COVID-19: From Zoonotic Spillover to Host and Pathogen Interaction in Human Disease

Key Points Answered in this Article

1. What constitutes a spillover?

2. What are the contributing factors?

3. How does SARS-CoV-2 cause infection in human pneumocytes

4. What are the contributing factors to more severe disease.



The United States prepares itself for the impact of COVID-19  that will likely be unprecedented.  Although we can say that most people who become infected will have a milder disease, we cannot always predict who is at greater risk for a severe outcome.  Particular attention goes to healthcare workers, lower-income communities, and people with advanced age and chronic health conditions.  To those unfortunate ones who develop severe disease and require hospitalization, the US health system faces shortages of ventilators, personal protective equipment (PPE), bedspace and the even the healthcare workers to attend to them.  Worst-case scenarios project hospitals to become flooded with those who have severe disease, particularly if cases were to occur with the same momentum as Italy or China.  The hope is that through the social distancing measures recently implemented, we may be able to blunt the outbreak peak and prevent overburdening our healthcare system.

The general audience has had access to many resources on COVID-19, such as the CDC, WHO, health blogs, video posts, and primary literature.  As we face this outbreak, never before has the nation’s working knowledge of viral infections been greater.  Since the outbreak was declared in December, we have had three months to learn more about this virus.

This post will go one step further into understanding the contributing factors to a viral emergence and how this likely is not the last outbreak we will have in the coming years.  What happens when a virus infects our bodies?  What occurs inside that leads to a certain presentation of a disease state?  Although COVID-19 is shrouded in mystery, it adheres to natural rules, many of which we still need to define.  The mechanism by which a pathogen causes an infection is a clue to how it can be defeated.


Viruses are Host and Cell-specific, until they cross species.

Viruses are intracellular pathogens that are species- and cell-specific. This means that they are usually only capable of infecting one animal.  Though there may be some fluidity to this concept.  A virus can reside in an animal, whether it is actively infecting the animal or not.  An animal virus is called a zoonotic virus, and the animal carrying it is a reservoir.  In viral zoonotic spread, mammals (e.g. bats, primates, etc) are the most common reservoir followed by birds.  When the conditions are right and several barriers are able to be breached, viruses can jump species, infecting other animals including humans. The process by which a virus jumps species and causes human infection is termed a spillover, an example of which is our current COVID-19 pandemic.

Over 75% of new or emerging diseases originate from animals.  From 1940 to 2004,Jones et al. (2008) determined that there were a total of 335 emerged diseases, 60% originating from animals.  In most outbreaks, human behaviors  shaped the conditions that made it possible.   The principal factor relates to human encroachment into animal habitats.  It is no coincidence that an acceleration of outbreak has occurred in the last sixty years (fourfold increase) in the setting of a massive population boom.  Eerily, a Times article  describing spillovers written in May 2017 was entitled The World is Not Ready for the Next Pandemic.


“We cut the trees; we kill the animals or cage them and send them to markets. We disrupt ecosystems, and we shake viruses loose from their natural hosts. When that happens, they need a new host. Often, we are it.”  David Quammen, author of Spillover: Animal Infections and the Next Pandemic writing in New York Times.


From the 1800’s, it took approximately 127 years for the population to increase by one billion, i.e. from one to two billion, an achievement that only took thirteen year intervals over the last several decades to achieve 7 billion.  The population growth may be a driving force for disputes over settlements, habitat invasion, the use of exotic animals as a food source in the setting of growing food insecurity,  or the trade and introduction of exotic animals to be used as products or pets.  Certain features directly related to the virus, including mutations, deletions and recombination, enable the virus to survive and then flourish within an introduced animal.

Ingredients of a Spillover Event.
Contributing Factors to a Spillover are related to human and animal behavior, as well as ability for the virus to persist in an introduced host.

Adapted form Nat Rev Microbiol. 2017; 15(8): 502–510.doi: 10.1038/nrmicro.2017.45

population growth chart



Ingredients for a Spillover Event. 

