Virus, Bacteria, What Does It Matter Now?
Dr. Michael Manson, April 23rd, 2020.
Viruses and bacteria are both just germs, right? So why does it matter that COVID-19 is caused by a viral infection rather than a bacterial infection?
It actually matters a great deal. That is because viruses and bacteria, although they both come in many types and each can cause very many illnesses, are very different things.
Bacteria are cells. That means that they are alive. They can live in or on us, but they can also live without us. They are organisms, and they can grow and divide without any help from us. Most of them are very small, invisible without a microscope. But if you look at them in a microscope, you can see that they are alive. Many of them can swim or crawl, and you can watch them get bigger and then split in two to create two new daughter cells out of one mother cell.
Because they are alive, they can also be killed. Fortunately, even though they have to do the same things our cells do to stay alive, they do those things differently. That means that chemicals that disrupt their life processes do not always disrupt ours.
Chemicals that kill bacteria and not us are antibiotics. Bacteria that live in or on us can be killed if we ingest or apply topical antibiotics that are harmless to us. Of course, bacteria can become resistant to antibiotics, but there is always the hope that new antibiotics can be developed that will be effective against bacteria that have become resistant to old ones.
Viruses cannot live without us or some other host organism. They exist on their own, but they cannot grow or reproduce. To do that, they have to get into cells. There are millions of types of viruses, and every cellular organism on earth has its own set of viruses. All animals have viruses, all plants have viruses, and even bacteria have viruses.
To be successful, a virus has to recognize the cell it infects. It does that by binding very specifically to proteins, called receptors. Different receptors exist on the surface of every type of cell. The virus that causes COVID-19 is a corona virus, one of very many families of different types of virus. It is closely related to a virus that causes common colds.
But the COVID-19 virus is different. It recognizes a receptor called ACE-2 on the surface of cells in the lining of our lungs. When it binds to that receptor, it induces the cell to take it up. Once it gets inside, the virus becomes alive. It starts reproducing itself, not just by dividing in two, but by making hundreds or thousand of copies of itself, all using the cellular machinery that keeps our cells alive. Anything that keeps the virus from replicating inside of a cell will also kill that cell. That is why there are no antibiotics against viruses, because chemicals that prevent them from reproducing would also kill us.
The infected cell produces viruses, and those viruses can then leave the cell they originally infected and go find another cell to infect. That cell could be in the person they first infected, so the virus can spread rapidly within a body. The virus can also be released from the infected person by coughing or sneezing and be breathed in by a different person, who will then have his or her lung cells infected. That is why COVID-19 is so contagious.
Some viruses can reproduce within cells without harming those cells. Others, like the cold virus, only make the cells somewhat sick. A few viruses can cause a very bad reaction in the cells they infect, and that reaction can be made worse by the body’s attempt to mount an immune response against the virus. (More about the immune system in a subsequent report.) COVID-19 can cause a very bad reaction in some people, particularly the elderly or those with compromised immune systems. Some people infected by COVID-19 can have only a mild reaction, or no obvious reaction at all. Those latter people are called asymptomatic. The only way to combat the virus is to prevent its spread, as by social distancing, or to produce a vaccine against it. The vaccine requires the help of the immune system, so we will talk about vaccines in a later report.
The Body’s Security Force: The Immune System
Dr. Michael Manson, April 25th, 2020.
The human body is host to about ten times as many foreign cells as our own cells. But these visitors that call us home added together have only 1% of the weight of our own cells. The simple math says that those cells are, on average, a thousand times smaller than ours.
The majority of those cells are bacteria. If you magically took away all of our cells, all the surfaces, external and internal, of our bodies would still be visible in the distribution of the bacteria that live in and on us. You would see our skin, our lungs, our bladders, our ears, noses and eyes, our mouths and our entire digestive system from entrance to exit. Different bacteria inhabit only very particular parts of the body. Most of the time, these settlers live in peace with us, despite occasional uprisings that make us sick or itchy for a bit.
Why are they so peaceful? Well, it turns out that we have a very good security force to keep them in place. It is the most brilliantly conceived, intricate defense system in the world: our immune system. Life would be impossible without it. You only have to think about how quickly after death a body starts stinking and decaying to appreciate its importance. It helps to keep the different bacteria in their place and quickly eliminates them when they wander. The danger of their wandering becomes clear when you think of what happens when there is a tear in the intestinal wall. Gut bacteria get into the body cavity with disastrous consequences. The septic shock that kills in such cases is, in fact, an overreaction of the immune system to the sudden rush of invaders leaving the place where they belong and remain harmless into a space in which they represent extreme danger.
The immune system is a complicated collection of different cells, as complex as the nervous system. Immune cells are constantly on patrol. Some move through the blood. Others move through a second circulatory network, the lymphatic system. (You think about the lymph mainly when you have an infection and your lymph nodes swell and hurt.)
