Friday, June 11, 2021

Biology of a Virus


 

It has been over a year since the world population has been dealing with the COVID-19 pandemic.  As a result of intense scientific investigation and study, effective vaccines have been developed and are being distributed worldwide.  

Given this reality, it would be of value to more fully understand what viruses are and how they function.

The following document may be of some help in this regard.

Sunday, February 7, 2021

The Basis of Antiviral Immunity

     Models of COVID-19 and the Spike Protein

The human immune system is a highly sophisticated and powerful system that the body utilizes on an ongoing basis in order to ensure the continued survival of the individual in a hostile environment. It is comprised of a heterogeneous population of cells, factors and organs that function together to maintain the general health of the individual. The immune system is, in fact, a product of millions of years of evolution. Rudimentary immune systems and processes can be found in many more primitive forms of life including single-celled organisms.

Immunologists have delineated two arms of the human immune system – innate and adaptive. The innate branch of the immune system possesses pattern recognition mechanisms designed to recognize any non-self antigen – an antigen is any substance, usually protein, that can elicit an immune response. When an antigen is recognized as foreign, the innate immune system is designed to mobilize quickly to neutralize the foreign organism that carries this antigen.

The other part of the immune system is referred to as the adaptive immune system. As the name infers, the adaptive immune system can adapt to new foreign invasive bacteria and viruses that find their way into the host. It is precisely this arm of the human immune system that responds to SARS-COV-2 (COVID-19). It is this system that neutralizes virally-infected cells and can induce the production of so-called, “memory cells.” It is this capability that is exploited and enhanced by vaccination strategies.

Both T-cells and B cells represent the primary cellular arsenal for the adaptive immune system essential for the eradication of invading viruses. The progenitors of the cellular components of the human immune system originate in the bone marrow. The COVID-19 pandemic has revealed the wide variability of the immune response to the COVID-19 virus ranging from an asymptomatic response to an acute and sometimes life threatening severe acute respiratory syndrome. This apparent variability has raised questions regarding the mechanisms through which antiviral responses are employed and the nature of the longevity of immunological memory.

As we are well aware, viral infections often lead to disease states within the impacted host. Viruses occupy a special place in regard to life on planet earth. They are essentially inert when outside a living cell showing no properties that are ordinarily assigned to living things. However, once they gain entry into a host cell, they subvert the cellular machinery, effectively diverting ordinary cell processes to a singular goal – the production of viral particles. This usually leads to the death of the host cell facilitating the release of new viral particles that go ahead and infect neighboring cells within the target tissue – in the case of COVID-19 its target tissue is found in the lungs.

The dynamics of the human body’s response to an invasion by a virus is intricate, immediate, and multi-faceted. The current understanding of this process is that it involves the integration of the two arms of the immune system we have previously referred to i.e. the innate and the adaptive. The first and rapid response is that of the innate system. The innate immune responses result in the production of factors that lead to inflammation at the site of entry – this is the so-called “inflammatory response.” This response leads to the activation of the adaptive immune system.

Viral particles are essentially composed of an inner core of either DNA or RNA and an outer shell of protein. It is the proteins on the viral surface that are potential antigens. Viral proteins and particles are subsequently taken up by specialized cells in the immune repertoire that are called dendritic cells (DCs) These cells transport the ingested antigen(s) to the lymphoid organs (lymph nodes and spleen for example), where they are specifically recognized by T and B cells. The T cells constitute the cellular branch of the adaptive system and the B cells represent the humoral branch responsible for the production of specific antibodies against the viral intruder. It is the cellular (T cell) and humoral (B cell) branches of adaptive immunity that collaborate to enable highly specific defenses against diverse viruses.

According to Dr. Linda Bradley from the Tumor and Microenvironment and Cancer Immunology Program at Sanford Burnham Prebys Medical Discovery Institute at La Jolla in a recent report in the prestigious journal, Science, “The magnitudes of the T and B cell responses are determined by such factors as the pathogenicity of the virus, the extent of inflammation, the frequencies of virus-specific T and B cells, and the kinetics of viral replication. CD8+ T cells differentiate into effector cells that limit viral replication through production of cytokines and direct killing of infected cells."