Although outbreaks are infrequent events, current conditions may allow for an increased risk.  For a virus to jump species from an animal reservoir to to human to human spread, usually several conditions would need to be met.  First, animals infected with a virus need to be stable and have persistent shedding of virus, while not succumbing to it.  Second, the animals would need to be in close proximity to humans.  Next, an exchange of infected fluids, such as saliva, mucus, feces or blood, or the ingestion of an animal allows for a sufficient amount of virus to be introduced into the new animal by its usual infection route.  While inside the human, some of the virus must possess a specific (enough) receptor mutation to allow for avidity (or connection) of the virus to a host receptor to gain entry into the specific cell.  Finally, it must be able to propagate and infect other cells, without being identified and neutralized by the host’s innate immunity.  Once it is able to survive and replicate within the human host, it must be able to be transmitted from one human to another.  If any of these conditions are not sustained, a spillover does not occur.

Street Light Diagram
Street Light Diagram of Components to A Spillover:  Adapted from RNA viruses: a case study of the biology of emerging infectious diseases.  Woolhouse M. et al. Oct 2013.  Microbiol Spectrum.

From the “Street Light Diagram,”  yellow (level 2) is intended to connote caution.   Red (level 3) indicates higher risk of pandemic potential, but certain viral and non-viral kinetics (e.g. population density, behaviors) prevent easy transmission.  These factors influence the basic reproductive number (Ro), with an Ro of greater than one to allow for risk  of exponential growth.  The black (level 4) designation is related to epidemic spread.  For a detailed list of RNA viruses that are recognized as causing infections in humans and their respective levels, refer to Woolhouse M. et al (list).

Of particular concern are the 180 and counting (2 newly identified per year) RNA viruses capable of infecting humans, the majority (89%) of which are zoonotic.  Examples of recent RNA viruses that have emerged include HIV, influenza virus, NIPAH virus and the Coronaviruses SARS, MERS and SARS-CoV-2.  RNA viruses may more easily jump species, because of their tendency to mutate and adapt more easily when introduced.  Not all RNA pathogens that cause infection in humans from animals are capable of being spread from human to humans.  The majority of zoonotic RNA viruses are restricted to level 2 (approx 107 out of 180 species).  An example of this would be avian influenza (H5, N2 or H9, N2), which does readily not cause human-to-human transmission.  It may be related to the cell type infected, the sialic acid receptor, which is in the upper respiratory tract of poultry and lower in humans. This is fortunate because it has an estimated case fatality rate of 14-30%.  Level 3 spread is seen only in about 73 species and spread is limited in 26 of these RNA viruses.  The remainder (47 Level 4 RNA viruses) can spread human to human, causing epidemics..

Very rarely, a virus may already be able to adapt to a human and lead to an outbreak, termed “off-the-shelf” virusesMore likely, viruses eventually adapt from repeated animal to human transmission and evolve to be more transmissable between humans (Level 3 to Level 4).  HIV probably crossed over from chimpanzees to humans in what is now the Democratic Republic of the Congo in the 1920’s, possibly from hunters who ate “bush meat” or had cuts and wounds contaminated with chimpanzee blood infected with Simian immunodeficiency virus (SIV), a milder disease which does not alter the lifespan of the infected animal.  The ability of HIV to cause a prolonged infection and be transmitted via various routes including bloodborne and sexually enabled it to become a level 4 pathogen and reach global transmission.

The SARS-CoV-2 emerged likely from bats with the possiblity of a secondary animal reservoir the pangolin.  Bats are known carriers of coronaviruses and have been determined to be the likely reservois for SARS and MERS.  Andersen et al.  published a recent correspondence entitled the proximal origin of SARS-CoV-2.   The authors discusss several possible and contributing scenarios.  On account of a 96% identical genome with a sampled bat coronavirus, bats were likely the original reservoir of SARS-CoV-2.  However, SARS-CoV-2 may have evolved the protein stucture of the S-spike to allow for better binding to human ACE2 receptors from pangolin through natural selection.  It is possible that a polybasic cleavage site (necessary for cell-cell fusion) may have evolved after being introduced into humans.


From Spillover to Infection and Disease

When COVID-19 emerged from an animal source and was capable of human to human transmission, humans had no prior memory of this virus.  The immune system was caught off-guard with minimal defense.  As a virus infects cells and increases its numbers in the host, the disease develops, a time when a person presents with signs and symptoms.  Even in the setting of a novel virus, most of the way a disease manifests is due to the host inflammatory response and not because of a distinct genetics, appearances (e.g. receptor sites) and other characteristics of a virus.