We generally think of our skeleton as a frame that determines the shape of our body and connects to muscles to allow movement. A less-appreciated function of the skeleton is to contain the bone marrow that produces all of the cells in our blood and lymph. The doughnut-shaped red blood cells (RBCs) that contain the hemoglobin that carries oxygen throughout our bodies are made there. RBCs just float along with the blood plasma as it is pumped out from the heart in arteries and flows back through veins, stopping off to unload carbon dioxide and upload oxygen in the lungs. Healthy RBCs do not change shape.
White blood cells (WBCs) also are made in the bone marrow. WBCs come in all shapes and sizes. A high percentage of them are integral parts of the immune system. They also flow with the blood and circulate with the lymphatic fluid, but many can also move by themselves along surfaces and through tissues. They are fantastic shape shifters, looking and acting like amoebae. Like amoebae, they are looking for bacteria and viruses to eat, not because they need them for nourishment, as the amoeba does, but as part of their duty as a security force. Their job is to ingest and destroy dangerous alien interlopers.
Various kinds of these WBCs have fancy names like platelets, macrophages, neutrophils, eosinophils and lymphocytes. Each of them has a very specific function, and their collective activity is what provides immunity. If any one of them is lost, bad things happen. AIDS results from the loss of one type of T lymphocyte. When tight control of their production is lost, other problems arise. Leukemia is a blood cancer that overproduces immature WBCs.
The immune system is conventionally divided into two parts. The innate immune system consists of all of those germ-eating, germ-destroying cells. It is the rapid response team. There is also the acquired immune system, which provides the long term protection against specific invaders that we call immunity. The acquired immune system makes vaccines possible. Its elegance almost, but not quite, surpasses human understanding. As we will discuss in a future report, innate and acquired immunity work together in an amazing ways.
A Very Special Protein: The Antibody
Dr. Michael Manson, April 27th, 2020.
The word antibody is working its way into the popular vocabulary as the COVID-19 crisis continues. Antibodies will somehow, and sooner or later, come to our rescue. What, then, are these potential saviors of our health and welfare?
Antibodies are nothing magical. They are proteins, plain and simple. But they are the most versatile proteins in our arsenal. The human genome contains something like 25,000 different genes. Most genes encode one protein, or at most two or three. That means you might think that we can make no more than 100,000 proteins. But, strangely enough, we have the potential to make millions of different antibodies. How can that be?
First, we have to discuss what a protein is. A protein is made up of one or more polypeptides. That somewhat forbidding word simply means a linear string of amino acids. Some polypeptides are only a few dozen amino acids long, others contain multiple thousands of amino acids. There are 20 different amino acids, each with unique chemical properties.
The number of possible combinations of amino acids in a polypeptide is staggering. A tiny peptide only ten amino acids long has 20 times 20 times 20, etc. possibilities, which equals slightly over ten trillion different sequences, a number equal to the number of cells in our body and 100 times greater than the 100 billion stars in our Milky Way galaxy. So, 25,000 genes encoding proteins that are hundreds or thousands of amino acids long produce a miniscule fraction of possible polypeptides.
That is all right, though. Most of the possible polypeptides would be utterly useless. To become useful, a polypeptide chain has to fold up into a very specific three-dimensional shape. The way it folds is determined by the interactions among its amino acids, and the vast majority of amino acids sequences will not have the right set of interactions to fold into a stable and functional structure. Even the change of one amino acid by a mutation can disrupt the interactions so much that the protein misfolds and loses its structure and its function.
Some proteins contain only one polypeptide chain. Other proteins form when multiple polypeptides come together to form the final structure. It can be multiple copies of the same polypeptide, mixtures of two or more different polypeptides, or a combination of the two. One common combination is six copies each of two different proteins
An antibody is a protein called an immunoglobulin, literally meaning a globule that confers immunity. The simplest sort of immunoglobulin contains four polypeptide chains, two identical short ones and two identical long ones. Think of it as looking like the letter Y. The first part of each long chain interacts with one of the short chains, forming the two arms of the Y. The remainder of the long chains interact with each other to form the stem of the Y. Every immunoglobulin has this same structure. What is so special about it?
The tips of the two arms, which you can think of as being in the position of hands, act like hands; they grab things. The two hands of any given immunoglobulin molecule grab only one thing. What they grab is determined by the precise way the polypeptide chains that form the hands fold. Any single antibody-producing B cell, a lymphocyte, makes all of its immunoglobulins with the same two hands, which recognize and grab (or bind, to use the term favored by biochemists) the same thing. But, different B cells produce immunoglobulins with different hands. The rest of the Y, the arms and the stem, are identical, but there are millions of different hands made by the millions of different B cells. Because millions of B cells make immunoglobulins with millions of different hands, almost any conceivable molecule that will fit into the ‘hand’ will be recognized by the immunoglobulin produced by one or more of the B cells.
