Day: December 2, 2023

  • A Look Back At How America’s Covid Response Failed

    A Look Back At How America’s Covid Response Failed

    Do you remember the days of 2020? Do you remember the uncertainty, the anxiety, and the constantly changing advice? Do you remember waking up every day, checking the news hoping for something better, but just seeing bad news after bad news? Perhaps, one of the most disheartening aspects of it was the expectations of scientists vs. what actually happened. At every turn, the virus proved more mysterious, complex, and unpredictable than what was anticipated. Every time, we thought that it was over and that we could declare mission accomplished, there was always something unexpected waiting for us. Taking a look back at some of these different moments during the Pandemic, my hope is to depict how the virus surprised us at every turn, and the lessons that we can take away for the next major Infectious Disease Outbreak.

    The first surprise that the virus threw at us was that the majority of us believed that our vaccines produced something known as sterilizing immunity. This was the ideal scenario because it meant that not only did the vaccine reduce the incidence of symptomatic and severe disease. However, it also reduced the incidence of infection and how frequently it was transmitted. This meant that, even if someone could not or chose not to get vaccinated, they would effectively be protected because the people around them could not spread the infection. This would decrease the overall community burden of Covid, along with the number of hospitalizations and deaths. Initially, it seemed like our vaccines had the potential to do this. For instance, there were studies in early 2021 showing that “The Pfizer vaccine reduced asymptomatic cases by 89.4%, and symptomatic cases by 93.7%”(Israeli Studies find Pfizer Covid-19 Vaccine reduces transmission). Similarly, many Israeli studies in the early part of 2021 observed the phenomenon that “Vaccines reduced the viral load in the respiratory tract of infected individuals, compared to unvaccinated people who were infected”(Israeli Studies find Pfizer Covid-19 Vaccine reduces transmission). Additionally, as Israel and the United States begun vaccinating their population, cases dramatically decreased. For instance, from January to May, Covid cases in Israel decreased from “1000 million per day to less than 3 per million”(What pushed Israel out of herd immunity? Modeling Covid-19 Spread of Delta and Waning Immunity). Unfortunately, these early signs of optimism were misplaced, and it clouded our judgement and took our eyes off the ball for the challenges that were about to come next.

    Around the same time that the incidence of Covid was decreasing in first world countries like the US, Israel, and the UK, the situation was extremely dire in India. In India, the number of infections were significantly increasing, along with the number of hospitalizations and deaths. The cause was not known yet, at the time. However, in April 2021 in India, “56-65-year-olds were spending an average of 13 days in the hospital”(Covid-19 Mortality in the Delta Wave in India: A Hospital-Based Study from Ramanagara District, Karnataka). Additionally, “77-84.62% of individuals in hospitals were completely out of breath, and WBC count was significantly elevated in over 40% of cases”(Covid-19 Mortality in the Delta Wave in India: A Hospital-Based Study from Ramanagara District, Karnataka).  In other words, there were early indications that there was something going on in India that was causing the pathogenicity of Covid to increase, and a significant number of people to get Covid to become seriously ill. To some extent, it was even more than what was seen during the initial Covid wave in New York or during the 2020 winter Covid wave in the United States. This was corroborated by the number of individuals “…needing significant levels of Oxygen”(Covid-19 Mortality in the Delta Wave in India: A Hospital-Based Study from Ramanagara District, Karnataka). Perhaps the largest red flag and warning sign in this situation should have been the fact that most of the population in India had already been infected, and supposedly developed immunity. According to some studies, “55% of India’s population may have been infected by January 2021″(India says it contains spread of COVID-19, no new cases in fifth of country). This only further proves that a new, pathogenic variant that was clearly immune-evasive, and especially adept at penetrating immunity induced by natural infection had arisen and would prove a significant threat to the United States, where so many people had still not been vaccinated. Indeed, the story of what happened in India repeated almost exactly in the United States 2-3 months later.

    So, America experienced the catastrophic effects of the Delta variant surge and then believed that everything was over. Surely there was enough immunity in America, so everything would be okay now, right? Unfortunately, the virus was still not done with us. Not only did our cases end up at a higher baseline than they were prior to the Delta surge. However, we then had a new variant arise in South Africa, which was good at evading all the immunity obtained from the Delta Variant, and previous variants. Specifically, “The reinfection rate of individuals who had been infected by other variants was up to 56% according to studies done by Qatar”(Protection against the Omicron Variant from Previous SARS-CoV-2 Infection). On the bright side, there were some positives on the horizon, though. The variant seemed to induce clinically milder symptoms and may have carried a lower risk of Long Covid. The variant also seemed to confer stronger protection to previous variants, suggesting that it was favored to be the dominant variant. For instance, studies showed that after having the Delta Variant, “Many individuals had a 6-fold increase in neutralization ability/capacity”(Omicron infection enhances Delta antibody immunity in vaccinated persons). This was unique to the Omicron variant, as other variants did not appear to provide such a broad immune response, especially to variants that were so dissimilar to it. This raised the hope that Omicron could signal a start to a more stable state with Covid because Omicron would be able to block reinfection, and infection, even if Covid experienced a significant number of mutations. Plus, the lower pathogenicity of Omicron would give it a survival advantage across populations, given that it would be less likely to kill its hosts. All that being said, while this prediction turned out to be somewhat true and the pandemic has remained stable after that point, with deaths and hospitalizations staying relatively stable in the US (albeit at a high level), and all subvariants being offshoots of Omicron, the 2021 winter Omicron wave caused a high rate of hospitalizations, deaths, and cases, even if it induced immunity in the process. 

