One source I have read recently is an article called SARS-CoV-2 and COVID-19: The most important research questions. Though this article was written in March, I thought it would be interesting to see their perspective of the pandemic back then and what their suggestions for research are. This article presented nine research questions about COVID-19 that they believe would be important to investigate. These included topics such as the origin of the virus, viral pathogenesis, vaccines, treatment & diagnosis, transmission, and asymptomatic and presymptomatic virus shedding.

When reading this article, I learned about the factors that must be addressed when fighting a pandemic. One intriguing possibility presented was the ability for the disease to be transmitted via sewage, waste, contaminated water, air condition systems, and even aerosols. Due to the gastrointestinal involvement in some COVID-19 patients as well as isolation of the disease in fecal samples, the fecal-oral transmission is probable and would explain cases like the Diamond Princess cruise ship. What is also interesting is that in comparison to other coronaviruses, COVID-19 has less specified symptoms, making it harder to control. 12.1% of the persons infected don’t exhibit a fever while SARS-CoV only has 1% and MERS-CoV has 2%. The article concluded that there are two possible outcomes from the pandemic: we eradicate the disease with a vaccine, or it becomes a community-acquired human coronavirus that causes mild respiratory tract disease like the common cold. This provides some cautious optimism.

I also listened to a podcast featuring Siddhartha Mukherjee, an oncologist, and virologist, about the various ineptitudes of the COVID response. He discussed various topics like lack of testing and equipment, slow response, the federal system, masks, traveling, and more. An interesting term he used was a “quasi-lockdown”. He used this term to describe the many states whose lockdown didn’t prevent the spread because people were still able to go out, but also hurt the economy because businesses were forced to close. He believes that businesses should try to run as long as they can, but people should be ordered to stay home. He also brought up the FDA’s and CDC’s slowness to authorize a test. Many private labs came up with their tests and tried to get them authorized but the FDA’s slow response, partly due to snail mail, hampered progress. Mukherjee’s solution was to pre-authorize academic/private laboratories so that they can create an interim test while the FDA and CDC develop their own. Another disturbing piece of information he presented was the initial issue of people rushing to the hospital with symptoms and then being discharged because they weren’t sick enough for a bed. He mentioned how many of those people would return to the nursing homes from the hospital. These nursing homes often did not have enough protective equipment for the staff and residents, exposing the vulnerable elderly to the disease.

For more information, check out my note page for "August 17th Journal Notes".

Sources:

Harris, Sam, director. #214 - A Conversation with Siddhartha Mukherjee (AUGUST 13,

2020). YouTube, 13 Aug. 2020, youtu.be/YX7Mu5NsKVo.

Yuen, Kit-San et al. “SARS-CoV-2 and COVID-19: The most important research questions.” Cell

& bioscience vol. 10 40. 16 Mar. 2020, doi:10.1186/s13578-020-00404-4

Question: What are the human challenge trials and the benefits and dangers associated with it?

This is the most pressing question out of all of those of my last post because recently, there has been a lot of news released about the race to develop a vaccine for COVID-19. Many companies who are developing vaccines are entering their third phase of human trials (i.e. Johnson & Johnson, Merck, AstraZeneca, Moderna, GSK, Bionteck, Pfizer, Sanofi, and NovavazAB). However, the leading company, AstraZeneca has put their trials on hold due to one of their volunteers experiencing an unexplained illness.

The speed at which these companies are going through the vaccine development process raises quite a bit of concern. Usually, vaccine development takes 10 years consisting of multiple phases: preclinical phase, three phases of human trials, licensed phase, manufactured phase, and then the distribution phase. Somehow, companies are finding a way to shorten this process to only 1.5 years, promising a vaccine by the end of 2020. How did they manage to cut 8.5 years of development? I think the answer lies with human challenge trials, which is when people volunteer to be infected with a disease and then take a vaccine to speed up the human trial phases. This method was successful in 2016 with typhoid, but there are still major risks associated with it. By answering the question above, we can have a better understanding of how vaccines are being currently developed. This information could even shed light on the effectiveness of the vaccines produced and whether or not we should take the first full-use public vaccine. Overall, this question is the most important one to me because it’s the most applicable to current events and the concept of human challenge trials is very risky, but also very interesting.

