Why is Home Sweet Habitat writing about the Coronavirus?
The Short Answer: I want to help in some small way.
The Long Answer: This global crisis has left people with more questions than answers, more fear than comfort, and frankly, much more time to dwell on these negative emotions than usual. I’m also someone who can’t sit still when people are in need, and this is about the only thing I can do to help. No, there isn’t much habitat in this post (though there will be a few animals to discuss). Still, with graduate school dominating my life at the moment, I basically read scientific papers for a living. I chose grad school to help me be of service to society and to nature. There’s no reason I should have to wait until I graduate to start.
That said, it is important for me to hedge my conclusions. My training is in vertebrate zoology and more recently botany. I’m not an epidemiologist or doctor, though I did take an infectious disease ecology course a few years back. I’m writing this post under a more condensed timeframe than normal, on a subject I understand less, and on an event that is still rapidly changing. Some of the things I say may end up being factually wrong, either because new discoveries refute currently-held understandings of the virus, or simply because I misinterpreted something. Still, an imperfect understanding is better than no understanding, so let’s begin.
What is the Coronavirus?
The Short Answer: Coronaviruses are a group of disease-causing viruses. The one causing so much strife is known as SARS-CoV-2. The disease it causes is known as COVID-19.
The Long Answer: Especially upon initial discovery, scientists tend to give organisms, mechanisms, or phenomena technical names rather than something you could actually remember. Gone are the days when diseases like “The Black Death” were named so vividly. The uninspired terminology of this new pathogen has led to us simply calling it “The Coronavirus” or “COVID-19”. These technically aren’t the same thing.
Coronavirus: Coronaviruses are a group of disease-causing viruses that infect animals, including humans. Coronaviruses get their name from their unique shape, as Corona is Latin for “Crown”. Each virus individual is spherical and covered in protein “spikes”, giving them a crown-like appearance. These characteristic protein spikes help coronaviruses bind to—and ultimately infect—host cells. Crucially, each “strain” of coronavirus is genetically optimized to infect a host species, so bats don’t usually get infected by the same coronavirus as, say, camels. When they do jump species, coronaviruses usually evolve some form of structural change facilitating its infection of the new host (more on this later).
SARS-CoV-2: When the first reports of a problematic new coronavirus emerged, it needed a name. Colloquially called the “Novel Coronavirus”, this was shorthanded to 2019-nCoV in scientific circles. As the scientific community learned more about the virus, they updated its name from 2019-nCoV to SARS-CoV-2. That is, “Novel Coronavirus discovered in 2019” became “Severe Acute Respiratory Syndrome Coronavirus #2”. This name was chosen because the pathogen’s closest human-infecting relative is the coronavirus that caused SARS, or Severe Acute Respiratory Syndrome, back in 2002 – 2004.
COVID-19: While the virus may be called SARS-CoV-2, the disease is called COVID-19. Similar to naming the virus, a need for a standardized term in a short period of time led to the rather uncreative disease name COVID-19, or “Coronavirus Disease discovered in 2019”. I personally think calling the disease SARS-2 would have been more consistent with the virus name and would have actually hinted at the respiratory effects of the disease. But I’m not paid to name diseases, so there’s that.
Why did the Coronavirus show up in Humans?
The Short Answer: SARS-CoV-2 most likely spread to humans from an animal host in China. We do not yet know what animal facilitated the first transfer to humans, and we don’t know how long the virus “silently” infected humans before it became pathogenic, or disease-causing. We will likely get these answers in the coming months and years, as an unprecedented amount of research is being conducted to help us understand and fight this new virus.
The Long Answer: Reports of a new pathogenic coronavirus began to emerge out of Wuhan, China in late 2019. This coronavirus was causing symptoms of the disease we now refer to as COVID-19: a dry cough, shortness of breath, fever, difficulty breathing, and in some, death. As an emergent virus, the coronavirus posed three problems: 1) No one in the human population will have immunity towards it; 2) There is currently no vaccine to prevent against it; and 3) If the spread is not stopped, the virus will become one more infectious agent the world must cope with going forward.
In an attempt to stop the spread, wide travel restrictions and distancing measures were placed on the city of Wuhan and eventually China at large. Unfortunately, infected individuals still managed to board planes and carry the disease to other airports, and ultimately, countries. Prior to the travel restrictions, these were likely individuals who were unaware that their fever or cough were anything special before travel restrictions were put in place. In fact, many who have spread the disease were not showing any symptoms at the time they spread the disease to others. This is known as asymptomatic spread. Asymptomatic spread has been linked to the spread of the coronavirus to Germany, as well as other places across the world. Unfortunately, international efforts to contain the virus were ultimately unsuccessful, leading to our current state of quarantine and distancing. We are now in damage control mode, rather than containment mode.
