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I had a super interesting time researching SAR-CoV-2. Obviously, we all lived through and experienced the pandemic, but I found it fascinating to look back in retrospect just how crazy the entire thing was.
The most revealing aspect I learned about this disease is just how little we know about it, even three years later. Just during the course of this semester, we had 2 completely opposing theories published about the origins of COVID-19: First in February with the Dept. of Energy announcing (with little confidence) that the virus was a lab leak, then in April, when researchers provided new evidence supporting a zoonosis hypothesis based on new virus samples. Both stories gained media attention.
The most surprising thing I learned during this project is related to patient zero. I was living in Seattle attending UW at the time of the outbreak. I remember getting an email from my institution, acknowledging that a man in a neighboring town tested positive for COVID; that man was later known to be patient zero from Everett, WA. I remember all of us students being LIVID that the school was still requiring in-person attendance, knowing that patient zero had just been  discovered so close by. So as you can imagine, watching Prof. Worobey's lecture pointing out that the Everett man was not actually patient zero, and that the virus was spreading communally prior to that, completely changed my perspective.
Tying that back into my Padlet assignment, I wish I would have learned that tidbit of information earlier, as I had already mentioned that anecdote prior to Worobey’s lecture. I would like to go back and apologize to said Everett man for ever putting any slander on his name lol. Other than that, I would have liked to write more about the different vaccines that were created to combat SARS-CoV-2. I mentioned in my padlets that there were multiple available; mRNA, protein-subunit, and viral vector, but did not really get to compare their mechanisms further than that.

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The emergence of SARS-CoV-2 arguably caused a divide throughout our country. Not only did the pandemic hit the medical community hard, but it also impacted our culture socially, economically, even politically.

Obviously the physical effects of COVID were intense. Overall, more than 100 million cases were reported, 1.1 million people have died; and this is just in the US alone! Many had mild cases, some still suffer with lasting symptoms in what is called “long covid”. Society had to change their social behaviors. Immediately we were told to mask up, stop seeing people in close proximity, limit outings to only essential trips like groceries. Schools closed down, which meant that afterschool programs and sports often did as well. People began working from home, no longer commuting to-and-from urban areas. Many up and left urban areas to move to more spacious, rural areas. Travel halted, borders closed, economies were impacted… Even 3 years into the pandemic, we are still dealing with these long-term effects.

Some argued that the effects from a long-term lockdown would actually be detrimental to society overall. There was a really interesting paper published in Frontiers in Psychology in 2020 that explores these societal phenomena. The author argues that overall, many people belonging to already “vulnerable” categories suffered due to the COVID-19 lockdown. Things mentioned included weakened immune systems from constantly being inside, morsened mental health due to stress of the lockdown, deaths from treatable illnesses that were sidelined by overwhelmed hospitals, personal financial insecurities leading to furthered inequalities, children falling behind in their education; the list seems endless.

The author of the article also brings up the concept of agnotology, which is defined as “the study of deliberate, culturally induced ignorance or doubt, typically to sell a product, influence opinion, or win favor, particularly through the publication of inaccurate or misleading scientific data (disinformation)”. Unfortunately, the COVID-19 lockdown occurred at a point of political contention in our country. One could argue that our society has been the most divided it has been in decades. Far-leaning political groups were using disinformation to sway their bases in certain ways. One side pushed xenophobic rhetoric against China, painting the entire country as a monolith, with the goal of taking down the United States. They also pushed the messaging that the pandemic was manufactured by a one-world-government in order to destabilize our presidential election. They told people that the vaccine was not real, it either had microchip/tracking devices in them, or were designed by scientists to alter your DNA. Hell, you didn’t even NEED a vaccine, as Ivermectin (a horse dewormer) was readily available at your local feed store to treat you… The levels of disinformation being ACCEPTED by portions of the public was truly terrifying. Did these people learn from the pandemic? Of course not. They only became emboldened in their ways, and will, without a doubt, act the same way during the next epidemic. Did society overall learn? Of course. This was, without a doubt, the largest scale pandemic we’ve seen in modern history. Not only is the average American more knowledgeable about the basics of epidemiology, but the government had hopefully refined their pandemic protocols as well; leaving us more prepared for the future.