Cell infection

A virus is an obligatory intracellular pathogen, meaning it can only thrive within cells.  A specific virus infects a specific type of cell.  Hepatitis C virus infects hepatocytes; BK virus infects the transitional cells of the bladder;  influenza virus and coronaviruses infect type I and type II pneumocytes in the respiratory tract;  HIV infects CD4 lymphocytes and Langhans cells.  The specificity of cell-type is not accidental and relates to a lock-and-key mechanism that a virus has with the cell it infects.  Think of it as a parasite requiring the mechanics of the host to build more copies of itself.  It enters the lining of the respiratory tract and attaches onto cells by means of a receptor interaction.  Specifically, this is between an outer membrane receptor of the virus (Spike glycoprotein (S)) and a receptor(s) on the host cell.  The virus then enters the cell by a process known as endocytosis.

Upon entry, the virus hijacks the cell’s ability to read nucleic acids and produce proteins.  COVID-19 is a positive strand RNA virus,  with the viral RNA serving as a messenger RNA, leading to the production of hundreds of copies of virus RNA and proteins in a single cell (known as replication). These copies self-assemble and form multiple viruses, or progeny.  This results in stress on the cell and cause changes in the cell membrane (membrane rearrangements), damages the infected cell, and go on to infect other cells.

The extent to which a virus can infect cells in known as its pathogenicity.  The speed at which a virus can spread through the body and infect other cells is known as the virus lifecycle.  In the case of viruses, typically thousands of copies can be generated in a period of a day and lead to significant inflammatory changes in the body as a response to infection.



ACE2 as a SARS-CoV-2 receptor

The S receptor on the SARS-CoV-2 binds to a specific receptor that lines the cells of the lung tissue, as well as heart kidney, endothelium (the inner lining of blood vessels) and the intestines, known as the Angiotensin-converting enzyme 2 (ACE2) receptor.  This interaction is a required step for viral entry into the cell.  Using a mouse model, an increased expression of the ACE2 receptor allowed for more viral entry into the cells and resulted in greater disease severity.  Further studies will have to sort out the speculation that medications such as ACE inhibitors, Angiotensin receptor blockers (ARBs), ibuprofen, or thiazolidinediones,  all of which upregulate ACE2 receptors would potentially worsen COVID-19 disease.  As for now, it does not appear to be the case.  In the realm of vaccine and therapy options, it remains to be seen if blocking these receptors, for instance through antibody therapies, or providing a vaccine that triggers antibodies to the S receptor would alter pathogenesis of the virus.



How does our immune system recognize these invaders?

The evolution of the immune system occurred in the face of the continuous onslaught of microbes from the environment.The human immune system consists of innate and adaptive immunity.

Innate Immune System

The innate immune system is the first branch to respond to a viral assault.  The components of the innate immune system include cells, such as natural killer cells, dendritic cells, monocytes and neutrophils, and complement proteins.  The innate system senses changes that occur to the cell from viral products and cell damage (Pattern Recognition Receptors).  This triggers the release of interferons (IFN), which promote inflammation (activate molecules known as cytokines) and reduce virus replication.  The cytokines signal special cells, known as natural killer and dendritic cells, which destroy infected host cells to reduce the spread of the viral infection.  The PRRs also trigger a process known as autophagy, in which an infected cell degrades itself to reduce (or the intent to reduce) further infection.

The complement system consists of several proteins that form a complex, leading to cell breakdown (lysis).  They can also signal certain cells such as activated macrophages to engulf infected cells, a process known as opsonization.

Adaptive Immune System

Adaptive immunity requires antibody production and cell-mediated mechanisms.  Some natural antibodies may already be circulating for a given virus that can provide some initial immunity (known as IgM class antibodies).  These are generated by antibody-producing white blood cells known as B cells.  Otherwise specific cells known as Activated macrophages can engulf cells to produce antigen that express more pathogen-specific antibodies by B cells.  The dominant antibody types in humans are IgM, IgD, IgG, IgA, and IgE, each of which has specific roles in the immune response.  The IgG is involved in the memory responses and form to neutralize a virus.

Another white blood cell line, known as T lymphocytes (T cells), are produced in a small gland known as the thymus, which is inside the front part of the chest (behind the sternum and in between the lungs).   These T cells provide cell-mediated immunity. Specific cells are produced that have receptors for a given pathogen and can neutralize them.