A natural question to ask is, why are we going through this? What happened? Where did this all come from? And that’s a valid question, both emotionally and scientifically. If we understand where this particular coronavirus came from, we will be able to understand it more fully and take steps to prevent other novel coronaviruses from disrupting the world in the future.
Here’s what we do know. We know the first victims of COVID-19 were linked to a live animal market in Wuhan, China. Because these markets pack many species of live animals—and sometimes, illegal exotic animals— in close proximity, the potential for close contact with sick, stressed wildlife is high. This creates an environment where a virus population might jump ship from its host species into another one, including humans. This has happened before in well-known coronaviruses. The virus strain that caused SARS in 2002 was liked to civets, while Middle East Respiratory Syndrome (MERS) appears to have been repeatedly spread to humans by close contact with camels.
In the case of SARS-CoV-2, we do not yet know what animal transmitted the virus to us, though we have some clues. The virus’s genes give us two hints. Looking at the entire genome, the most genetically similar coronavirus is one that infects the intermediate horseshoe bat, (Rhinolophus affinis). The two coronaviruses share approximately 96% of their genes, and these bats are found in Wuhan. That would appear to be a solid match, but there are two problems. First, considering we share half of our genes with bananas, a 4% difference is quite large in the genetic world. Second, some of the genes that don’t match up are functionally the most important genes. As I mentioned before, coronaviruses are covered in “protein spikes” which allow them to infect their host. Briefly, these protein spikes bind to a host cell, allowing them to hijack the cell, inject genetic material into the cell, and create copies of itself using the cell’s own machinery. Differences in protein spike genetics affect how a coronavirus binds to a host cell as well as what host species they can successfully infect. The protein spike genetics between the horseshoe bat coronavirus and SARS-CoV-2 are quite different, suggesting humans were not directly infected by horseshoe bats.
Another option for a host species is the pangolin. Pangolins, also known as scaly anteaters, are endangered mammals that also act as hosts for coronaviruses. They are illegally trafficked for their meat and scales, which are used in alternative medicines. If the live animal market in Wuhan was breaking exotic animal laws, then pangolins may have been present at the market where the outbreak occurred. Additionally, the protein spike genetics between certain pangolin coronaviruses and SARS-CoV-2 are extremely similar; this means that the same genes that were not matching up with the bat coronavirus match up extremely well with the pangolin coronavirus. We can conclude that the way the pangolin virus infects its hosts (and which species it can infect) are remarkably similar.
Still, there are additional problems with pangolins as our direct host. Namely, as a whole, the pangolin coronavirus is much less genetically similar to SARS-CoV-2 than the bat coronavirus. It shines in one particular place in the genome, but the rest of the genes are nothing to write home about. Imagine a dachshund and a chihuahua. The two dogs are probably genetically similar in the genes that control height, weight, and to some degree, shape. However, given the dachshund was bred in Germany and the chihuahua was bred in Mexico, the two breeds are not closely related and likely have many closer relatives.
A third possibility is one of these two animals (or an unknown animal) transmitted the disease to humans, and it “silently” evolved inside the human population. That means, some human contracted the virus and showed no symptoms. That person then unknowingly “infected” family, friends, and neighbors with a virus that did no harm. But a virus that does no harm has certain disadvantages. It is harder to keep your species alive if you have to wait for your hosts to get close enough to spread the virus. If someone has to breathe on or kiss someone to spread the virus, that virus won’t be as successful as one that can force the issue. So, over time, the virus evolved to not only optimize its ability to infect humans, but to produce disease. Humans can’t always control when or where they cough or sneeze. Thus, a virus that causes disease can spread much more effectively than a virus that must wait for its host to be socially warm.
More time and research will be required to know exactly where the virus came from. However, there are possibilities we can definitively rule out.
Is it possible that the new coronavirus originated in a lab? Was it released onto the world accidentally or on purpose?
The Short Answer: No. SARS-CoV-2 was not created in a lab, and there is evidence to support this.
