What’s Important To Know About Immunity In The Age Of Covid-19

Mike Murray
16 min readMay 7, 2020


By Kaique Rocha from Pexels

Questions, questions, questions.

“Can we test for antibodies to the coronavirus to see how many people have been infected?” Well, it depends on the accuracy of the test.

“If I have antibodies to the coronavirus, am I protected from infection?” Well, it depends on which experts you listen to, and the World Health Organization has gone so far as to specify that there is no evidence that prior infection is protective.

“Will vaccination finally put an end to the pandemic?” Well, it depends on what part of the coronavirus the vaccine targets and whether that stimulates a protective immune response. Previous attempts to make an effective vaccine against the SARS coronavirus of the early 2000’s were met with several failures.

As we proceed through the uncharted territory of the Covid-19 pandemic, we are bombarded by a slew of scientific and pseudoscientific information about virology, epidemiology, disease manifestations, treatment, and preventive measures. At the center of these topics is immunity; how our bodies respond to a viral infection and how vaccination may work. What we hear and read about almost exclusively is antibodies, but when it comes to our immune system’s response to viral infections, antibodies are really just a part of the immunity story, and not necessarily the most important part at that. That’s why I would like to provide a broader picture of how we respond to infections by viruses and how different approaches to vaccination may be implemented. My intention isn’t to present a highly technical treatise on immunology, but rather to explain the parts of immunology that people will benefit from understanding as they consider how this pandemic may play out, including how we might begin to get back to our normal lives.

First, a little background information about me. I am a veterinarian and I am board certified in large animal internal medicine. I am not a specialist in virology, immunology, or epidemiology, but throughout my career I have conducted research on infectious diseases in collaboration with many highly talented scientists in these fields. At one point I was the head of the global pets’ vaccines franchise for a major animal health company, and in this and other roles I had the privilege to work with brilliant scientists who were at the forefront of vaccine innovation. Many of these innovations are now being incorporated in the development of vaccines targeting SARS-CoV-2. I also was part of a team that my company sent to Australia to help coordinate the use of a novel recombinant equine influenza vaccine during the 2007 Australian equine influenza epidemic. This vaccine was credited with helping extinguish the rapid spread of the virus in a population of horses that was previously unvaccinated and immunologically naïve to the influenza virus.


So, let’s start at the beginning, with what comprises our immune system. The elegance and complexity of the mammalian immune system is one of the great wonders of nature. It is designed to detect and stop, or at least attenuate, a host of viruses, bacteria, fungi, protozoa, worms, and other potential invaders that can infect and kill us. Like a sophisticated army, a successful defense is based on detecting a potential threat, having an effective communication infrastructure, and possessing the capability to mount a rapid response. As such, the key components of the immune system are concentrated where potential invaders are most likely to gain entry: the skin, the gut, and the nose and throat. The primary soldiers of the immune system are cells called lymphocytes. These are small, spherical cells that can be found throughout the body and in the blood. They are most abundant in the intestinal tract and in specialized lymphoid tissues such as lymph nodes, tonsils, the spleen, and the thymus in young animals. There are many different types of lymphocytes, each with unique functions. Some are programmed to produce antibodies (B cells), some help to ramp up a response to an invader (T helper cells), while others directly kill cells infected with viruses (cytotoxic T cells and Natural Killer cells). Some lymphocytes produce chemicals (cytokines) that enhance an inflammatory response, while others dampen inflammation. Lymphocytes communicate with each other and other cell types via chemical messengers, and some even communicate with our nervous system via these chemical signals. When we are healthy, there is a constant, coordinated symphony playing throughout our bodies that engages the immune system with our entire being, constantly on the lookout for potentially dangerous invaders.

One of the most fantastic aspects of the immune system is that we have lymphocytes that are pre-programmed to target virtually any potential pathogen of the past, present, and future. There are literally billions of lymphocyte “clones” that are specific for individual pathogens, including those that have not yet come into existence! That’s how we can mount an effective immune response to the newly emerged SARS-CoV-2. Each of these clones recognizes a particular chemical structure (antigen) of the invading organism, usually a sequence of amino acids in a protein. Often there are lymphocyte clones that recognize different parts of a virus, so that when we are exposed to that virus the immune system launches a “polyclonal” response.

Antibodies are what we hear about all the time, of course. These molecules can be thought of as highly specific handcuffs that can only be used on a thief with a specific fingerprint. The specificity of antibodies is based on amino acid sequences in their binding sites that are perfectly complementary to amino acid sequences in proteins in the virus. These viral amino acid sequences are called antigens, which are the targets for antibodies. The coronavirus SARS-CoV-2 is comprised of many proteins and amino acid sequences that could be targets for antibodies. Importantly, these targets need to be accessible to antibodies. If we look at the familiar spike protein on the surface of the virus, for example, it’s structure consists of long chains of amino acids in various folds, loops, and other configurations. Many of its amino acids are not accessible to antibodies, being buried within those folds. Also, there can be specific antibodies produced to different chemical sequences within the spike protein, and these antibodies may not all be equal in their ability to prevent the virus from infecting us. These variables pose challenges for manufacturers of antibody tests and certain types of vaccines.