The amazing way that enormous diversity of hands is made by only a handful of genes is the subject of the next report. A related and equally fascinating story is the way that cells that make the ‘right’ immunoglobulins are recruited to produce an acquired immune response.
Creating Diversity from Simplicity – The Hypervariable “Hands” of Antibodies
Dr. Michael Manson, 2020
I used the metaphor “hands” to describe the tips of the “arms” of the Y-shaped immunoglobulin molecules that are commonly called antibodies. The genes that encode these molecules look like ordinary genes, but they are expressed only in a very few cell types, including the B cells of the immune system, and they are expressed in a peculiar way.
Most genes remain exactly the way they were from the time of fertilization of the egg throughout life. Every time those genes are expressed, the same protein or, in some cases, a few different but closely related proteins, are made. But the genes that encode antibodies are different. Each antibody protein consists of two identical short chains and two identical long chains that come together to form the Y-shaped immunoglobulin. At the very beginning of each of those chains is a small region that makes up half of a hand. It is only in those small regions that the process I am about to describe occurs.
In the chromosome of every cell in the body, the gene that encodes the kappa short chain has, at the beginning of its protein-coding sequence, 40 repeats of a sequence called V (variable) and 5 repeats of a sequence called J (joining). The gene that encodes the lambda short chain has 30 V sequences and 3 J sequences. However, these are not perfect repeats. Each V and each J is the same size, but it encodes a different short string of amino acids. The same is true of the repeats in the J region. In the gene that encodes the long chain, the beginning of the gene has 44 V sequences, 27 D (diversity) sequences, and 6 J sequences. In most cell types, these genes are silent, meaning they are not expressed and make no protein.
Most cells do not express these genes, but B cells do. But, before they are expressed, something quite remarkable happens. In the genes encoding the short chain, 1 of the 40 V sequences and 1 of the 6 J sequences are selected and joined together. The choice is random and occurs independently in every individual B cell. The same thing happens in the gene encoding the long chain; 1 V sequence, one D sequence and 1 J sequence are chosen and joined together, again randomly and independently in each individual B cell.
Think of the possibilities. There are 40 x 5 = 200 combinations for the kappa short chain, 30 x 3 = 90 combinations for the lambda short chain, each different. There are 44 x 27 x 6 = 7,128 possible combinations for the long chain. This process occurs separately and without any communication. Thus, when the two chains join, there are 200 x 90 x 7,128 = 128 million possibilities. The number is actually even higher because the joining is quite imprecise, which means that there are even more possibilities. All the rest of the short chain and all the rest of the long chain is the same in every B cell. Because only one short chain and one long chain is made in any given cell, each arm of the Y will have the same hand that grabs the same thing. In the population of B cells, there are many millions of different hands.
The process of choosing V, D and J sequences is random. But the sequences are enough alike that they all can, when joined, fold into some kind of a structure that acts like a hand. However, what that hand can grab – or bind, to use the biochemistry term – is different for each combination. Different B cells will make antibodies that recognize different things. The range of things they can recognize is vast. Some recognize nothing, some recognize proteins, some recognize carbohydrates, some recognize nucleic acids (RNA and DNA). And, they recognize different proteins, different carbohydrates, different nucleic acids. They also bind what they recognize with great specificity and high affinity, which means very tightly.
But, the process of making a B cell that produces an effective antibody is far from over. There are many millions of immature B cells, only a few of which will make any particular antibody. In the immature B cells, the immunoglobulins are not being produced in large amounts, and they are not secreted. They are embedded in the cell membrane with the arms of the Y extending out from the cell surface into the surroundings. The process of selecting which B cells will mature and produce antibodies will be the topic of the next report.
Picking and Choosing: The Maturation of a B Cell
Dr. Michael Manson, May 3rd, 2020.
It is convenient, but not correct, to think that B lymphocytes, or B cells, are called that because they begin to develop in the bone marrow. The processes that I discussed in the last report take place in the bone marrow, and the precursor B cells start to differentiate there.
The millions of different Y-shaped immunoglobulins are originally expressed as membrane proteins, or B cell receptors. The arms of the Y extend out of the cell so that the hands are positioned to bind things floating there. At this stage, these cells are waiting to receive the signal to begin development. As you have probably guessed, the signal for any specific B cell is the binding of the molecule that the hands on the receptor recognize.
Something important has to happen first. In infants, a B cell is not activated when its receptor binds what its hands recognize. Instead, during this period, a B cell whose receptor binds something is most likely recognizing a molecule that should be present. It is either something that is secreted by, or is present on, the surface of our own cells. It is self.