    So you might be wondering, what exactly was the point of going down memory lane with Covid? What was the point of discussing all these events? What I hope that you gleamed from this article is that while the Covid-19 Pandemic had an end of sorts, and while we appear to be out of the unstable, uncertain phase of the Pandemic now, America’s response fell quite short in many ways. Any future Pandemics could be made worse, and if we do not focus on how to significantly improve our response, the level of suffering that we undergo then could be made way worse. For one, we needed to be way more proactive, not reactive. We needed to stop hoping that Covid would end by itself, and we needed to actually take the steps to end it. We needed to tightly restrict travel from other countries and put a lot of security measures in place to prevent variants from coming to our country. Similarly, we needed to distribute the vaccine much more equitably and put a much more all hands-on deck effort in getting the world vaccinated by early 2022. It would not have been easy, but it could have been done. Additionally, we needed to keep slight restrictions in place until the world was vaccinated, like having a Federal Mask Mandate to keep cases as low as possible, while vaccinating the world. Finally, with the level of genomic analysis that we have available in today’s day and age, we should have worked on predicting worst case mutations that Covid-19 could undergo and created backup vaccine formulas based on those mutations to have immediately ready the second that we heard of these new variants. All of that would have minimized the level of hospitalizations, deaths, and disruption that society had to undergo throughout this pandemic. So, if nothing else, I hope you as a reader takeaway one point from this article: We needed to do way better in our response, and we are lucky that this was not way worse than it already was!

    Sources:

    Lubell, Maayan. “Israeli Studies Find Pfizer COVID-19 Vaccine Reduces Transmission.” Reuters, Thomson Reuters, 19 Feb. 2021, www.reuters.com/article/health-coronavirus-israel-vaccine-int/israeli-studies-find-pfizer-covid-19-vaccine-reduces-transmission-idUSKBN2AJ08J/.

    De-Leon, Hilla, and Dvir Aran. “What pushed Israel out of herd immunity? modeling covid-19 spread of Delta and waning immunity.” medRxiv, 2021, https://doi.org/10.1101/2021.09.12.21263451.

    Mukhopadhyay, Amita, et al. “Covid-19 mortality in the Delta Wave in India: A hospital-based study from Ramanagara District, Karnataka.” Cureus, 2023, https://doi.org/10.7759/cureus.43678.

    Das, Krishna N. “India Says It Contains Spread of Covid-19, No New Cases in Fifth of Country.” Reuters, Thomson Reuters, 28 Jan. 2021, www.reuters.com/world/india/india-says-it-contains-spread-covid-19-no-new-cases-fifth-country-2021-01-28/.

    Altarawneh, Heba N., et al. “Protection against the Omicron variant from previous SARS-COV-2 infection.” New England Journal of Medicine, vol. 386, no. 13, 2022, pp. 1288–1290, https://doi.org/10.1056/nejmc2200133.

    Khan, Khadija, et al. “Omicron infection enhances Delta antibody immunity in vaccinated persons.” Nature, vol. 607, no. 7918, 2022, pp. 356–359, https://doi.org/10.1038/s41586-022-04830-x.

     

     

     

     

  • Diary of an Undergraduate Thesis

    Diary of an Undergraduate Thesis

    The Georgia Tech Research Option is available to all undergraduate students in the College of Sciences. It includes the completion of an undergraduate thesis. Students who choose to take on all this additional work are generally considered a bit sick in the head. Through these diary entries, I hope I can provide some insight into the joys and trials of completing this process. Particularly, for those who (for some reason) want to take on the same path.