The Long Answer: Rumors have been circulating that SARS-CoV-2 is a human invention, created by genetically manipulating an existing coronavirus. We can again look at the genetics of the virus to prove this is untrue. As I have previously stated, we know three things about the genetics of SARS-CoV-2:
1) The closest genetic match is a coronavirus in horseshoe bats. 2) The virus with the most similar infection mechanisms (protein spikes) is found in pangolins. 3) The most similar human coronavirus is SARS-CoV, responsible for the Severe Acute Respiratory Syndrome outbreak from 2002 – 2004.
If I were trying to synthesize a new coronavirus, for either research or war purposes, I would only be able to use known human coronaviruses as a starting point. Make a few genetic changes, and maybe I could make the SARS virus much more deadly and infectious. Thus, if SARS-CoV-2 was created by artificially manipulating an existing virus, it would look much more like the SARS virus than it would any unstudied viruses that occur in nature. Alternatively, if SARS-CoV-2 is a natural invention, it may look much more like viruses that occur in nature, even when those viruses are not yet known to cause disease in humans.
A recent study came out indicating that the latter scenario fits the genetic data. Namely, the genetics of the bat and pangolin coronaviruses are closer to SARS-CoV-2 than is the original SARS coronavirus. If I were trying to manipulate a virus in a lab, it would be virtually impossible to create a virus that matched bat and pangolin coronaviruses if these viruses don’t infect humans! Even if I was aware of bat and pangolin coronaviruses, I still would have structured virus to closely match SARS, because I would already know such a virus is deadly and infectious. I wouldn’t waste my time trying to supercharge a bat or pangolin virus with no evidence of human infection.
Second, the manner in which the coronavirus binds to host cells was not known to science previously. Those spike proteins—which enable a virus to stick to host cells, hijack them, and inject them with genetic material—operate differently than the first SARS virus does. The way the new coronavirus binds to cells is so radically different from the way the first SARS virus binds to cells that our disease models predicted the new coronavirus would actually be a pathetic human pathogen! Using what we previously knew about coronaviruses, our disease models indicated that it would have a very hard time binding to our cells. Clearly that is not the case, so it must be using some as-yet-undescribed binding method to actually do the job very well.
An artificially-manipulated coronavirus would look a lot like the viruses we currently know to exist. Both in terms of genetics and its manner of infection, SARS-CoV-2 looks much more like viruses we didn’t know could be a threat to humans. Therefore, the virus was not man-made.
So, what do we do?
The Short Answer: Stay inside whenever possible. When you can’t, wear a mask and stay 6 feet apart.
The Long Answer: Guidelines from the Center for Disease Control are crucial to follow at this given time. You have already heard about hand-washing, staying six feet apart, wearing masks, and limiting social contact. All I can really do is reiterate how important these things are. The virus appears to spread through droplets expelled from our bodies when we cough, sneeze, yawn, or even just talk. This is why it is crucially important to prevent these droplets from spreading to others whenever possible.
Even if you don’t feel sick, you might be contagious. In fact, a recent study estimated that before travel restrictions began in China, 86% of people infected with SARS-CoV-2 were undocumented infections. Nobody knew these individuals were anything more than “under the weather”. Remarkably, this study found that these individuals were approximately half as contagious as infected individuals who actually had symptoms, and these asymptomatic individuals were responsible for 79% of the disease spread before travel restrictions! In the same way, you and I may not be exhibiting symptoms yet, or we might not recognize these as coronavirus symptoms. If we assume the worst and hope for the best, then we can keep ourselves safe. Here's a great resource for making your own face coverings.
Stay Inside: When possible, the best way you can protect yourself and others is simply staying inside. You can’t breathe on someone who isn’t around you, and your computer screen won’t mind infectious breath!
When You Feel Ill, Assume You Have the Virus: If you are feeling at all under the weather, just stay home. Hopefully it’s just a cold. But it could be worse, and you have the power to prevent the spread of this virus.
When Going Out, Assume You Have the Virus: Of course, you may not be able to work from home, you may be an essential employee, or you might just need to stock up on groceries. In the event you have to leave home, wear a mask. Masks partially protect you from getting the virus, but they greatly protect those around you. A mask won’t prevent someone from sneezing or breathing onto your eyes, but it will protect your nose and mouth from infection. At the same time, all of your respiratory parts will be covered and you will be much less likely to spread the virus if you have it. Masks, along with keeping six feet apart, will greatly reduce your ability to spread or contract the virus.