A molecule that binds to a B cell receptor is called an antigen, because it generates an antibody response. However, it would be useless, or even dangerous, to raise an immune response against antigens that should be present. In infants, B cells that bind self-antigens undergo programmed cell death, or apoptosis. The population of B cells is purged of cells with receptors that recognize self. As a result, our immune system does not attack us. If this process fails, a very dangerous situation called autoimmunity can arise. Our immune system, once it becomes activated, will attack us, with often disastrous consequences.
The process of destroying B cells that recognize self is called clonal deletion. It also has a downside. At this stage, the body cannot raise an immune response against a dangerous invader. This is why newborns are so susceptible to infection and why infant mortality is so high in societies without good hygiene, and in our own society until quite recently.
After this important but very hazardous time, usually about a year in humans, the B cells respond very differently. Now, any molecule they have not seen before is likely to have been produced either by one of our normal set of microorganisms, our microbiota, that has gotten to the wrong place, or by an invader, which could be a very dangerous pathogen.
What happens now is the opposite of what happened during the time of clonal deletion. The surviving B cells migrate out of the bone marrow to the spleen and transform into what are called naive B cells. They are on the prowl for foreign antigens. When a particular naive B cell whose randomly generated hand binds a foreign antigen it becomes activated, whether the antigen is on a virus or a bacterium or a molecule just floating in the blood, . This is a complex process that involves interaction with T helper cells. It is the T helper cells that are attacked and killed by the HIV virus, with the result that people infected with HIV develop the acquired immunodeficiency syndrome we call AIDS.
A naive B cell only interacts with a T helper cell after it has recognized the antigen its receptors bind. Interaction with the T helper cell does several things. First, it induces the B cell to divide and make many cells that bind the same antigen. Second, it induces maturation of the B cell, which now starts producing antibodies. These have the same Y-shaped structure as receptors, and they are encoded by the same rearranged genes that produced the receptor. However, they do not remain attached to the B cell; they are secreted out into the blood.
These antibodies bind the antigen that they recognize. Each has two hands, and it tightly binds and coats any virus or bacterium that has that antigen on its surface. An object coated with antibody is tagged for engulfment and destruction by cells of the innate immune system.
What produces the long-term immunity that protects us from subsequent infection? Most mature B cells produce antibodies and die. A few become long-lived memory B cells. These remain in the body for many years, acting as sentinels to provide a much quicker immune response to previously encountered invaders. Memory B cells make vaccines possible
Destroy the Infected – Cellular Immunity Mediated by Killer T Cells
Dr. Michael Manson, May 4th, 2020.
Antibodies produced by B cells are only part of the guard against reinfection. A parallel system is afforded by killer T cells. Killer T cells also generate myriads of different surface receptors, one type per cell. Killer T cells undergo clonal deletion of those that recognize self-antigens. They remain immature until their receptor binds the antigen it recognizes. They are activated in the thymus by helper T cells. Activated T cells also start to multiply.
There is one important difference from B cells. Mature killer T cells do not secrete antibodies. They patrol the body looking for our own cells that have the antigen they recognize on their surface. When they find a cell with a foreign antigen, they bind to it and induce the cell to undergo programmed death, the cellular suicide called apoptosis.
Their only option is to destroy, not to cure. This property of killer T cells makes it clear why all of them that recognize self-antigens have to be removed from the population of immature killer T cells. Otherwise, they would cause our own cells to commit suicide. Failure to delete killer T cells that recognize self is a major contributor to autoimmune disease.
The objective of this seemingly harsh enforcement is two fold: control of infection and control of cancer. Most viruses that infect us, including corona viruses, do not kill the cell they infect. Most viruses get released from our cells by budding, unlike viruses that infect bacteria, which essentially explode the cell to be released. Once the virus has replicated its genome, either DNA or, as in corona viruses, RNA, viral genes are expressed to produce proteins, which are made by the host synthetic machinery. Some of these bind to the RNA to stabilize it for packaging into the virus particle. Other proteins that will be present on the outer coat of the virus are exported to the membrane of the infected cell.
For a brief time before the viral RNA and associated proteins arrive, these viral coat proteins are exposed on the surface of the infected cell. They are recognized as foreign by the killer T cells that have receptors for them. The appropriate killer T cells bind and inform the unlucky infected cells they should kill themselves rather than produce viruses. If the infected cell is not killed, a mature virus buds off the cell and is released into the external milieu. The COVID-19 virus infects cells in the lungs, and thus the infection spreads through the lungs.
Like the antibody response of B cells, it takes some time after infection before mature killer T cells can be produced. It takes one to two weeks to produce a full acquired immune response. Until that happens, a person harboring the virus is infectious, whether or not they show disease symptoms. The COVID-19 viruses produced in the lungs can be expelled into the air with a sneeze or cough and be inhaled by another person. This scenario of infection, virus replication and spread, and virus release explains the importance of social distancing.