For this assignment, it took me about 4-5 hours over the Monday and Tuesday before it was due to complete. The week before, I brainstormed with Mrs. Gergen, and finally decided on a topic and type of project on my own. I had trouble executing my project because I wasn’t sure how to format it. However, after looking up the lab report and case study analysis paper formats, I felt organized enough to start my piece.

There were a couple of things that I would have done differently. Firstly, I would have started the project a lot earlier. It would have been less stressful and I think that the project would have been more “put together.” I would have more time to brainstorm, research, outline, and edit.

I also wished I had found a way to incorporate data and graphs into my case study. Conducting this study would have been impossible since it’s all fictional and I don’t have the resources for that; however, with some research, I think I might have been able to create my data and graphs based on what I would think would occur if this were real.

I liked my concept for this project. I think it was creative because it’s interesting to tell a story through science. I learned a lot about not only how to write lab/case study reports, but also how much goes into coming up with your study with a small margin of error. Communication-wise, Mrs. Gergen and I were on the same page, and during our meeting, I asked her about quite a few different formats I could use for my project. I didn’t need much help on my project, but I did bounce some ideas off with a classmate.

This month, the issue I have been focusing on is the elimination of viruses. I have recently created an outline of my research for this year and I have decided to focus on 21st-century epidemics/pandemics. Here is the list:

• SARS (2002 - 2003) - 770 deaths

• Swine Flu (2009 - 2010) - 200,000 deaths

• MERS (2012 - present) - 850 deaths and counting

• Ebola (2014 - 2016) - 11,300 deaths

• COVID-19 (present) - 1.12 million deaths and counting

With this focus on the 21st century, I want to investigate the evolution of certain factors of disease over the past two decades. How have technology, traveling, population, and even politics changed the spread of diseases and the severity of epidemics/pandemics? Why did only 770 people die of SARS, but it had the largest R0 value of 3.5 (most contagious) out of all the other diseases listed? By selecting a small-time period to study, I will be able to dive deeper into these questions.

Based on this development, for this SDA, I would like to talk about mutations and how they can help viruses to adapt to their environment to increase infectivity. I want to look into how SARS from 2002 and COVID-19 are related, specifically if COVID-19 is a mutation of SARS. It would be interesting to inspect how the coronavirus strains have evolved over the last two decades and how COVID-19 is mutating now.

Project wise, making a timeline would be an interesting way to organize the various mutations chronologically. It would be easier for the viewer to see the progression of the coronavirus family. To accomplish this, I would probably have to have a visual project. I haven’t decided yet if it would be better to do this on paper or digitally. If I do it on paper, I have some large sheets of construction paper I can use to write out the timeline, the only issue is that my printer is awful at its job. If I do it digitally, I could use a program like Prezi to make an interactive slideshow of some sort. I could even use Kami to combine the two mediums.

I would love to hit all five Cs, but for this project, I am mainly focusing on critical thinking. I want the viewer to be able to analyze the progression of coronavirus mutations when looking at my SDA. It should be like a broken down analysis of the strains of the coronavirus. I am looking forward to the research aspect of this project, but I am dreading the actual execution of the SDA. It’s going to be so much organizing and I can feel the impending frustration I’ll experience, especially if I make it digitally. I am also worried about time management. I need to find a way to break this project up into stages. Regardless, I will get it done, I just don’t exactly know how yet.

Essential Question: How did SARS originate in China? Does it have something to do with the climate, population density, etc?

Recently, I watched this documentary by CBS (it was originally aired in November of 2003) about the SARS outbreak. They delved into the vital months before the WHO declared a global warning about the disease in March of 2003. The documentary went date by date, explaining how the WHO had multiple opportunities to check in with Guangdong province (the origin place of SARS), investigate the disease, and potentially stop the spread. On November 23rd, 2002, a WHO official went to Beijing for a WHO conference. At the conference, he was told by a concerned doctor from Guangdong province that recently, there have been cases of unknown atypical pneumonia that has not only greatly affected patients, but also healthcare workers. After hearing this, the WHO official did nothing. He did not ask doctors from a WHO-affiliated lab in Hong Kong to check out the situation, nor did he inform the head WHO official in the Beijing office about this news. He reasoned that since there wasn’t anything abnormal in the official flu reports from Guangdong, no further investigation was needed. It wouldn’t be until the week of February 10th, 2003, that the world would learn of this disease from a retired US Navy epidemiologist. This man had received an alarming warning from a doctor in Guangdong of an outbreak of cases of atypical pneumonia in hospitals. Concerned and curious, he proceeded to ask online if anyone had heard of this outbreak, and many people responded. Due to the new media attention, Guangdong publicly admitted to the outbreak, and on March 12th, WHO finally issued a global alert.

