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The biggest struggle with the Covid-19 pandemic was mental health. First and foremost, there was a lot of unknown. We did not know how to stop the disease, how to prevent deaths, how to create a solution for it? There was so much speculation and polarization on the topic that everyone was on edge and frustrated with one another. Second off, everyone was fearing for their loved ones, or feeling disconnected from them. There was a general air of helplessness in the face of a lot of tragedy and everyone was trying to keep the people they loved away from it. Additionally, people were cooped up, and they had to adjust their reality to being at home all the time and avoiding contact. This recipe only lead to anxiety and depression, an experience that the majority of people would liken Covid-19 too.

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Due to social distancing measures, it was harder for humans to connect with one another. The majority of people were forced to stay in their homes and remove themselves from their social circles, in order to curb the spread of the disease. As very social creatures, this created a lot of unrest and dissatisfaction.

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The majority of jobs were forced to transfer to online platforms as well. Remote work and online communication have never been so prevalent as during the pandemic. This was to help promote social distancing while still allowing people to make money. Some jobs however were unable to go fully online, such as grocery stores, etc. Thus, employees were always seen wearing masks, and working behind plastic barriers to avoid acquiring the disease. This also highlights a class divide, in that minimum wage jobs, were not able to protect their employees as well, because there was no feasible way for them to move to an online platform.

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In terms of education, society as a whole has typically conformed to an in person, classroom model throughout history. With the onset of the pandemic, there became a huge shift towards online school. This was a difficult adjustment for many students and teachers. Additionally, not all students, and not all schools, have access to electronic devices needed to support online classes. Thus, the imbalance in education due to poverty was starkly highlighted in this situation, and many communities didn't have the same access and resources to make this switch.

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The Covid-19 pandemic created an upheaval of life as we knew it. Almost every single person in the world was affected by it in someway or another. The pandemic left no stone unturned and essentially altered every aspect of our lives including politics, the economy, healthcare, education, social interactions and cultural practices.

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World Health Organization. (2020). Coronavirus Disease (COVID-19) Dashboard. https://covid19.who.int/

Gov.sg. (2020). TraceTogether: How it works. https://www.gov.sg/article/tracetogether-how-it-works

The Lancet. (2020). COVID-19: learning from experience. https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)31180-6/fulltext

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Clearly pandemics are extremely hard to mitigate. It is difficult to predict what methods will work and what methods will be a waste of time and resources. However, if one had to critique leadership and suggest what could have been done better, some improvements include, increasing research funding, direct money towards the development of treatments/vaccines, implement stricter measures to enforce social distancing/mask wearing, as well as just communicating with the public. A lot of misinformation and speculation was spread through social media, stoking fear and drastic behavior. This could have been avoided by extra and consistent communication. Last but not least on a global scale, more coordination between governments could have helped reduce transmission through travel.

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In regards to managing Covid-19, many innovative initiatives came out of the pandemic. The primary goal was to reduce the spread of covid-19 and thus mitigate it's consequences. Some initiatives that embodied this, included contact tracing, mass testing, social distancing measures, and technology that tracked the spread of the virus. For example, in Singapore, a mobile app called TraceTogether, aided the country in tracing the disease and curbing it. For many apple users, notifications that they had been exposed to covid-19 were activated, so that the individual would be notified and could go get tested.

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LEADERSHIP/GOVERNMENT BODIES RESPONSE ~ 

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LEADERSHIP/GOVERNMENT BODIES RESPONSE ~ 

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The Covid-19 pandemic caught the world by surprise, and the response from leadership and governmental bodies has varied significantly from country to country. Some countries have been successful in controlling the virus spread, mortality rates, and economy, whereas others have struggled to contain it, as well as mitigate it's consequences.

New Zealand for example, has been consistently praised for how it responded to the Covid-19 pandemic! Because the government reacted fast and implemented a strict lockdown super early on, closed the country's borders, enforced social distancing, and provided elaborate tracing as well as testing, they managed to lower mortality and infection rates!

The United States however, has been criticized for how it handled Covid-19. Upon the Virus hitting the US, there was a lot of polarization amongst the governmental parties, and the disagreements slowed progress. Additionally the federal government to state government relationship made it hard to maintain consistency. Unfortunately the United States has some of the highest Covid-19 cases and death rates in the entire world.

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Edward C. Holmes, Stephen A. Goldstein, Angela L. Rasmussen, David L. Robertson, Alexander Crits-Christoph, Joel O. Wertheim, Simon J. Anthony, Wendy S. Barclay, Maciej F. Boni, Peter C. Doherty, Jeremy Farrar, Jemma L. Geoghegan, Xiaowei Jiang, Julian L. Leibowitz, Stuart J.D. Neil, Tim Skern, Susan R. Weiss, Michael Worobey, Kristian G. Andersen, Robert F. Garry, Andrew Rambaut,

The origins of SARS-CoV-2: A critical review,

Cell,

Volume 184, Issue 19,

2021,

Pages 4848-4856,

ISSN 0092-8674,

https://doi.org/10.1016/j.cell.2021.08.017.