    August 24, 2023

    Finally figured out the direction that I want my thesis to go in! This has been stressing me out quite a bit, so I’m glad I’m able to figure things out. I talked with my PI and we sort of figured out that I can do a project that combines the calcium sensors our lab has been developing and the dopamine recordings in freely moving mice that we’ve been doing. There’s still a lot of directions this project can go, but this sounds like a good place for me to start thinking (and just as importantly, looking at sources for the background section of my thesis). What I found super helpful is that my PI gave me a set of next steps if I want to pursue this project, which alleviated a lot of my uncertainty. Here they are:

    1. Get trained on stereotactic surgery (mouse brain surgery)
    2. Learning how to run and handle mice in our behavior rig
    3. Injecting mice with whichever thing we want to test (probably dopamine and the sensor at first)
    4. Running in vivo experiments

    As you can see, running experiments is step 4, after having to learn a lot of other stuff. Hopefully, I’ll be able to start that step in October/November, but if not I should be able to do it in spring. 

    We also discussed how there’s a huge gap in the literature that I honestly hadn’t really considered: we don’t really know how dopamine impacts the excitability of neuron populations. This seems like something really basic to the field, but we haven’t really had the tools to measure it until very recently. I don’t want to get too deep into the particulars of the field, but basically I’m glad that we’ve found something that I can reasonably say fills a need in this field of research. In addition to that being a required part of my thesis’ introduction, it makes me feel a lot more passionate about the work. I think a big challenge of this thesis will be staying motivated as the going gets tough, so this is good.

    My next steps will be to get trained on the techniques I’m planning to use and look at some papers for background.

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    October 6, 2023

    I have been super busy this past month and change. I have been practicing stereotactic surgery, which has proven to be really hard. While I’ve been working on experimental techniques, I’ve also been reading a ton of articles.

    Right now, I have around 25 articles in my Zotero (research sorting app), and I’ve read about 7. Although I’m improving in my ability to read research articles, it’s still taking such a long time. 

    Now, my literature review is due in two days, and I haven’t read all the papers yet. However, since it’s just a draft, I’ll try to use the background section of my PURA proposal as a base for it. I’m going on a trip tomorrow, so I really don’t want to work on it during my trip.

    I’m going to work on it now and just submit the draft. This thesis process has taught me to just turn something in, even if it isn’t perfect.

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    November 4, 2023

    Well–I think I’m at the point of the semester where it all feels like I’m fighting an uphill battle. Looking at my 4 step plan from August, I’m still working through step 1. My plan of conducting actual experiments in October was a little too rosy. One thing that’s slowed my progress is that although I’ve been practicing mouse surgery, I can only pretty much do one mouse per week. I share the surgery room with other people in the lab, and with scheduling around classes and other lab tasks, that’s all the time I have for practice. 

    Still, I feel like I’m making progress, slow as it is. This week, I’m going to be doing my first survival surgery, which is one step closer to being able to put in implants and biosensors into mice.

    On the writing side, it’s time for me to revise my lit review, introduction, and work plan and put them together. It’s also necessary for me to get all three (all together they’re called the proposal) signed off by my research advisor and second reader. Honestly, this part kind of scares me because I feel like I haven’t gone in depth enough for my lit review in particular. I’m meeting with my advisor later this week to show him my proposal, so I’ve got to get working on this today and tomorrow (the weekend). Currently feeling stressed out. But I keep telling myself that it’ll pass.

    The thing is–I really like doing research, and I find reading articles and learning more information about the topic interesting. But deadlines and expectations always scare me. Even so, I’m trying to tell myself that I have all the tools I need to succeed. I just need to be patient with myself.

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    December 1st, 2023

    Well, I’ve basically done all my revisions. My readers gave me some really helpful feedback, and it turned out that my proposal was in better shape than I originally thought. I just need to check some of the formatting, and then I’ll wait for the approval form to come out so I can submit it. 

    One thing I noticed–that I also talked to my advisor about–is the fact that when I’ve been working on my thesis, it’s made me think about why I am doing what I’m doing. Like it’s simple enough to say I’m working on a project that uses a biosensor, but when I started writing, I started thinking more about the details in a way that I never really did while just doing bench work. Why do we choose this type of biosensor? What gives our approach the advantage over another? In what way does our experimental setup even work?

    I think as undergrads, a lot of stuff is technically really complex and hard to grasp. So the researchers who are mentoring us simplify things so we can get a general gist of what’s going on. But when you’re writing your own thesis, or even making a presentation on your research, you’re encouraged to delve deeper into the reasoning behind what you do. And in that way, I think I finally kind of understand why a thesis was put into the curriculum of the research option. 

    As the semester is nearing its end, I’ve been thinking a lot about what I’ve done so far. And I feel like while I’m behind on my work plan, I still feel proud about what I’ve accomplished. It’s just an undergraduate thesis–I’m not really expected to produce groundbreaking. Still, I feel like the skills I’m learning (reading journal papers, scientific writing, study design, coordinating with my research advisor) are going to be really helpful in the future.

    Or, maybe I just feel like this because the pressure is off, for now. I’m going to put the final touches on my proposal now–see you next semester!


    Here is my followup to this article–the finale of my undergrad thesis journey!