Furthermore, in regard to immune responses to COVID-19, this report goes on to state that, “Viral recognition elicits cytokine-producing effector cells, such as T helper 1 (TH1) cells, which inhibit viral replication and support CD8+ T cell as well as B cell differentiation. Effector T cells can enter the circulation and relocate to tissue sites of infection, where they mediate local antiviral responses. CD4+ T cells also differentiate into T follicular helper (TFH) cells that are crucial for the development of antibody-producing B cells (plasma cells) in lymphoid tissues and support memory B cell development. Antibodies can neutralize viruses by preventing host cell entry or promoting the lysis of infected cells. As a result of the coordinated interplay of innate and adaptive responses, the peak T and B cell responses lead to decreasing viral load and subsiding inflammation, often within 1 week of infection."

It is an understanding of the mode of action of a particular virus and the immune system’s responses to it, as outlined above, that plays a critical role in developing a vaccine that can effectively augment the natural immunity. For a virus to successfully infect a host it must gain entry to the host, successfully evade the immune response, gain entry into the host cell, and successfully commandeer the host cells machinery to make more viral particle and spread the infection. Any vaccine that successfully interdicts any of these mechanisms will necessarily prove efficacious.

 

Wednesday, December 23, 2020

Holiday Message for the Coming Year - 2021

The year 2020 has been in many ways disturbing and unsettling.  What, of course, comes to mind almost immediately is the COVID 19 pandemic that has claimed so many lives and has been so economically devastating to many facets of the national economy, and especially for those who have lost their livelihoods and businesses.  Added to this national burden are the deep fractures that have been exposed in regard to a national sense of unity, shared-mission and purpose.

Along with this overwhelming sense of loss, however, is the untold bravery, courage and unwavering energy displayed by so many who have risked their own lives and safety to come to the aid of all of us for the unselfish commitment to the greater good.  These individuals have come from many diverse positions - as doctors, nurses, emergency response teams, members of the police and fire departments and first responders of all kinds.  To this list, we should include all those responsible for providing food; for delivering the mail; for the taxi and bus drivers, train operators and pilots; for the teachers; for all those who care for the elderly and for all those who provide the essential services that we all too often take for granted.

My wish for the New Year (2021) is that we grow wiser from the events that have befallen us and see the future as a time for healing and learning from our collective missteps.  My hope is that the new year will be a time of new beginnings.  My dream is that we will finally come to recognize that regardless of our national origin, religious affiliation, skin color or sexual orientation we are all members of the same species with the same physical bodies, the same architecture of the brain, the same genetic makeup, the same constellation of feelings, of hopes and of dreams.  Each of us is worthy of the same opportunities to grow and develop as sentient beings on this most remarkable planet that also needs our kindness, care, and attention.  Earth is, after all, our only home.

Best Wishes to All

CRISPR and Other Tools May Radically Change the Treatment of Intractable Genetic Disorders

Genetic diseases such as Sickle Cell Anemia and others have posed a serious and seemingly intractable problem for the science of medicine since any cure would require the repair of the damaged gene(s) involved.  However a number of significant technological breakthroughs in recent years have begun to change that bleak impasse.  In 2003, the complete mapping of the human genome was accomplished.  This technology and the information provided with its use have led to discoveries that have pinpointed the genetic origin of many diseases and continues to do so.  In 2012 a new tool was fashioned – the genomic editor referred to as CRISPR.  This remarkable tool can precisely edit particular sequences within the introns of targeted genes.  The designers of this capability, Jennifer Doudna and Emmanuelle Charpentier were awarded the Nobel Prize in Chemistry in 2020.  These two advances are changing the prospects for the treatment of genetic diseases.  CRISPR and an additional methodology (described below) have demonstrated great promise.