(https://www.sciencedirect.com/science/article/pii/S0092867421009910)

Mario Cannataro, Andrew Harrison, Bioinformatics helping to mitigate the impact of COVID-19 – Editorial, Briefings in Bioinformatics, Volume 22, Issue 2, March 2021, Pages 613–615, https://doi.org/10.1093/bib/bbab063

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The health care community were the hero's of the covid-19 pandemic. However, they were understaffed, underpaid, and overworked as millions of people required hospital care and medical attention. Many healthcare workers, were exposed to the disease themselves, or became ill from the stress that the mass influx of patients caused. Covid-19 highlighted the unfortunate reality, that our society was not equipped to handle such a devastating pandemic, and lack of resources, and enough qualified individuals to handle such mass hospitalization rates, showed that the healthcare system desperately needs more attention/funding.

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The scienctifical communities response to Covid-19 has been focused on not only how we can mitigate the disease, but how can we better understand it. With this in mind, bioinformatics technology has been critical to combatting the disease.
Below are some examples of the role bioinformatics has played:

1. ) Determining if the origination was a zoonotic emergence: In order to determine whether or not covid-19 was passed from animals to humans, scientist used bioinformatics to track possible host and their environments and map it to the first cases of covid-19. They found that the virus most likely originated from the Wuhan animal market or the bat caves in Yunaan. It is suggested that the virus's original host was a bat, and the intermediate host was a pangolin (which is similar to an anteater)! Scientist's were able to compare the genomes of the virus within an infected bat, and the genome of a virus within an infected human, and found that they share 96 percent of genetic material. With this information in mind, scientist were also able to trace the first appearances in humans bath to October 2019, several months before it was reported in December.

2.) Determining if the origination was lab leak: Bioinformatics allowed scientist to discover several unique features of covid-19 compared to other human coronoviruses. They detected a unique genetic feature called a furin cleavage site, which was not present in any other human coronaviruses. Some scientist suggest that this was the result of artificial manipulation, whereas some argue that it could have evolved naturally. By examining the virus through bioinformatics, we can trace it to its origination based on whether mutations that have occurred would have had to been altered in a lab.

3. ) Tracing the evolution of Covid 19: Bioinformatics has allowed us to trace Covid around the globe. Scientist can take samples of Covid from different regions or different strains, and compare their genomes, allowing us to better understand how the virus is spreading and mutating.

4.) Developing diagnostic test: Bioinformatics has been used to design and develop diagnostic tests that can detect the virus. One example of this would be PCR!

5.) Drug targets: Bioinformatics has been used to predict drug targets for Covid-19. Computational methods have allowed us to identify compounds that maybe be able to bind to the virus and inhibit its replication.

6.) Vaccine: Bioinformatics was used to generate a vaccine that would illicit an immune response against the virus, and thus prevent vaccinated individuals from acquiring as harsh of symptoms.

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Different Strains of Covid-19 Across the world

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- https://www.ncbi.nlm.nih.gov/books/NBK554776/
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5243249/

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SARS-CoV is particularly virulent and has the capability to cause a worldwide pandemic as seen with the shutdown and social distancing caused by Covid-19.

The Coronavirus family tree can be categorized as follows:

Genera ~
Alphacoronovirus
Betacoronavirus
Deltacoronavirus
Gammacoronavirus

Within these groups, there are 7 subgroups of known coronavirus that are capable of affecting humans, and can cross species barriers, which is particularly confounding to scientists.

"SARS" AND "MERS" cause the most severe symptoms, and thus are the most virulent. The respiratory symptoms that these two strains cause are long lasting and often very intense. The entire world has first hand experience with SARS-CoV-2 (Known as Covid-19), and the travesty it caused. Many people were very ill, and some even had long lasting symptoms such as loss of taste and smell.

There are many variations of human coronavirus that are not as virulent, such as HCoV-0C43 and HCoV-HLU1. The respiratory symptoms partial to these strains, are much more mild, and far less consequential.

In summary, SARS-CoV which is of the Betacoronovirus family, is extremely virulent and has a harsh array of symptoms when transmitted from one individual to another. In particular SARS-CoV-2 is highest on the spectrum of virulence compared to other SARS-CoV. There was a SARS-CoV scare in Wuhan, China in both 2002, and 2004, however it did not have such a disastrous and far reaching impact as SARS-CoV-2 in 2019. The Virulence has only increased as the original virus continuously mutates and evolves, reducing the effectiveness of the vaccine and slowing down our progress in curbing it.

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The basic definition of virulence based off of the article "Bacterial Virulence Factors," From NCBI ,"is the ability of an organism to infect the host and cause a disease."

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5243249/

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“CDC Museum Covid-19 Timeline.” Centers for Disease Control and Prevention, Centers for Disease Control and Prevention, 15 Mar. 2023,
https://www.cdc.gov/museum/timeline/covid19.html.