Stay Sane by Planning Ahead: Current recommendations (at least in California) allow for people to enjoy nature in wide open spaces away from other people. If you head to an area early in the morning or late at night, you can get some nature in (perhaps a dreamy night of stargazing?) without risking anyone. In my own life, I have an overweight dog that needs daily walks. So, I wake up at 4:30, throw on a mask, and give him a 5am walk. He wakes up immediately and enjoys the whole thing. I wake up gradually, enjoying the waking birds.
Cuddle Your Pets: While there have been reports of human-to-pet transmission of SARS-CoV-2, the risk to your pets is exceedingly low. I can count on my hands the number of human-to-animal transmissions documented in nature, though apparently a tiger at the Bronx Zoo has tested positive. Either way, with over 1 million documented human cases worldwide and less than 10 documented pet cases, you can safely cuddle your dog or cat. If you do test positive for COVID-19, then simply limit contact with your pet (including face-licking, food-sharing, and yes, cuddles) until you have recovered.
Are We Blowing This Whole Thing Out of Proportion?
The Short Answer: No, we’re not, but I’m not going to berate you if you disagree.
The Long Answer: I used to conduct call surveys for the Northern Spotted Owl. Since spotted owls are nocturnal, I would have to drive deep into the forest on unpaved roads to check for owl presence, all in the dead of night. So, at 2am, I would find myself at a predetermined call point, playing a recorded spotted owl call, listening for a response for a real owl. I was alone, often over a mile from my truck if the roads were too poor to drive.
You don’t really know fear until your flashlight goes out in the middle of the forest and you hear something massive moving towards you.
When this happened, I had to move slowly, but deliberately. The first thing I did was find a tree to place my back against. Now, I was only vulnerable on three sides rather than four. Next, I quietly reached into my pack and found the spare battery I needed, listening all the while for continued movement. Finally, I was able to get the flashlight on, only to find that whatever was moving was still not visible to me. I cautiously made my way back to the truck and to safety.
If what had scared me was a bear, my actions would have been completely justified. Running away screaming in the dark would likely leave me injured even if the bear had no intention of harming me! I could easily trip and fall, or run headlong into the bear, thus giving it a reason to be upset. Thus, my best option was to move slowly and deliberately.
If the “massive” beast was really a squirrel who just happened to disrupt many branches all at once, then my actions were still justified. I would have felt foolish in hindsight, but in my state of ignorance I had to assume the worst. If I did otherwise and it really was a bear, potentially with her cubs, I also would have felt foolish…foolish and dead, that is. I could have just walked back calmly, feeling for the road, waiting for my eyes to adjust. But that ultimately would have been the wrong call.
I’m not saying that bears are vicious beasts. They are not. However, they are animals capable of harming humans unless given proper space and respect. In the darkness, I was powerless to provide either space or respect to whatever it was, and so I acted in the only way that was safe. I moved slowly as I gathered information.
The current SARS-CoV-2 pandemic is quite similar to my fateful night in the forest. Some may feel we are overreacting, and the damage to the economy is not worth stopping this disease. How many will die, especially in impoverished countries, as a result of loss of livelihood over the coming months and years? Certainly this is difficult to know, and it is a valid concern. Still, we have an opportunity to save lives. Over 1.2 million people have contracted the disease from December to April, and over 67,000 people have died. These are numbers as of today, so many of these deaths occurred in spite of the tremendous isolation efforts that have been enacted globally. Simply put, had we done nothing, these numbers would be much much higher. In the United States, nearly 9,000 people have died from COVID-19, with over 300,000 people infected, despite our efforts. We may reach a peak where over 3,000 people die in a single day in the US. To put that in perspective, that is how many people died in the September 11th terrorist attacks, which launched us into a decades-long conflict in the Middle East costing trillions of dollars. Maybe our reaction isn’t so extreme after all.
You may not agree with me, and that’s fine. You may think I’m right on the money, and that’s fine too. Ultimately, this is everyone’s first coronavirus pandemic. No one really knows what they’re doing, so it is important we don’t point fingers. I’d prefer it if you stayed inside and didn’t hoard toilet paper, but I’m not mad at you if you do. We are humans, fallible, and allowed to overreact or underreact to complex situations that we don’t fully understand. Our social media society has a habit of throwing certain groups or behaviors under the bus, and I want you to know I will never participate in that. All I can ask is that you consider the sincerity of my words, the urgency of my pleas, and the credibility of my sources. Whatever you choose, you’ll still have a friend in me after this is all over.
By the way, I never found out what scared me that night in the forest. Fortunately, I never had to. I sincerely hope the same for you and your own. Godspeed, and God bless you.