It has recently been reported in the prestigious scientific journal Science that, “Two strategies for directly fixing malfunctioning blood cells have dramatically improved the health of a handful of people with these genetic diseases.  One relies on CRISPR, marking the first inherited disease clearly helped by the powerful tool created just 8 years ago. And both treatments are among a wave of genetic strategies poised to expand who can get durable relief from the blood disorders. The only current cure, a bone marrow transplant, is risky, and matched donors are often scarce.”

The two genetic diseases referred to are so-called, “blood disorders.”  One is Sickle Cell Anemia, and the other is Beta Thalassemia.  Sickle Cell Anemia is a disease in which the red blood cells are mishappen and their ability to carry oxygen to the tissues is seriously compromised.  The origin of this disease is genetic -the alteration of both alleles that carry the blueprint for hemoglobin protein, the protein responsible for binding oxygen.  This disease particularly impacts the African-American population.  In Beta Thalassemia, the patient makes little or no functional hemoglobin.  The result, for the patient, is a dangerous and debilitating anemia since the body’s tissue cannot receive enough oxygen to effectively function.

The treatment devised that has been applied to both Sickle Cell Anemia and Beta Thalassemia involve modifying the genes that carry the information for the structure of hemoglobin in the following way.  The stem cells responsible for producing red blood cells resident in the bone marrow are harvested from the patient, and the BCL11A gene responsible for shutting off the fetal form of hemoglobin is disabled thereby allowing it to be produced.  The research tool utilized for this kind of genetic modification is CRISPR.  The patient then receives chemotherapy to destroy any resident diseased cells and the modified stem cells are then reintroduced into the patient.  If successful, the patient will then produce red blood cells with the completely functional fetal hemoglobin.

In addition, Dr. David Williams from Boston Children’s Hospital has achieved the same result using a novel technique - a specially genetically engineered virus is utilized to introduce a fragment of DNA encoded RNA into the harvested stem cells that effectively silences the BCL11A gene (referred to earlier).

It has been reported that, “Patients treated in both trials have begun to make sufficiently high levels of fetal hemoglobin and no longer have sickle cell crises or, except in one case, a need for transfusions.”  The Boston team described a particular case in of a teenager, “who can now swim without pain, and a young man who once needed transfusions but has gone without them for nearly 2.5 years.”

These are, indeed, exciting developments, but represent only the beginnings of what could be an amazing era in the approach to many other diseases of this kind. 

Wednesday, October 21, 2020

The Role of Microglia in Alzheimer's and Parkinson's Diseases

 

Alzheimer’s and Parkinson’s are diseases that directly impact and impair brain functions. They are degenerative and devastating illnesses that result in severe dementia in the case of Alzheimer’s and a serious degradation of motor control in the case of Parkinson’s disease. There is no cure in either case and no known biomarkers that could predict onset of these conditions. There is a type of cell resident in the brain referred to as microglia that function as amyloid phagocytes – they are cells capable of monitoring the local environment and can ingest and clear amyloid protein.

It seems that in addition to this known role, microglia may play an additional and essential role in maintaining neuronal function and homeostasis. In fact, the build up of amyloid protein in brain tissue may not be the primary cause of dementia that is the result of neuronal dysfunction and cognitive decline in neurodegenerative disease – some centenarians have been found to display good cognitive health and a build up of amyloid proteins in their brain tissue. It seems that accumulated patient data demonstrate that some aging individuals with accumulated amyloid protein show cognitive dysfunction while others do not. It is important from a therapeutic standpoint to understand the nature of this difference.

Several genetic studies indicate that microglia may provide the answer to this difference in health outcomes. According to Soyon Hong from the UK Dimentia Research Institute at University College, London, “Emerging data in developing, adult, and diseased brains collectively suggest that microglia are critical to neuronal homeostasis and health. These observations raise the question of whether, and which, microglia-neuron interactions may be impaired in Alzheimer’s disease (AD) and Parkinson’s disease (PD) to confer neurodegeneration. Insight into this question will enable the development of methods to assess and modulate microglia-neuron interactions in the aging brain and allow for a desperately needed expansion of focus from clearing amyloids alone to monitoring neuronal health in biomarker and target engagement efforts.”