When we become infected with a new virus, whether it’s new to the world or just new to us, we have some defenses already in place, which are part of the innate immune response. This consists of certain chemicals (interferons) and a type of lymphocyte called a natural killer cell. If the infecting virus particles get past this innate immune response and infect our body’s cells, these cells will become “hijacked” to produce new viral particles. In the process, though, these cells can also send a call for help, by presenting a portion of viral protein on the surface of their cell membranes that alerts the immune system that they are under attack. Several cell types, including specialized antigen processing cells, are particularly effective at alerting the immune system that the body is under attack.

B Cell Lymphocytes: The Antibody Factories

One way that the immune system can recognize a viral infection is by direct interaction of the virus with B cell lymphocytes, which comprise the humoral, or antibody, response of the immune system. These cells are found in specialized lymphoid tissues, including those in the nose and throat (the tonsils, for instance). When a virus interacts with a B cell that is specific for that virus (remember that we are born with these), the B cell becomes activated to produce antibody AND it alerts other lymphocytes called helper T cells that secrete chemicals that cause the B cells that are specific for that virus to replicate many-fold. It’s like a massive callup of new recruits for a military campaign. Early in the process of this activation, the B cells produce a type of antibody called IgM, and then after a few days they switch to produce IgG antibody. As a result, we can usually detect an IgM antibody response to an infection 5–7 days after the initial infection and a more pronounced IgG antibody response 14–21 days after infection. Both IgM and IgG antibodies can bind to viruses and neutralize them, preventing them from infecting more cells in our body. Another type of antibody, called secretory IgA is produced by lymphocytes in the mucosal linings of the respiratory tract, gut, genitourinary tract, and mammary tissues. It is produced along the same timeline as IgG, so while secretory IgA is considered to be the first line of defense against many infections, with a novel virus like SARS-CoV-2 it will not be produced in time to prevent spread of the virus within an individual.

T Cells: Communications, Logistics, and Hand-To-Hand Combat

There are many different types of T lymphocytes, and in collaboration with other cells types, especially the specialized antigen processing cells, they comprise the cell mediated immune response (CMI). T helper cells recognize the call for help from cells infected with the invading virus, and they carry that message to other parts of the immune system. This results in a rapid proliferation of cell types, including B cells for antibody production and T cells that can directly stop the spread of the virus. Cytotoxic T cells are the soldiers of the immune system that kill virus-infected cells before they can manufacture and release thousands of new copies of the virus. With some infections, these T cells can be activated and proliferate with just a few days, blunting the propagation of a viral infection even before there is much antibody production. This is particularly crucial when we are infected with a virus to which our body has not previously been exposed, either naturally or through vaccination, like the novel SARS-CoV-2. This is probably one of the key factors why many people who are infected develop no symptoms or mild symptoms. If you can stop the virus before it propagates, you’ll be fine. If, on the other hand, the virus gets a toe-hold and starts to spread into the lungs and other organs, the body goes into DEFCON 1, triggering a cascade of harmful chemicals in an all out effort to stop the invader, essentially shooting first and asking questions later. It’s a scorched earth tactic to destroy the virus, but it can also devastate us in the process.


When we want to determine the immune status of people against a virus like SARS-CoV-2, we are limited to looking for the presence of IgM and/or IgG antibodies in their blood. But as we know, these antibodies only comprise a portion of the actual protection provided by the immune system. Secretory IgA on the mucosal surfaces of the respiratory tract and gut is vital to neutralize virus particles before they can invade and propagate, and the lymphocytes of the CMI are key players to eliminating infected cells before they can manufacture and release new virus. However, measuring IgA and CMI, while possible, is not clinically feasible, especially on a large scale. Consequently, the tools we have to assess immunity, either after an infection or vaccination, provide somewhat limited information as to the actual immune status of the person. Yes, it matters whether you have produced IgM and IgG, but it is just a part of the story. Another confounder is the accuracy of these tests that are being rapidly deployed. Many of these tests are known to have flaws with their sensitivity (the ability to detect antibody when it is present) and their specificity (the ability to report a negative result when the antibody is not present). This makes it difficult to develop a clear picture of the extent of infection, given that a large proportion of infected people do not have symptoms and are not tested for the presence of the SARS-CoV-2 virus.