The goal of the lockdown was to slow the spread of the virus. Everyone shelters in place, then when the vaccine comes out, everyone vaccinates, and we can hopefully mitigate as many unnecessary deaths as possible. So although we tried to save our most vulnerable (mostly sick/elderly) through swift lockdowns, did we end up doing more harm to our society than good? I would argue no. Although we could have done so much differently, lockdowns were an essential part of weakening the COVID-19 pandemic, as we witnessed in other countries that were successful in their lockdowns. The ultimate downfall, in my opinion, was not the lockdown itself, but the mishandling of the lockdown by our government, as well as the American public's unwillingness to cooperate with rules and regulations.

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Once the news that the emerging coronavirus has spread outside of Chinese borders, economies worldwide began to see change. Businesses were forced to shut their doors, school campuses closed down, international travel was restricted, public gatherings were banned, many stopped commuting altogether and began working from home.

At first, it seemed as though the government was banking on this pandemic being a 2-week stint. Instead, deaths ramped up and our economy began showing signs of downturn. Quickly, it became apparent that our government needed to step in and intervene, and deal with the new hardships Americans were facing during this unprecedented pandemic.

In March of 2020, roughly 4 months into the pandemic, Congress came up with their plan. It would come in 3 parts:

1. Coronavirus Preparedness and Response Supplemental Appropriations Act - Passed on March 6. Immediately provided roughly 8 billion dollars to be used to combat immediate needs; funding to support hospitals and medical reporting agencies, fund research into the virus and a subsequent vaccine, community education/preparedness, etc.

2. Families First Coronavirus Response Act - Passed on March 18. Established emergency paid sick and medical leave for American workers, funded free-testing for COVID-19 for the public, bolstered unemployment benefits, and most importantly, increased funding to food stamp programs for American families.

3. Coronavirus Aid, Relief, and Economic Security Act - Passed on March 27th. The last phase of the 3-part plan. This act created a new government committee, the Pandemic Response Accountability Committee (PRAC for short), who would be responsible for the roughly 2 TRILLION dollars set aside by the US government for pandemic related aid; making it the largest economic stimulus package ever in US history. The original proposal included only three things: $500 billion in stimulus checks directly to the American people, $208 billion for loans to “major industry”, and $300 billion for loans to small businesses. In the end, the bill instead included: $300 billion in stimulus checks to the American people ($200 billion less than intended), $260 billion in increased unemployment benefits, $669 billion for PPP loans for small businesses ($369 billion more than proposed), $500 billion in loans for corporations (Roughly $300 billion more than proposed), and $339.8 billion to state and local governments.

Although that all looks great on paper, the reality was more complicated.

Some of the things in these government acts were great. Science NEEDED funding to study the virus and come up with a vaccine; one year later the American public were able to choose from multiple safe, free, and effective vaccines for COVID-19. Rental protections helped paycheck-to-paycheck prevented families from being evicted when faced with pandemic job insecurities. Food-stamp benefits were increased for low-income families; many of whom rely on public schools to provide their children with meals for the day (which were now shut down).

Some things didn’t go as planned. Using the concept of universal basic income, stimulus checks for the American people were proposed to stimulate the economy. However, recurring payments turned into one… What was supposed to be a $2000 check became less… You only received them if you yourself had filed taxes in the previous year… In the end, the program became a drop in the bucket. Barely any money made it to the hands of the American people, and instead an increased amount of taxpayer money was given to corporations (shocker).

Unfortunately, many Americans felt like their leadership failed them when it came to stopping the spread of the pandemic. Our own President at the time chose to downplay the severity of the pandemic. While our congress was putting together the initial covid relief packages, our President was nowhere to be found. Instead, he was busy going around the country, pushing his narrative of 2020 election fraud. Public health officials were unclear when giving information to the public, leading many to distrust anything they were saying; and instead turned to (unreliable) sources of their choosing.

In the end, as of writing this post, 1,129,573 Americans have died from the virus. Was this death count inevitable? Or could stronger leadership in the early days of the outbreak have prevented such national tragedy? It’s up for discussion.

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As mentioned in a previous entry, prior to our knowledge of COVID-19, Chinese hospital workers were overwhelmed  dealing with a pneumonia-like illness that was unresponsive to standard courses of known treatment.

The cause turned out to be the novel virus SARS-CoV-2. It was the first SARS outbreak the world had seen since 2003. Also previously mentioned, initial variants of the virus were HIGHLY virulent; so the medical community around the world worked quickly to get ahead of the increasingly imminent pandemic; both in treatments and vaccination.

Every country/government around the world implemented their own strategies in order to combat the pandemic. For the purpose of this entry, I will focus mostly on how the pandemic was handled in the United States, not globally.