It seems that in addition to their role in clearing pathogens and amyloid protein and responding to the presence of injury and dying neurons present in the environment of the brain, microglia are involved in monitoring changes in neuronal activity and the modulation of such distinct functions as memory and learning. In AD, for example, synaptic loss and dysfunction have been shown to be associated with the disruption of cognitive ability in patients. It is, therefore, of great importance to understand the underlying mechanisms that are responsible for this degenerative process and the role that microglia play in maintaining synaptic integrity.

Thursday, July 2, 2020

Evidence for the Role of Dramatically Increased Numbers of Megakaryocytes Associated with Blood Clots in COVID-19

Disturbing new evidence is emerging from the post-mortems of patients who have died from COVID-19 disease that demonstrates the presence of blood clots (thrombi). These thrombi have been shown in this extensive study to be present in major organs and systems including the lungs, heart, kidney, and brain. 

In addition, a particular cell type referred to as a megakaryocyte has also been found associated with these thrombi. Platelets (thrombocytes) are often associated with thrombi. Platelets, themselves, are generated from so-called progenitor, promegakaryocytes that reside and multiply within the bone marrow. Megakaryocytes are formed from promegakaryocytes and from these megakaryocytes are formed that ultimately break up to produce platelets (see diagram below) that are released into the blood and tissues. The fact that megakaryocytes are evidenced in higher than usual numbers in tissues such as lung, heart, kidney, and brain in patients with COVID-19 disease is a cause for concern.





According to an abstract published by Lancet – a prestigious medical publication – and authored by Amy V. Rapkiewicz, “In seven patients (four female), regardless of anticoagulation status, all autopsies demonstrated platelet-rich thrombi in the pulmonary, hepatic, renal, and cardiac microvasculature. Megakaryocytes were seen in higher than usual numbers in the lungs and heart. Two cases had thrombi in the large pulmonary arteries, where casts conformed to the anatomic location. Thrombi in the IVC were not found, but the deep leg veins were not dissected. Two cases had cardiac venous thrombosis with one case exhibiting septal myocardial infarction associated with intramyocardial venous thrombosis, without atherosclerosis.” In addition, The presence of circulating megakaryocytes on autopsy in various organs was also found and thoroughly studied.

The fact that thrombi have been found in the post-mortems of a significant number of patients who died of COVID-19 disease can account for systemic organ failure in vital organs such as lung, kidneys and heart and such a set of conditions could easily lead to subsequent death.

These data are exceedingly troubling and leaves researchers with a profound question – how does COVID-19 infection trigger such a disastrous response?

The Apparent Efficacy of the Steroid Drug Dexamethasone as Therapy for COVID-19 Patients

As medical professionals, epidemiologists, immunologists, and molecular biologists work in the midst of the COVID-19 pandemic, many aspects of the biology of this virus are being studied and as a result, new understandings are emerging.

It seems that patients with advanced disease that require intervention using a ventilator may be suffering from a hyper-active immune response. In such cases, the use of steroid-based anti-inflammatory drugs may prove efficacious.

An extremely encouraging report from the highly respected Science journal, Nature, has shown the results of a trial study using the proven steroid drug Dexamethasone.

According to the report, the results have indicated that, “An inexpensive and commonly used steroid can save the lives of people seriously ill with COVID-19, a randomized, controlled clinical trial in the United Kingdom has found. The drug, called dexamethasone, is the first shown to reduce deaths from the coronavirus that has killed more than 440,000 people globally. In the trial, it cut deaths by about one-third in patients who were on ventilators because of coronavirus infection.”

This study was expansive involving 2100 participants who received the drug at what is considered a low to moderate dose – 6 milligrams (mg.) per day for 10 consecutive days. The results from the patients were then compared to the results from 4300 patients who received standard care for COVID-19 infection.

Although the drug had no noticeable impact on patients showing no severe symptoms, the positive effect was most striking on patients on ventilators and even on those undergoing just oxygen therapy (not on ventilators) where the rate of death was reduced by 20%.

These are, indeed, encouraging results.