In the documentary, they mentioned how officials believe that the disease spread from animals to humans in a Chinese wet market. Curious about why Southern China seemed to be the ideal place for disease to fester, I watched a video by Vox, explaining this topic. In Southern China, there is a high population density of both people and animals who live close to one another. Usually, it’s hard for viruses to transmit from humans to animals since they rarely come in contact. However, in wet markets, various exotic wild species come into close contact with each other and humans. The animals are packed into cages that are stacked on top of one another. They are often soaked in excrement, blood, and pus. What’s interesting is that only a small minority of China’s population consumes these animals: the rich. Originally, the consumption of these animals originated from the poor during the famines of the 1970s. However, over time, they became a prosperous market in China. Some theorize that the reason why China was and still is reluctant to permanently shut these markets down is because of the influence of the people who consume the products from this market.

Both of these videos provide information on how SARS came to be. Wet markets, the source of both SARS and COVID-19, are hard to shut down because of the influence of the wildlife industry. As long as they still run, there will be countless opportunities for new outbreaks and pandemic to occur again. On a different note, the lack of action taken by the WHO could be due to various reasons. In the documentary, the WHO officials that were interviewed said that they could receive tips, but couldn’t issue a global warning until the information was verified; and to verify, they have to talk to China. However, they can’t force a sovereign nation to give them information, especially one as powerful as China. Though the WHO may seem helpless, they still had many opportunities to stop the spread earlier. They have offices and officials established in China and they had the authority to step in when SARS had spread internationally. Still, they waited weeks while a global epidemic ensued. It seems that politics, population density, and sanitation all play a part in the origins of SARS in China.

For more information, check out my notes in the “Notes” under “November 13th Journal Notes”.

Citations:

“Covid-19 and Sars: How the World Battled a Deadly Respiratory Disease in 2003 - BBC World

Service.” YouTube, BBC, 4 Apr. 2020, www.youtube.com/watch?v=Hy5gplP0JVw.

“How Wildlife Trade Is Linked to Coronavirus.” YouTube, Vox, 6 Mar. 2020,

m.youtube.com/watch?v=TPpoJGYlW54&t=49s.

“Inside the 2003 SARS Outbreak - Who Was Really to Blame.” YouTube, CBS Studios, 2003,

m.youtube.com/watch?v=0n7pIVS3t08.

I am indifferent about my SDA. I think that it does a good job summarizing the industry and history of wet markets, but it lacked critical thinking. I could have discussed the different perspectives towards wet markets and created an argumentative piece. I could have also looked at wet markets outside of China and relate them to those in China. There are so many things I could have done differently. I kind of conveyed a “So What” - I addressed why wet markets can be bad. Then again, I didn’t dive deeply into how disease spreads in wet markets or how it relates to SARS or COVID-19. So I still lacked substance.

I had been researching this topic a couple of weeks before the deadline however, I constructed the entire project within a day. I need to stop waiting until the last moment to put my project together so that I don’t feel the need to omit certain topics from my project to save time. I wish I could have put more quality into the assignment. Despite this, I am improving on curiosity - I am allowing myself to digress into side topics that I find interesting. Research and interests naturally evolve anyway. The most important thing that I learned from this project is that I need to push myself out of my comfort zone. This applies to both how I present my projects and how I analyze them.

One thing I am proud of is my effort to change the sources I used. Instead of just using the websites, I started to watch videos and documentaries on YouTube. Though this still isn’t a very elevated source, it’s a different way to get information. I am planning on reading books in the foreseeable future to switch things up again. One thing I still need to work on is my collaboration. I need to reach out to more professionals whether they are inside or outside the school. I also need to collaborate with my fellow EMCer's like Nihal, Karsen, and Meryam and see if they would be willing to collaborate with me on an SDA in the future. I plan to research avian diseases that relate to the information that I had learned over this past month.