According to a review in the Iranian Journal of Medical Sciences, response/strategies to a pandemic from the medical community can be broken into the following categories:

1. Monitoring

2. Public Education

3. Crowd Control

4. Care Facilities Preparation

Let's review how the US fared in each of these categories.

Monitoring

According to the CDC, epidemiologists monitored the pandemic in various ways, including: Incidences of new case reporting's, prevalence of cases based on location, number of cases resulting in hospitalizations, and lastly, deaths.
Looking back, a few issues were presented here. Firstly, although a public test for COVID-19 was created on January 28th of 2020, there were restrictions on who could receive them. It wasn't until a few months later that these restrictions were relaxed. Even then, the government couldn't supply the amount of tests that were needed.

Although access to testing got better over time, throughout the duration of the pandemic, the US never reached the recommended threshold for controlling an outbreak according to the World Health Organization.

Public Education

Since so little was known about the virus, initial education to the public was all over the place. Looking back, the US government really mishandled how they rolled out information to the public. The information we were being presented was all over the place, to the point that even our public health leaders seemed to be confused.

Untrustworthy information from our government, coupled with a large population of under-educated individuals as a result of our under-funded education systems, created, in my opinion, the worst-case scenario of how a population could deal with a pandemic.

Crowd Control

Unfortunately, crowd control did not necessarily occur in the US. Other countries quickly implemented strict lockdowns and travel bans once they got word of the outbreak; we did not. The federal government basically left it up to the states on how they wanted to handle this: What jobs were essential, what public spaces could stay open, how many people could gather at a time. Unfortunately, not much was done regarding this matter, and if it was, much of the public chose not to follow.

Care Facilities Management

Our system simply wasn't ready to handle a pandemic of this magnitude. A public messaging of "flatten the curve" began to spread. Throughout the length of the pandemic, many major hospitals became overwhelmed. ICU's filled up with patients needing ventilators. COVID was a priority, and hospital beds quickly filled; leaving those that needed hospitalization for other reasons out-of-luck. Many COVID patients needed ventilators; there weren't enough. ICU's needed more nurses; there weren't enough. Hospital workers needed proper PPE in order to not get exposed to the virus themselves; there wasn't enough. In the hardest hit metro areas, the US military had to set up emergency triage centers to deal with the overwhelming number of cases. One can only assume that the lack of proper care facilities in the US contributed to our high pandemic death toll.

Although our public health/medical systems were not ready to handle the outbreak of the SARS-CoV-2 virus, our scientific communities were about to do something astounding; rapidly create mRNA vaccine for COVID-19; that has proven to be safe and effective years after it’s release. Roughly a year into the pandemic, the FDA was able to grant emergency access to mRNA vaccines being made available to the most at-risk public. Unlike a traditional vaccine that uses whole weakened/dead viruses to trigger our adaptive immune response, an mRNA vaccine only administers genetic material; the code for the surface binding proteins your immune system will need to detect the virus. Other types of vaccine were also developed, including protein-subunit  vaccines (which administer only the protein subunits), and viral vector (which uses another virus modified as a viral vector).

Also, there are now treatments available to the public for the treatment of COVID-19. These include antiviral drugs that prevent the virus from multiplying after infection.  Veklury is administered in hospital settings. Paxlovid and Lagevrio can be taken at home. Convalescent Plasma Therapy (blood transfusion from recovered individuals) is also an approved and effective treatment for COVID-19 per the CDC.

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How do we measure the harm a pathogen inflicts on its host? We have a term for that; it’s called virulence.

Virulence can be described as the harm caused by a pathogen onto its host following an infectious event. It’s a relative term, and could measure anything from specific symptoms a pathogen causes, to overall host fitness. In short, virulence measures the severity of disease a pathogen causes.

Let’s think back to the start of the pandemic, in late 2019. Our first introduction to the virus was HIGHLY virulent and caused an array of severe symptoms in their hosts; often resulting in long term detrimental health effects, frequently to the point of death. We had seen outbreaks of coronaviruses in the past, however none were as virulent as we were witnessing with SARS-CoV-2.

This led to scientists speculating about the source of COVID’s virulence. Although we are still learning about the virus, many different virulence factors about SARS-CoV-2 have been proposed, including: Structures of spike proteins that help the virus bind to host immune cells, unique FURIN cleavage sites, mechanisms that allow the virus to manipulate host immune cells, so-on and so-forth.