Of course, this description of how our immune system works is intentionally oversimplified. The immune system is highly complex and elegant, but so are the pathogens it has evolved over hundreds of millions of years to fight. These pathogens have also evolved over millions of years to evade the immune system, and so it is a constant “arms race” between the immune systems of animals of all stripes and the pathogens that try to make a living off of them. Many of these viruses have become very successful at evading the immune system, and in people HIV and herpesviruses are particularly notable in their ability to remain hidden in plain sight. How does SARS-CoV-2 compare to these expert immune evaders? While it’s too early to say for sure, the structure of the virus seems to optimize its transmission and invasiveness, but it also has properties that should make it a good target for the immune system. That will be good news for vaccine developers.


Vaccines use whole virus particles, alive or dead, or parts of the virus to “trick” the immune system into thinking there has been an infection and thus mount an effective response. The key to the success of vaccines is that the immune system has memory, and there is an entire cadre of lymphocytes dedicated to creating and maintaining this memory. Once the immune system has responded to a pathogen or vaccine, it “remembers” that specific organism, and if the person becomes infected again in the future, the body mounts a more rapid and pronounced immune response, with both antibodies and CMI, than with the first infection.

Because vaccines work by imitating an infection, the closer they can mimic an actual infection, the more robust the immune response. The first recorded vaccination in modern times was Edward Jenner’s use of ground up pustules from cowpox infections to immunize people against smallpox. In fact, Chinese doctors are believed to have used lesions from persons with actual smallpox to immunize others against the deadly disease hundreds of years ago. Both viruses share structural properties that our immune system recognizes. Vaccinating with smallpox virus infected tissues will literally give the recipient smallpox. The trick is to properly titrate the dose of virus given, a truly hit-or-miss proposition. With using coxpox, it’s also hit-or-miss with the dose, but because the virus is not adapted to humans, it only can replicate a few times before it is eliminated. And that’s the beauty. It replicates enough to make the immune system respond as if it is a real smallpox infection, but not enough to cause serious illness.

Today, we still employ this principle by using modified-live viruses, viruses that have been weakened, but not killed, and which can replicate a few times and cause the immune system to react as if it is a real infection. Examples of modified live virus vaccines include vaccines for measles, mumps, and rubella.

Many vaccines use killed virus, because this can be an effective way to stimulate antibodies as a first line of defense. Many influenza vaccines used killed virus. The immune response is not as robust, particularly a weaker cell mediated immune response, as with a modified live virus vaccine. For seasonal influenza, though, an antibody response is usually sufficient to stop or moderate an infection. These vaccines are typically injected into the muscle, and the killed virus particles are carried through lymphatic drainage to local lymph nodes where the inactivated virus particles can interact with lymphocytes, which recognize proteins on the surface of the killed virus.

Other vaccine technologies seek to optimize the immune response without using a live or inactivated version of the actual pathogen. Some vaccines include only specific viral proteins that trigger an immune response, while others use the DNA or RNA that codes for a specific viral protein amino acid sequence (peptide) to cause the individual to mount an immune response as if they were infected by the actual virus. The viral DNA or RNA gets into the vaccinated individual’s cells, causing the cells to manufacture that specific viral peptide, but not the entire virus. That viral peptide is expressed on the surface of the cell, alerting and activating the immune system as if there was an actual infection with the virus. One promising vaccine candidate to respond to the COVID-19 pandemic is based on the RNA sequence for a portion of the spike protein on the surface of the virus. An exciting feature of this vaccine is that it is relatively simple to manufacture, and millions of doses can be made relatively fast. Vaccines that use weakened or killed virus require that the virus be grown in eggs or in cell cultures, which are limited in capacity, thus restricting production.

Another method to accomplish this highly specific immune stimulation is using recombinant technology, in which the gene that codes for a viral peptide is inserted into another, non-pathogenic virus, which does replicate a few times in the vaccinated individual, but does not make them sick. Just like with a DNA or RNA vaccine, the vaccinated person’s cells make the target virus peptide, which is used by the cell as a call for help. The immune system detects the viral peptide and acts as if it is a real infection and mounts a robust response. This technology has been used extensively in veterinary medicine and examples include the use of a live, attenuated canarypox virus in which genes that code for peptides of canine distemper, feline leukemia virus, rabies, or equine influenza are inserted into the canarypox DNA. The recombinant equine influenza vaccine was shown to induce a rapid antibody and CMI response, and in a 2007 outbreak of equine influenza in Australia, where horses were naïve to this virus, there were cases in which local outbreaks were stopped within a few days of a single vaccination. The ability of a vaccine to rapidly induce protective immunity in the face of an outbreak in a population is exactly what is needed in the COVID-19 pandemic, particularly for those at greatest risk of getting infected.


Many questions remain unanswered about how our immune system responds to infection with SARS-CoV-2. What does seem to be clear is that people respond quite differently from each other. This has vexed physicians and stymied epidemiologists, who are trying to track the extent of COVID-19 disease through testing procedures, and it raises important questions about the effectiveness of vaccination.