The strength of the immune response to an invading pathogen varies based on the pathogen, the infectious load, and the health of the infected person. The immune system becomes less potent in old age, and thus the elderly, AIDS patients, and people taking immuno-suppressant drugs after an organ transplant are most vulnerable to any infection, including COVID-19. That is why so many COVID-19 deaths occur in nursing homes.
Killer T cells also have an anti-cancer function. When body cells become cancerous, they revert to an embryonic state and start growing and dividing. They also start making proteins normally present only in the embryo. Many of these proteins are exported to the cell surface. Because they were not present when the B and T cell population was being pruned of cells that recognize self in the infant, they are seen as “foreign.” Killer T cells perceive these cells as infected because they express “foreign” proteins, and they bind to them and initiate apoptosis. The cancer is killed in the cradle, as it were. This is why people with suppressed immune systems are more likely to develop cancers rarely seen in immuno-competent people.
Antibody production by B cells and killer T cells provides the acquired immunity that prevents reinfection. The next report explains how this immunity makes vaccines possible.
Vaccines: The Ultimate in Preventive Medicine
Dr. Michael Manson, May 5th, 2020.
Vaccines are all the rage now because of the COVID-19 crisis. Drs. Fauci, Birx and other public health officials tell us the corona virus pandemic will only be truly over when we have a vaccine. What does that mean, and why are they saying that it will take 12 to 18 months to produce one? Why can it not be done much faster? We already have flu vaccines.
One way to get immunized is to contract the disease. Your innate immune system, with its macrophages, neutrophils and natural killer cells has the first crack. These innate responses are generally more effective against bacteria, which can be recognized without prior experience because all bacteria share certain structural features that cells of the innate immune system inherently recognize. These cells bind the bacteria, engulf them, and destroy them. Viruses are more structurally diverse and usually not recognized by the innate system.
The innate system is ineffective against viruses because of their diversity and because they bind receptors on our own cells, which causes them to be engulfed and internalized. The COVID-19 virus binds the ACE-2 receptor of cells in the lung epithelium, the interior surface layer of the lung through which oxygen is absorbed and carbon dioxide is released. Once inside lung cells, the virus cannot be detected by cells of the innate immune system. Virus replication and budding occurs, and budded virus particles quickly infect other lung cells.
Not all is bleak. Some virus particles will have been bound by immature B cells and immature T cells, which will recognize them as foreign and dangerous. This process initiates the maturation of the specific B and T cells that have receptors for proteins present on the coat of the virus. Within a week or two, B cells secrete antibodies that cover any free-floating virus particle and tag it for destruction by phagocytes of the innate system. Cells infected with virus export viral coat proteins to their cell membranes and are recognized by killer T cells. These cells are sentenced for death by apoptosis before they can produce virus.
After the activated B and T cells have done their job and the infection is cleared, most of them die and are destroyed. However, a few memory B cells and memory T cells linger in the body for a few years to many years. This means someone who has recovered from infection is usually immune to reinfection. Upon reinfection by the same virus, the memory T and B cells recognize the viral antigens and get activated. Antibody producing B cells and killer T cells specific for the returning invader are quickly generated. Reactivation of memory cells is much faster than development of the initial acquired immunity from naive B and T cells. The infection can be cut off before it develops into a full-blown incidence of the disease.
It is possible to initiate this same process more gently than suffering through a bout of the disease. If the body is exposed to something relatively harmless that shares some of the same antigens as the pathogenic virus, the acquired immune system responds to it and makes memory B cells and T cells that recognize those antigens. If they are good enough mimics of the antigens on the pathogenic virus they will provide acquired immunity against the pathogenic virus. This process, called vaccination, was discovered by Edward Jenner in 1796. He found that milkmaids seldom got smallpox, but instead got a much milder disease called cowpox. The cowpox virus was similar enough to the smallpox virus that immunity against cowpox provided immunity against smallpox. His recommendation was that people should be artificially infected with cowpox to protect against smallpox. Remarkably, it worked.
We do not know of any virus similar enough to COVID-19 that it can be used in this way. Some cold viruses are corona viruses, but they are too dissimilar to provide strong protection. Another option is to use a virus that has been inactivated in some way. This can be dangerous if the inactivation was not completely successful. Another way is to clone a gene that encodes a protein unique to COVID-19 into a corona virus that is relatively harmless. The gene that encodes the spike protein of COVID-19, which binds the ACE-2 receptor on lung cells, has been proposed as a candidate. This tricky work will be discussed in the next report.
The Painful Wait: Why Does Vaccine Development Take So Long?