Katella, Kathy. “Our Pandemic Year-A Covid-19 Timeline.” Yale Medicine, Yale Medicine, 9 Mar. 2021,
https://www.yalemedicine.org/news/covid-timeline.

“Who Coronavirus (COVID-19) Dashboard.” World Health Organization, World Health Organization, https://covid19.who.int/.

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According to the WHO, as of March 23rd, 2023:

- 761,071,826 cases of Covid-19
- 6,879,677 reported deaths
- 13,260,401,200 vaccinations administered

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2019

- mysterious disease arises causing patients to have pneumonia like symptoms
- Animal markets closed to concerns of a repeat SARS-CoV outbreak (occurred in 2002 and 2004)
- Disease is identified as a coronavirus and dubbed "Covid 19 or SARS-CoV."

2020

- first death occurs in China
- By January four countries in total have confirmed cases: China, Japan, Thailand, Korea
- By February, the disease has reached the United States
- In Illinois... two people acquire covid, without having traveled in recent months
- By February, Italy has become a Covid-19 epicenter, with an extremely high number of cases
- By March there are over 4,000 recorded deaths
- The end of March brings the arrival of lockdowns and social distancing
- By April the United States has more confirmed cases than Italy, the previous highest.
- In August, the first case of reinfection occurs in Hong Kong and covid becomes the third leading cause of death
- In December, a vaccine is in the works, but a variant called "B.11.7" reaches the United States creating more confusion and anguish.

2021

- more variants
- spread to almost every location in the world
- the only reported country that has been untouched is Turkmenistan

2022
- although Covid-19 still rages onward, life in the United States, has started to get back to normal again

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This video does an excellent job of showing the spread of Covid-19 from December 2019 through the end of 2022. We can see how it started in Wuhan China, conquered Europe, and then the entire world.

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History of Coronavirus in 90 Seconds | First 500 Million Cases

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Experts believe that Covid-19 is transferred from one individual to another through droplets containing the virus. This can occur when an individual breaths, coughs, sneezes, etc. and another individual comes into contact with it.

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https://www.sciencedirect.com/science/article/pii/S0092867421009910

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The second theory has stirred up more political controversy and has resulted in lots of accusations and tension. Wuhan China is home to the Wuhan Institute of Virology, which specifically studies the SARS-CoV Virus. The laboratory team was thoroughly investigated and they seem to have followed all safety protocols. Although they successfully managed to culture three SARs-CoV genes from bats through their fecal samples, investigators could not link Covid-19 to a breach from this experiment. In addition, many scientist would argue that The Wuhan institute of virology could not have conceivable created conditions for which an animal based virus could transfer to a human host. Thus, most scientist dismiss this idea as fictional, although there is coincidental similarities.

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Most scientist would argue that a zoonotic emergence is the most plausible explanation for Covid-19's origination. Wuhan, China is home to an exotic animal market in which different strains of Covid 19 have manifested in years prior (2002 and 2004). Scientist believe that the this virus could be linked to animals found in the exotic market such as civets and raccoon dogs. These particular species were traced to the market in relation to all instances of SARS-CoV. Additionally, near Wuhan (in Yunnan province) is a cave system home to a species of bat that may also be a carrier, as the closets known relatives of SARS-CoV and SARS-CoV-2, have been found within their genomes.

There are two struggles in identifying whether or not a zoonotic emergence is in actuality the cause of the Covid-19 pandemic. First and foremost, it is nearly impossible to explain why the virus emerged within animals in the first place. Secondly, it is difficult to trace how it would have been able to pass from animals to humans considering the changes the virus would have to undergo to adapt to a human host.

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SARS-CoV-2 was first detected in Wuhan China around December of 2019. There has been much controversy and speculation in regards to its origin. I will present to you the two most popular theories of origination.

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- Discovered December of 2019 in Wuhan China
- Variety of symptoms but most common are respiratory (Flue, cold, pneumonia)
- Typically spreads via nose and mouth droplets
- More severe symptoms are common amongst those with prior or pre-existing health issues
- Hundreds of thousands of people died from Covid-19 in the United States
- Vaccine caused major political controversy
- Multiple Variants of Covid-19

Information found from the CDC ~ https://www.cdc.gov/coronavirus/2019-ncov/your-health/about-covid-19/basics-covid-19.html

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Common name: Covid -19

Scientific Name: SARS-CoV-2

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I chose this research question, due to the worldwide upheaval the emergence of Covid-19 caused. I would argue that almost every single person was affected by this pandemic in one way or another. Covid 19 not only affected the economy, politics, and healthcare, but took a toll on societies mental and physical health. It essentially resulted in a complete shutdown of life as we knew it. In the aftermath, we are still trying to reset from a battle that is still not won. Covid-19, especially the vaccine, and the government response, has been highly controversial, and polarizing! With this in mind, I am excited to look at Covid-19 from a strictly epidemiological lens, without the bias of politics or personal experiences threatening my outlook!