There have been many variants of SARS-CoV-2 that have emerged since the outbreak began in late 2019. Starting with alpha, onto the dominant strain as of writing this post; omicron. Each one seemingly different than the next. The 5 main pandemic strains of concern are as follows:

Alpha - First seen in the UK in December of 2020. This strain contained a few key mutations distinguishing it from the original we saw in Wuhan: N501Y mutation, affecting spike proteins,  D614G mutation affecting replication, and P681H mutation whose function is still unclear. Compared to the original Wuhan strain, alpha is considered slightly less virulent, but more transmissible. Alpha was also the most sensitive to vaccines and antibody treatments.

Beta - Detected in South Africa in December of 2020. In addition to alpha’s mutations, it also contained a K417N mutation, which is believed to help the virus evade antibodies. This meant that the strain remained highly virulent in hosts that were previously infected with SARS-CoV-2, and those who were vaccinated. Also, the strain appeared to be significantly MORE transmissible than previous variants.

Gamma - Detected in Brazil in January 2021. It contained a new mutation, K417T, that affected how it binded to human cells; AKA increased transmission. Luckily, this gamma strain responded well to vaccination.

Delta - First detected in India in May 2021, delta quickly became the dominant strain around the globe. It contained many genetic mutations distinguishing it from previous variants. L452R mutation not only made the virus more infectious, it also helped with evading the host immune system (alongside another T478K mutation that did the same). P681R mutation, associated with increased disease symptom severity, and K417N mutation found in strains called “Delta Plus”. The delta strain was HIGHLY transmissible, even when compared to the alpha strain. Not only that, but the vaccine did not seem to prevent the transmission of the delta strain, only lessened the virulence in those infected.

Omicron - First identified in South Africa in November of 2021. The latest strain that is here to stay. Omicron had the largest number of identifiable mutations distinguishing it from earlier strains. Despite this, omicron appears to be the least clinically virulent strain on the list, while also having the highest transmissibility.

Based on the characteristics of the above variants, can we say that the virulence of SARS-CoV-2 has changed overtime? I would say yes. We can definitely see a pattern of virulent factors developing in the virus overtime. However, in a clinical sense, one could argue that the virus is evolving to become LESS virulent. Clinicians could tell you how they are seeing less severe COVID cases during omicron, fewer patients dying of the disease than at previous points in the pandemic. Concurrently, we also see the virus become MORE transmissible over time, with human-to-human spread increasing due to the variant.

Could this be the evolutionary strategy taking place? As time goes on, we are seeing COVID-19 transform into a community disease; meaning, it is present in the population for the long-term. Could an evolution towards low virulence, high transmissibility be the best strategy for the virus itself to achieve the highest fitness? Get the host sick enough that they are shedding the virus, but not sick to the point that they are incapacitated/dead?

It’s now been over a year since Omiron was first identified, and it is STILL the dominant strain of SARS-CoV-2 in our population. Perhaps the virus is getting closer to finding its “happy medium”. After all, as we’ve learned in class, the dominant hypothesis is that intermediate virulence will always be preferred in the virulence/transmission trade-off… I guess only time will tell.

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Map of international flights leaving Wuhan, China during the Lunar New Year Holiday in 2020, before lockdown was implemented.

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By the time the authorities were able to identify the virus spreading in China, it was already too late. You see, between the time the first COVID death occurred in China and the start of the Chinese lockdown, a major Chinese holiday took place; Lunar New Year. Probably one of China’s largest holidays, it is said that roughly 5 million people traveled outside of Wuhan during this period, before travel restrictions could be implemented.

On January 13th, 2 days following the first death in China, Thailand confirmed their first case of coronavirus. 2 days later, on January 15th, the Japanese government found a positive case in an individual who had just returned from a trip to Wuhan.

It wasn't until January 21st that the first case was confirmed in the Americas; a man residing in Everett, Washington State. (I still remember the news of this vividly, because at the time, I was studying at the University of Washington in Seattle; the same school as the man's son was attending. Side note, the university decided that this info wasn't cause for alarm to close the campus down, and mandated that students show up in-person to class for the remainder of the quarter... Hindsight is 20/20, as we then had to witness the virus decimating our local elderly communities).

During this time period, many other countries in the neighboring regions also witnessed their first cases. By January 22nd, the virus was confirmed in South Korea, Taiwan, Hong Kong, and Macau. This triggered the WHO to meet and discuss whether or not the spreading virus was a public heath emergency, but ultimately decide to decline to call it so... but by January 24th, the virus was confirmed to be spreading in both West Asian and European regions.

