were comparable in measure and were far better in repelling ticks than water or the Sawyer Picaridin Insect Repellent. All in all, it is important to note that the use of tick repellent will deter ticks from biting a host and prevent tick-borne disease from arising.

Mathematical Modeling of COVID-19 and the Potential Effects on Eastern Washington University’s Student Population

By Brinae Brown, Tiffany Jordan and Zack Wright

COVID-19 potential health outcomes at EWU with no interventions

The World Health Organization announced the official name of COVID-19 on February 11, 2020 to identify the novel coronavirus outbreak first identified in Wuhan China. We understand that COVID-19 spreads through respiratory droplets, coming in close contact with people can increase the spread of this virus. There’s an assumed straightforward connection between social distancing parameters and the rate of COVID-19 infection. To predict the outcome of COVID-19 on Eastern Washington University, we need to understand which parameters would have the greatest impact on the given population. Once we understand the importance of the given parameters, social distancing, testing of exposed or infectious and tracing of exposed or infectious, we can apply each to the simulation population and observe the effects. We can make important conclusions such as, if reopening class at EWU for fall 2020 is safe. This is important because we can implement rules before the quarter starts to prevent new infections and deaths.

Eastern Washington University is located in Cheney, Washington with a student population of 12,326 as of Fall 2019 according to EWU’s enrollment page. We used a software, Covasim; a stochastic agent-based simulator designed to be used for COVID-19 epidemic analyses. The model explores potential impacts of different interventions (https://covasim.idmod.org/). Each individual is categorized by the susceptible, exposed, infectious, and recovered/dead as per the SIR disease model. The model creates a simulation object with parameters and a population with demographics and comorbidities is additionally generated. Agents in a network are then looped in an integration of dynamic scaling, health constraints, agent updates, disease progression, importation events, applied intervention, calculated disease transmission events across the contact network, and finally the collation of outputs in results arrays (Kerr & Stuart et al. 2020).

We used a control and manipulated comparison of treatments where the total cumulative infections will be our measurement of severity of outbreak. More specifically, we analyzed the data by comparing statistical significance by a one-tailed t-test with a significance value set at 0.05.  Our control was defined as having 0% intervention on all four general parameters with variation among infectiousness (beta), the level of different interventions, the number of people on campus, and the length of the quarter. Our initial infections was set to one to represent a hypothetical initial infection coming into the EWU community. Each scenario was tested ten times each to account for variability and compared to the control treatment and to each other to find statistical significance.

COVID-19 potential health outcomes with only 7000 people on campus with 50% social distancing with a 40 day quarter

Our evidence shows a significant difference between moderate and aggressive social distancing at almost all levels excluding outbreaks starting with three infections. In all 3 population parameters, quite similar result patterns appear despite the differences in initial numbers. In every scenario tested, statistical differences were seen in every differing treatment level where 80% social distancing would always be better than 50%. It was interesting to note the ineffectiveness of light 10% testing where 10% of people showing symptoms are tested per day. It was shown to be statistically insignificant to test people while also social distancing and it could be reasonably assumed that if more interventions were put in place it would be even harder to notice the difference strictly by looking at cumulative infection numbers. It could be reasonably assumed that in a larger population with more networking that testing would make a more significant impact on reducing subsequent infections. We also saw separately that the only way to avoid fatalities related to spread on campus was to have no more than 50% of the population on campus for only half the quarter, with at least 50% social distancing. This does bring good news however, because the data supports that moderating your social contacts which does not cost money is the most effective way to reduce the spread and therefore the prevention of a local outbreak at EWU is economically feasible.


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