From Infection to Disease

When a person becomes infected with a virus or bacteria, there is a period of time at  which s/he is symptomatic.  The term that is used from onset of the infection and expression of the disease is known as incubation period.  Various viral infections have different incubation periods.  For instance, influenza’s incubation period is one to four days; COVID-19 may take one to fourteen days (average of 6) to show symptoms.  During the prodromal phase, the person develops early symptoms of a viral disease.  This could be the beginning of nasal congestion, sore throat, cough and tiredness.  After a threshold is reached and enough cells become infected, a more sizable inflammatory response is generated.  It is at this time, the person becomes symptomatic.

During the invasive phase, the number of circulating virus intensifies, while the body responds to the infection with a maelstrom of inflammatory markers.  The severity of the presentation correlates to the intensity of infection and the inflammatory response.  Eventually, the inflammation subsides as neutralization of the virus as a result of the immune system.  It is at this point that a person’s symptoms gradually resolve.  stages of an infection


Viral Disease: It’s all about inflammation

In approximately 80-85% of those infected with SARS-CoV-2, only a mild disease is seen.  In the remaining, a severe infection can lead to hypoxia (low oxygen levels) and need for mechanical ventilation. Owing to increased cellular damage, the subsequent inflammatory response may pose a threat on life.

Risk Factors: In a study of clinical course and risk factors for mortality in COVID-19, risk factors were identified in almost half of the patients, with hypertension, diabetes and coronary heart disease.  Smoking likely leads to a two-fold risk of more severe disease than a non-smoker.  Advanced age is also a significant mortality risk.  From the Wuhan epicenter data:  80+ years, 14.8%; 70-79 years, 8%; 60-69 years, 3.6%; 50-59 years 1.3%.  This is likely on account of dysfunctional innate immunity, IL-2 signaling (not down-regulating) and T-cell mediated immune system with aging.  What still remains unknown for COVID-19 infection is whether there exist genetic determinants (as seen in other viral diseases) that lead to a greater risk of a more severe infections.  This could explain why we are hearing reports of severe disease in the “otherwise healthy” youth.

Pathogenecity and Inflammation Contribute to Disease Manifestations.  The extent to which someone presents with more severe disease relates to an interaction of amount of cell destruction from viral burden and host response.  Below is a depiction of the contributing effects of Viral Pathogenicity and Host Inflammatory Response in disease.  Increased viral infection burden is likely an important contributor to a greater immune response.   It may be that type 2 pneumocyte infection in the lower respiratory tract may cause a greater cytokine release than infection in upper respiratory cells.

disease manifestations
Disease:  A “dance” between viral infection and immune response


Disease Presentation

The most common symptoms on admission were fever and cough, sometimes with sputum production and fatigue.  Interestingly, the average time of presentation of respiratory complaints, such as shortness of breath, is approximately 7 days and need for invasive ventilation is 14.5 days (range 12-19 days), suggesting that the latter part of infection may be when greater inflammation develops “cytokine storm”.  The most frequently observed complication was sepsis, followed by respiratory failure, ARDS, heart failure and septic shock.


**The shortness of breath (“Dyspnea” in blue) started around day 7 in both groups**


Laboratory Findings for Hospital Management

There is a significant inflammatory response in more severe infections of COVID-19.  Patients may develop ARDS, which is the leading cause of mortality.  Several findings of the disease support a hypercytokine, hyperinflammatory response that contribute to a more severe presentation.  These patients have a persistent fever, low white blood cell count, elevated cytokines (IL-2, IL-7, IL-6, GM-CSF, Interferon gamma and others), an elevated ferritin, and an elevated D-dimer.

Future Therapy

In an unprecedented move, the FDA has granted emergency authorization for the use of hydroxychloroquine along with azithromycin based on early clinical data that there may be a benefit of hydroxychloroquine in reducing viral load and inflammatory state.   We await further progress in other therapeutics and vaccine trials, many of which are now underway.


The COVID-19 outbreak was a spillover event of a novel coronavirus from an animal reservoir that led human to human transmission.  Further research is required to understanding the way the infection can lead to various disease manifestations, including who may be susceptible to more severe presentations.  Hydroxychloroquine along with azithromycin may provide some benefit in treating those with severe disease.  As for now, we await for the results on the treatment and vaccination fronts.



References are embedded in the Text

Simon A, Hollander G, McMichael A.  Evolution of the immune systen in humans from infancy to old age.  Proceedings of the Royal Society B.  22 Dec 2015.

Zhou F, Yu T, Du R, Fan, G, Liu Y, Liu Z et al.  Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study.  The Lancet.  Vol 395, issue 10229, p 1054-1062.  28 Mar 2020.