Dr. Michael Manson, May 6th, 2020.
In the last report, I mentioned Edward Jenner and the smallpox vaccine. There had been earlier attempts at variolation – prior exposure to smallpox to prevent subsequent infection – but Jenner’s was the first controlled study. Jenner took pus from a skin lesion of a young milkmaid named Sarah Nelms, who was mildly ill from cowpox, and scratched it into the skin of 8-year old James Phipps, the son of Jenner’s gardener. No parental consent forms are on file. The boy became ill with cowpox but recovered after ten days. Jenner then inoculated James with smallpox several times over a period of months, and James did not develop the deadly disease. Voilá! A vaccine had been born. That was in 1796. Why so slow now?
Jenner was fortunate in several ways. First, the cowpox virus is similar enough to the smallpox virus that they share many of the same antigens. Second, cowpox causes an illness far milder than smallpox. Third, acquired immunity to cowpox protects against smallpox. Fourth, cowpox virus was readily available from milkmaids, who must have been fairly numerous in England in those days. Fifth, there was no CDC, FDA or other organization to monitor testing on human subjects. Jenner’s status as a country gentleman also helped.
None of these conditions apply to development of a COVID-19 vaccine. There is no relatively harmless virus similar enough to Covid-19 to produce cross-immunity. SARS-1 (COVID-19 is SARS-2) is similar, but it is also lethal, although less infectious. Exposure to the corona virus that causes common colds does not provide much immunity to COVID-19. Exposure of COVID-19 virus to intense UV irradiation or high temperature should render it incapable of causing infection, and the proteins of the virus might remain intact. One might think dead virus could be used as a vaccine. However, debilitated viruses cannot replicate in the body, so a great number would have to be injected to evoke a good immune response. The consequences of that are uncertain. Also, in a population of supposedly killed viruses, some might survive and be capable of causing a full-blown COVID-19 infection.
One option is to genetically engineer a relatively harmless virus to produce an antigen from COVID-19. A good candidate antigen is the COVID-19 spike protein that binds the ACE-2 receptor on lung cells. The gene encoding the spike protein could be cloned to replace the gene encoding the spike protein of a cold-causing corona virus. This engineered virus could infect our cells, replicate, bud out and infect other cells. Vaccination with this virus would generate mild or asymptomatic infections but evoke strong acquired immunity. Among the memory B and killer T cells produced, some will recognize the COVID-19 spike protein. Thus, the acquired immune system of a person vaccinated with this engineered virus should recognize the spike protein of the actual COVID-19 virus. Upon subsequent infection with COVID-19, they would rapidly produce antibodies and killer T cells to protect against it.
That may sound simple, but not so fast. First, the virus has to be genetically engineered. Second, it has to be shown to reproduce in human lung cells, probably first in tissue culture. Next, it has to be tested for safety in animals. If they do not get seriously ill, it must be tested for safety in small, well-controlled trials in volunteer human subjects. If it proves safe in those trials, it must be tested in humans to see if it produces an immune response that recognizes the COVID-19 spike protein. Then, it must be demonstrated that this immune response actually protects against infection by COVID-19. If it does, then a way must be found to produce the engineered virus in sufficient amounts to be used as a vaccine for large human populations. Meanwhile, the virus has to pass a number of time-consuming but essential tests for it to be certified as safe by the CDA, FDA and other public health agencies.
Laboratories worldwide are pursuing this and other alternatives for producing vaccines. Most of the required tests must be done in series rather than in parallel. Thus, 12 to 18 months is a reasonable estimate for how long it will take. Tragically, many people will get ill and die over that time. In the next report, I will discuss some faster potential alternatives.
Temporary Measures: The Search for Therapies Short of a Vaccine
Dr. Michael Manson, May 6th, 2020.
An effective vaccine that provides long-term protection against COVID-19 is the best option for diminishing the ravages of the disease for the future. But its development and approval will take time. What can be done in the interim?
Two alternatives also involve the immune system. The first is the possibility that those infected with COVID-19 can be given a transfusion of serum from a person who has been infected with COVID-19, recovered, and has antibodies that neutralize the virus. When all of the red and white blood cells have been removed from the blood, the remaining serum still has soluble antibodies that target the virus. When this antibody-containing serum mixes with the blood of the patient receiving the transfusion, those antibodies will bind to the virus before it can enter lung cells and target it for destruction by the phagocytic cells of the innate immune system. Using serum avoids most of the problems with blood-type incompatibility.
There are clear limitations to this therapy. One is finding blood donors. People recently recovered from a serious illness seem unlikely to want to give blood, and giving blood may prove health threatening to them. Blood donors will presumably come from those who had mild or asymptomatic infections. However, because of the milder infection they also may not have as many antibodies as those who were more severely ill. Because the antibodies do not reproduce, multiple transfusions may be required. Also, this approach does not provide the killer T cells that will attack and destroy COVID-19 infected cells in the lungs.