By February 9th, less than 2 months after the virus was first discovered, the death toll of this new emerging virus surpassed the pervious SARS outbreak from 2002. However, it's not until a MONTH later, on March 11th, 2020, that the WHO declares the COVID-19 outbreak as a pandemic.

We are now 3 years into the pandemic, and COVID-19 seems here to stay. Per the World Health Organization (link also includes an interactive map of confirmed COVID cases by country), as of writing this post:

761,402,282 cases of COVID-19 have been confirmed globally.

6,887,000 people have died by the virus.

Although the virus seems to be mutating towards lower virulence (as seen in omicron), and vaccination rates continue to increase, the COVID-19 virus continues to have devastating effects on the human population. For instance, in the US alone, roughly 2,000 COVID-related deaths occurred in the last week alone.

We now must accept that SARS‑CoV‑2 is a community virus that is probably here to stay; much to the likes of influenza and other common viral illnesses.

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In early December of 2019, doctors in China begin seeing cases of a pneumonia-like illness crop up in their hospitals. The illness was unlike anything they’ve seen, and was unresponsive to normal courses of treatment. Behind the scenes, Chinese officials contacted the WHO to uncover this mysterious illness. By investigating individual cases of each patient, they were able to trace the cause of the epidemic to a wet market in Wuhan, China. By January 1st, Chinese officials shut down the market to prevent further spreading of a potential virus.

Unfortunately, it was too late. On January 11th, the Chinese state media confirmed the first casualty of the illness; an elderly man who was a regular customer at the market. The WHO names the new virus “2019 Novel Coronavirus”, and begins publishing genetic sequencing data from viral samples in order to map out the viral genome.

The WHO identified the 2019 Coronavirus as a zoonotic disease (which they define as “any infection naturally transmissible from vertebrate animals to humans''). The most plausible, ongoing theory is that the virus must have spilled over from an animal in the market to human customers, then spread rapidly human-to-human around the globe.

However, 3 years after the outbreak, the original animal reservoir has yet to be confirmed. Early on, officials were able to enter the Wuhan wet market to swab cages, where 33 positive samples for the coronavirus were found. They were not able to collect data from actual animals, however, and the Chinese government has been less than complicit when dealing with scientists wanting to come collect data on the virus’ origins. This has led to the public creating their own theories about the origins of the virus; one being that the virus was a lab-leak, bio-engineered by the Chinese government to be unleashed onto the public for… who knows what reason.

Since we will probably never get to see genetic samples from the animals present at the market at the time of outbreak, scientists are relying on genomic sequencing to piece together the origins. Those samples taken from the market have been analyzed by scientists around the world. The latest findings link the virus to raccoon dogs found in the market (*I do want to note that these findings have yet to be peer reviewed). Previously scientists believed that the virus originated in bat specimen, but believed that another carrier animal was needed in between bats and humans; could raccoon dogs fill in the blank? Unfortunately, until international government cooperation is achieved, it’s seemingly unlikely that an exact origin of the virus will be uncovered anytime soon.

The question of origin still remains; was COVID-19 a zoonotic spillover? A bioweapon engineered by the Chinese government? Or maybe an accidental lab-leak from employees at a Wuhan laboratory who then visited the popular wet market… Hopefully one day we will find out.

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The infectious disease I am choosing to write about this quarter is COVID-19, which is caused by SARS-CoV-2, a betacoronavirus belonging to the subgenus Sarbecovirus.

Writing about this disease has probably been overdone, however recently the Dept. of Energy weirdly came out of nowhere and declared that they the virus was a lab leak; despite the amounting scientific data that is showing otherwise. My goal for this project is to learn more about the evolution and origin of this disease, and hopefully dispel some of the bigotry and misinformation that I have been hearing about the origins of the virus from friends and family.

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Disclaimer: The NCBI taxonomy database is not an authoritative source for nomenclature or classification - please consult the relevant scientific literature for the most reliable information.

Reference: How to cite this resource - Schoch CL, et al. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database (Oxford). 2020: baaa062. PubMed: 32761142 PMC: PMC7408187.

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national center for biotechnology information

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Taxonomy browser (Severe acute respiratory syndrome coronavirus 2)

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Disclaimer: The NCBI taxonomy database is not an authoritative source for nomenclature or classification - please consult the relevant scientific literature for the most reliable information. Reference: How to cite this resource - Schoch CL, et al. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database (Oxford). 2020: baaa062.