Overall, I hit Level Two the most in this project because I mainly summarized. I did show some cause and effect by describing the origins of wet markets in the Great Chinese Famine. Plus, I tried to answer some research questions like why it’s hard to ban wet markets as well.

For your reference, my notes for this journal are posted on my Notes page under January 14th Journal Notes.

I have used databases in the past, mainly use the Gale databases (i.e. Academic OneFile, Science, and Health and Medicine). I mostly read scholarly journals and lab reports. Scholarly journals are typically denser than the articles on the public web. However, they tend to be more organized as many are divided into sections, thoroughly addressing many different aspects of their chosen topic. They are more specific in the topics that they address than publicly accessible research texts. Many of the articles I read had a specific question that they were answering, rather than being compiled of superficial information.

Being limited to just scholarly articles proved to be more helpful than I had anticipated. I began skimming the Internet for relevant search terms and testing them out on various databases. Using articles from the databases that gave an overview of my initially broad topic, I found specific concepts that were briefly discussed that interested me. I then began to focus on those smaller topics mentioned and used terms mentioned in the "broader" article as my new search terms. After some trial and error, I found a good amount of articles that proved to be helpful. This experience helped the progress of my project, heightened my curiosity, and advanced my research skills. It was cool to find articles that piqued my interest. Being limited to scholarly articles challenged my patience at times but it was very rewarding in the end. I wouldn’t say the act of reading these journals was intriguing, but the content in them was.

The most challenging part about this SDA was organizing my information and outlining my project. Choosing and simplifying the topics I wanted to address was very difficult. Writing my abstract beforehand helped me to decide on what was the most important information on my topic.

Although I didn’t take the path I had necessarily intended for my SDA, I believe that I answered my essential question. My SDA explained the genetic transfer mechanisms of antibiotic resistance genes from livestock to eventually humans, and how these mechanisms leave humans more susceptible to diseases. My solutions section was vague, but I think I represented the current stance of most scientists on this issue.

In general, I am happy with how my SDA turned out. It was sweet and simple, and I managed to hit all the points I wanted to in about 11 minutes. Using Prezi Video made my project a lot easier to follow. I am proud that I was able to create a comprehensive video project for once. I do wish that I had more editing abilities with Prezi Video (they only allow you to trim the beginning and end of the video). What I am most proud of is incorporating the “So What?” element into my SDA. Unlike most of my projects, I think this time I successfully displayed my critical thinking on why antibiotic resistance is an issue by utilizing diagrams and images to emphasize how easy it is to acquire resistance genes. With the speaking element of my project, I believe my curiosity and enthusiasm for the project came off well, and I was able to communicate my ideas concisely. I am still weak in the collaboration department; hopefully, I can collaborate with my peers, teachers, and possibly interview a professional.

Next month, I will try to have a visual element to my SDA again - it enhances comprehension. I also want to continue practicing simplifying my research so that I become more familiar with the information I gathered. As of now, I am not quite sure what my new essential question for March will be. Originally I had planned to look into the MERS virus, but now I am interested in microbiology and food safety. I am also considering doing a project with the book Spillover by David Quammen and continue my focus on zoonotic transfer. Hopefully, with the help of my coordinator, I will be able to post my question soon.

As I have studied various diseases this year, I have kept seeing the topic of “bats” reappear over and over again. It was as if bats were some kind of "super" viral vector since COVID-19, SARS, the rabies virus, and others were all transferred to humans from bats. I began to wonder what made bats such fantastic viral reservoirs; was it something with their immune system, or their lineage? I think this topic is very significant now especially with COVID-19 because in order to learn about these diseases, we have to understand their origin. With the knowledge of how these viruses transfer from bats to humans, we can begin to search for solutions to prevent this zoonotic transfer from happening. As a result, we could prevent many future epidemics and pandemics.

Currently, I am looking into one of my vital questions from last week about bat flight behaviors (how has roosting and travel/flight behaviors of bats enhanced the spread of disease?).