Another possibility is using monoclonal antibodies. Monoclonal antibodies are produced from tissue-cultured mouse cells programmed to make one antibody that recognizes one particular epitope of the virus. An epitope is the name given to one specific element of an antigen that is recognized by only one specific antibody. One difficulty with this approach is to determine which epitope is most effective in binding to and neutralizing the virus. A logical candidate would a prominent exposed feature, like the spike protein that recognizes the ACE-2 receptor on lung cells. Binding of the monoclonal antibody, which must be injected into the patient in relatively large amounts, can bind to the spike protein and block the virus from binding to the ACE-2 receptor, and thus prevent it from entering the lung cells. This approach is labor-intensive and expensive, and it is probably most effective in preventing the initial infection rather than in dealing with an infection that has already established itself. An advantage it has is that it does not require humans donors.
I have described why antibiotics are more effective against bacteria than viruses. Bacteria are killed by drugs that have little effect on our cells. Because viruses replicate inside our cells, things that prevent their replication tend to be harmful to us. There are exceptions. One of these relies on the fact that corona viruses have RNA as their genetic material. To reproduce, they must use their RNA genomes as templates to make more of their RNA.
In the nuclei of our cells, all types of RNA are transcribed from the DNA in our genes. The enzymes that do this are DNA-dependent RNA polymerases. We cannot make RNA from RNA. For the virus to make RNA from RNA, even inside our cells, one of its genes has to encode an RNA-dependent RNA polymerase. This RNA-dependent RNA polymerase is different enough from our DNA-dependent RNA polymerases that drugs that block its function may not have any deleterious effect on our DNA-dependent RNA polymerases.
One drug receiving attention lately for inhibiting the viral RNA-dependent RNA polymerase is remdesivir. It proved useless against Ebola virus, but early clinical trials indicated that it shortened the time to recovery of COVID-19 patients from 15 to 11 days, although it had no effect on mortality. That might not seem like much, but it is a beginning. Thousands of already-existing drugs are being tested, and some of them may be far more effective than remdesivir. Another possibility is to use remdesivir together with other drugs to produce an anti-COVID-19 cocktail. That approach worked with HIV. So, there is hope.
Does the SARS-2 Virus Want To Kill Us?
Dr. Michael Manson, May 9th, 2020.
It does not. The virus that causes COVID-19 has the same goal as any other organism: to reproduce. Reproduction equals success in the biological world, and to die without issue is to impose extinction on your genetic lineage. Many humans do this voluntarily, but we seem in little danger of dying out as a species because of a failure to reproduce.
For a parasite, a host is essential. If a parasite has only one host, the extinction of the host is the extinction of the parasite. Thus, it is in the interest of a parasite not to be too deadly.
This reality explains why so many of the most ravaging diseases are zoonotic, meaning that they jump from another species to us. Sometimes that species is closely related, like the chimpanzees from which we acquired HIV. Some variant of that virus that had adapted to a relatively peaceful coexistence with chimpanzees ran wild when it transferred into humans. The bubonic plague bacillus transferred from gerbils in central Asia to rats to humans.
The best evidence is that SARS-2, like SARS-1, transferred from bats to humans, perhaps through pangolins. Ebola virus also seems to have transferred from bats to humans. Flu has come from pigs (swine-flu) and ducks (bird-flu). These diseases typically originate in places where humans and animals live in close contact, like China or parts of Africa.
I am not sure that we know the symptoms of a SARS-2 infection in bats; if elderly bats are dying, how would we know? One of the greatest challenges for a parasite is transmission. Any given individual host organism is going to die of something, sooner or later, so it is important to find a new host. The ways that different parasites do this is long and amazing. Some, like malaria and yellow fever, use mosquitoes. The trypanosome that causes sleeping sickness uses tsetse flies. The plague used rats and fleas, typhus uses rats and lice. The cholera bacterium uses contaminated drinking water as a vehicle for its dissemination.
Many viruses employ a more direct approach. Like flu and SARS, they make us cough and sneeze. Viruses are tiny, they float in the air, and they survive for a relatively long time outside a host. This is why masks are effective against spread of COVID-19. Mosquito nets work against malaria and yellow fever, but a virus can go right through a mosquito net.
A SARS-2 infection progresses like this. After we inhale the virus, it first comes in contact with the cells lining our nasal passages and throat. It infects these cells and starts replicating and budding. As long as it remains there, it is relatively benign. However, our innate immune system responds by making us sneeze and cough to rid ourselves of the virus, thus propelling it back into the environment, where it can spread and infect others.