At the center of both tracking infection and vaccination are antibodies. In theory, we should be able to identify who has been infected and the extent of infection on a population based on the presence of antibodies to SARS-CoV-2. While this seems largely true so far, it also seems that an unknown proportion of people with confirmed COVID-19 disease do not develop a robust antibody response. Importantly, how and which antibodies are detected really matters. Classical testing for antibodies uses serial dilutions of a person’s serum to detect a cutoff point at which antibodies that neutralize the virus can no longer be detected. This dilution is called the titer, and the person’s antibody titer can vary based on the sensitivity of the methodology. More and more, rapid antibody detection kits are available to laboratories, and these tests have a calibrated cutoff, an amount of antibody at which the test result is positive or negative. With SARS-CoV-2, we don’t yet know which of these tests has calibrated the cutoff point optimally, such that some tests are already showing a propensity for a high number of false positive or false negative results.

Furthermore, in consideration of whether testing positive for the antibody means you are protected from infection, infection with SARS-CoV-2 induces antibodies to different components of the virus. Most antibody tests look for antibodies against segments of the spike proteins on the surface of the virus, but antibodies to other components of the virus can also be produced. None of these tests indicate which antibodies are actually protective, so while a positive antibody test probably indicates you have been exposed to the virus, it does not definitely mean you are protected. Probably, but not definitely.

This testing also tells us nothing about the importance of the CMI response in fighting infection with SARS-CoV-2, but this is likely to be a critical piece of the puzzle. As mentioned, differences in the CMI response to the infection may be at the core of why some people are asymptomatic, while others become severely ill and succumb.

How our immune responses vary to this infection also weighs heavily on choices being made in how to successfully develop vaccines against SARS-CoV-2. For instance, a classical killed vaccine will likely induce an adequate array of antibodies in most recipients, although not a robust CMI response. The extent to which these antibodies confer protection, though, is still highly uncertain. Vaccination against other coronaviruses, including SARS-CoV (1), often resulted in inadequate protection. The RNA or viral vectored recombinant platforms described here should stimulate a more robust immune response, including both a strong antibody and CMI response, but scientists will have to have selected genetic sequences that code for coronavirus antigens against which our bodies produce a protective response. Targeting peptides in the SARS-CoV-2 surface spike proteins makes complete sense, but this is not guaranteed to work!

There is evidence that it might, though. Researchers with Oxford University in the UK have developed a vaccine based on recombinant technology, similar to that described for the equine influenza vaccine. In their case, the vaccine is based on a weakened simian adenovirus (which causes the common cold in Chimpanzes) that has the genetic material for the SARS-CoV-2 spike proteins inserted into its genome. The virus is also modified so that it cannot proliferate in people, but it can invade enough cells so that they express the spike proteins and “trick” the immune system into thinking there is an active coronavirus infection. Preliminary studies in which six Rhesus macaques were given one vaccination and then challenged with a heavy dose of SAR-CoV-2 virus yielded positive results, with no illness observed in the animals. Human trials will commence soon. Of course, there will be concerns about using a “monkey virus” in people, fearing a reversion to virulence, as well as concerns about using a genetically modified virus vaccine. The experience with administering millions of doses of recombinant vaccines in veterinary medicine should be reassuring in this regard.

Because the different vaccine technologies and compositions stimulate the immune system differently, the types of responses can be tailored to meet the specific needs of certain segments of the population. For example, medical professionals directly involved with treating COVID-19 patients, desperately need full immunologic protection ASAP, and a vaccine that stimulates a rapid CMI response could be highly beneficial for that group. Such a vaccine might be based on recombinant live virus technology or an RNA platform. A vaccine that employs killed virus or viral proteins and that stimulates a good antibody response could be particularly valuable for mass population vaccination, especially in young people who may be important silent spreaders of SARS-CoV-2.


We are still faced with a large degree of uncertainty to very important questions that relate to our immune response to SARS-CoV-2.

· Why do different people react to infection so differently?

· What does the antibody testing mean?

· If I do get infected with SARS-CoV-2 and recover, am I protected from reinfection, and for how long?

· How can we use antibody testing to get the country and the world back to work and resuming our lives?

· Why does it take so long to develop a vaccine?

As of the beginning of May 2020, the answer to these questions essentially is, “It depends”.

· It depends on your genetics.

· It depends on how your body’s inflammatory response system is calibrated (many chronic diseases promote a hyper-inflammatory state)

· It depends on the technology platform being employed.

· It depends on how lucky we are in getting the right technology platform, the right immune response, and the right capability to deliver these to people as quickly as possible.

They say that sometimes it’s better to be lucky than good. With SARS-CoV-2 and COVID-19, we’ll need both!