Recently I have been reading two journals that discuss flight in bats and its association with viruses. The first one is called Bats: Important Reservoir Hosts of Emerging Viruses which the author of Spillover, David Quammen, mentioned in his book (link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1539106). This journal focuses more on the flight patterns of bats. It describes how some bats not only fly daily for food but also have seasonal migration. For example, the Mexican free-tailed bats travel at least 800 miles from their summer caves in Texas and New Mexico to their winter homes in Mexico. Also, silver-haired bats travel seasonally from Alaska, across Canada, and then to Texas. Researchers have found rabies virus variants associated with the silver-haired bats along their migration paths. Their constant travel and their ability to reach distant places enhances the bats’ ability to spread any viruses that they are carrying to domestic animals, and then to humans.

My second journal is called Bat flight and zoonotic viruses (link: link.gale.com/apps/doc/A369064771/EAIM?u=nysl_ca_guild&sid=EAIM&xid=f81b1563). In this article, the authors present a hypothesis that the increase in metabolic activity and higher body temperatures that bats experience when flying may boost their immune system. Bats experience a 15-16 fold increase in metabolic rates when flying. A study mentioned on lab mice with high metabolisms showed that these mice exhibited a stronger immune response than mice with lower metabolic rates. Researchers also saw an increase in leukocyte counts and the size of lymphatic organs (produce immune cells that recognize and eliminate antigens) in mice with higher metabolisms. This study supports the hypothesis and suggests that the daily cycle of flight of bats may activate an immune response within them and allow viruses to persist in the bats without harming them.

My main goal is to show my audience that we need to be paying more attention to bats. There is a major lack of research on bats, and it seems that the general public is unaware of how dangerous they can be. I want to inform my audience more about bats as viral reservoirs so that I can help them understand the impact bats have had and will have on our lives unless we find a solution to prevent these zoonotic transfers. I also plan to discuss ways that we have been encouraging bats to spread disease as well (i.e. via the destruction of caves) so that we can be more aware of our actions.

Citations:

Calisher, Charles H et al. “Bats: important reservoir hosts of emerging viruses.” Clinical

microbiology reviews vol. 19,3 (2006): 531-45. doi:10.1128/CMR.00017-06

O'Shea, Thomas J., et al. "Bat flight and zoonotic viruses." Emerging Infectious Diseases, vol. 20,

no. 5, 2014, p. 741+. Gale Academic OneFile Select, link.gale.com/apps/doc/A369064771/EAIM?u=nysl_ca_guild&sid=EAIM&xid=f81b1563. Accessed 8 Mar. 2021.

Here are my three most pressing questions currently:

1. What are the signs that a pandemic is ending?

2. How do organizations like the CDC and WHO address outbreaks of disease?

3. Why does the COVID-19 pandemic seem to have a much larger impact on everyone’s lives in comparison to other epidemics/pandemics in the last few decades?

Over this past year, I focused on various specific topics related to pandemics (especially their causes) like wet markets, antibiotic resistance in microbes, bats, etc. However, I never really focused on the big picture of pandemics; for example, the phases of a pandemic, how they are addressed, and their impact on daily life. I also haven’t dedicated much time to the current pandemic and how it compares to those of the past. For the symposium, I want to focus on bringing the past and the present together to reflect on this current pandemic while creating possible predictions for future outbreaks.

I am currently leaning towards my first question to use as the basis for my symposium presentation. I want to look more into some past pandemics of similar diseases to COVID-19 (i.e. SARS, MERS, Spanish Influenza) and learn more about how they ended. Then, I can predict some possible endings for the current pandemic as well. Maybe I could also incorporate some of the data and graphs from the disease projection models like the SIR model to gain more statistical insight on how the COVID-19 pandemic could come to a close.

The second question is a good reflective question as well. I specifically want to know more about what kind of team and procedures these organizations have to address outbreaks. This topic could become more of an argument piece as I could analyze what these teams did right and wrong for this pandemic and give an overall evaluation of their performance. Then I could present ideas of how they could improve in the future, or talk about changes that these organizations are already making.

The third question is one that I am more curious about for myself. Though I could make this my symposium topic, I think it may be too subjective. However, I want to know why this pandemic has such a substantial impact on daily life globally. How do scientists categorize which diseases are more dangerous than others? Is COVID-19 more dangerous than SARS or Ebola for example? Was its impact heightened because of social media, politics, population increases, traveling, or globalization? There are so many possible factors that could have culminated to create something so universally influential like the COVID-19 pandemic.