Serious illness results when the virus moves into the airways of our lungs. It invades cells there that have the ACE-2 receptor, and again it goes through its replicative cycle. Now, the consequences are more severe. The innate immune system responds more strongly and produces chemicals known as cytokines that attract more of phagocytic cells of the innate immune system, like neutrophils and macrophages. The result is inflammation, which can result in difficult breathing and other systemic responses, like headache and fatigue.
The most-serious manifestation of the disease is when the virus attacks the lung cells that carry out gas exchange, taking in oxygen and expelling carbon dioxide. Patients in which the infection reaches this stage are the ones who require ventilators and are at risk of dying when the gas-exchange function of their lungs is seriously compromised. The disease is most likely to progress to this stage in those with compromised immune systems, like the elderly.
There is a scary reality here. The virus does not “want” to kill anyone. By killing off the elderly and others with compromised health, it is really not hurting its chances of reproducing. These are the least mobile and least interactive segments of the population. This cruel fact lies behind the calls to open the economy and take some risks. Relatively few children or healthy adults will die. The question now becomes a moral, ethical and political one. What is a human life worth, and what risks with lives will we accept to return to “normal?”
What in the World Is an mRNA Vaccine?
Dr. Michael Manson, December 14th, 2020.
Immune responses are typically raised against proteins, macromolecules that assume particular shapes that can be recognized by the receptors that trigger an immune response. Nucleic acids, DNA and RNA, are primarily information coders, specifying the sequence of amino acids in polypeptides (long strings of amino acids) that, given the correct sequence, can fold up into functional proteins. Thus, vaccines have typically been attenuated or inactivated infectious agents or purified proteins or derived from them. Why then, if an RNA is unlikely to assume a shape that can be recognized by the cells of the immune system, can it be used as a vaccine? The answer lies in the ability of an RNA to encode a specific protein.
Proteins are made in the cytosol – the extranuclear compartment of a cell. Ribosomes convert a sequence of RNA into a sequence of amino acids that forms a protein. RNA molecules are made as copies of DNA sequences of genes in the nucleus in a process called transcription. RNA molecules that are exported from the nucleus into the cytosol to be translated by ribosomes into polypeptides are called messenger RNA (mRNA).
Ribosomes have no way of “knowing” the origin of RNA molecules that appear in the cytosol. When the SARS 2 corona virus that causes COVID-19 binds to, and is taken up by, a cell, it releases its genetic material, an RNA rather than DNA, into the cell cytosol. This viral RNA can act as an mRNA, being translated by ribosomes into the proteins that are required to make a new virus. Unlike an mRNA, the viral RNA can also be replicated into many copies by a protein it encodes, an enzyme called RNA-dependent RNA polymerase. Virus can then bud off from the cell when new copies of viral RNA are coated with proteins that form the virus “coat.” Some of these proteins are first incorporated into the cell membrane, so that the virus particle actually forms at the cell membrane before it is released from the cell.
Therein lies the “secret” of an mRNA vaccine. Scientists can construct an RNA molecule that encodes one of those proteins that coat the virus. In the case of SARS 2, that is the spike protein that sticks out from the virus particle and recognizes the ACE2 receptor on the surface of the epithelial cells in the nasal passages and lungs. If a cell takes up this “mRNA,” it will make the spike protein and export it to the cell surface. There, it can be recognized by cells of the immune system, which will then raise an immune response against that protein.\
The trick is how to get this artificial mRNA into the cells. It could be introduced by a “harmless” helper virus that will bind to and be taken up by cells. However, this helper virus will only bind to cells that have the receptor they recognize, which is unlikely to be a cell of the immune system. There may also be side effects of the “harmless” helper virus.
The artificial mRNA that encodes the spike protein can be packaged with lipid (basically fatty) nanoparticles. Because cell membranes contain lipids, these nanoparticles will fuse with any cell and release the RNA they carry into the cytosol, where it can be translated by ribosomes to make the spike protein, which will be exported to, and exposed on, the cell surface. This spike protein can be recognized by cells of the immune system that will start producing B cells that make antibodies against the spike protein and CD8+ killer T cells that will attack and kill cells expressing the spike protein. Thus, new virus can be coated with antibodies and tagged for destruction by the innate immune system, and cells that have been infected by the virus and produce spike protein can be destroyed by the killer T cells.
Of course, it is not simple to produce such an mRNA vaccine. The mRNA must be stable enough to survive and contain the right structure to be read by ribosomes. Researchers have introduced mutations into the mRNA that make the spike protein they encode more stable. The lipid nanoparticles must be designed to be maximally effective in delivering the mRNA. Also, it is difficult to predict side effects or effectiveness in eliciting an immune response. However, the original trials of the Pfizer/BioNtech and Moderna mRNA-based vaccines have been very promising, with 95% effectiveness and few, if any, deleterious side effects.