The pandemic is not over yet, or finally is, but not for the governmental institutions in US and other countries, especially in my own country, Italy. News and reports are controversial, and we do not know who or what to believe anymore.
We know that vaccines are necessary in life in specific cases, like those important to do when we are born, or in medical work environment, or other environments, or when traveling in wild area of the world, but they can also cause side effects and even death in rare cases. Certainly, I do not believe other type of data that show about terrible things inside these vaccines, or of risks of transferring even other type of pathogens. Who could do such a thing to the humanity. It is too unrealistic for me to believe this, perhaps accidentally, but even in this case hard to believe for the process of safety and control vaccines go through.
This disease is not so dangerous as it was at begin, it looks like, and as the majority of naturopaths I believe that natural immunity is the most important tool to fight a disease. Especially with coronaviruses there is a history that makes realize that we have been certainly in contact in the past with other types of SARS coronaviruses, and currently since the begin, we all have been exposed in way or another to the SARS-CoV-2 coronavirus and developed some sort of immunity against even though the strains are different and even though we did not get sick.
The same Dr. Robert Malone, the inventor of the mRNA and DNA gene therapy’s techniques talks about the concept of cross-reactivity and previous exposures, besides the other concerns he seems to have for the use of a genic therapy as the same he has invented in collaboration with other scientists, as for the errors that can develop from the insertion of mRNA into the human cells.
This from one of his articles in cooperation with his wife, I have assembled through copy and paste of their original article just cutting parts:
“What Do Covid, HIV And Many Common Colds Have in Common” By Drs. Jill & Robert W. Malone
“The RNA genome of a coronavirus can be infectious; the RNA alone, if transferred into a cell, can cause that cell to produce complete and infectious new coronaviruses. This is why mRNA vaccines only use a fragment of the mRNA genome, so that the mRNA cannot reproduce virus.”
The same inventor tests that we should be secure at least for this part, but not for the errors that can develop.
“Using RNA as the genetic material- the article continues- is very efficient, but it is also very likely to develop errors during replication relative to using double stranded DNA (like human beings use). Among other problems with this viral strategy viruses that use RNA often mutate very fast. Good thing that human beings use DNA to store their genetic information!”
“The high mutation rate of RNA viruses is one reason why it is difficult to make effective vaccines against many of these types of viruses, this is why there is no vaccine for HIV and the common cold.”
“RNA viruses account for a large fraction of all known human viruses, including many well-known pathogens such as HIV (the AIDS virus), hepatitis C virus (liver cancer), rhinoviruses (common cold), West Nile virus, Dengue virus, Zika, SARS and MERS coronaviruses, and COVID-19.”
“As the virus undergoes pressure from the vaccine with a target of a single protein (spike in this case), it will mutate to escape the vaccine and these escape mutants will often become more deadly.”
This is what the inventor of the mRNA and DNA gene therapies thinks.
Yes, right now cases are surging again all around the world and hospitals seems also cannot contain as they say and show on TV and media. They are admitting that omicron variant is more infectious and less dangerous and most of the cases are resolving as a regular cold or flu, but then other news report that some doctors warn in regard saying that it is not always this way and that also omicron can be very dangerous, and especially for the unvaccinated, is this true?
The conclusion is that we all do what we think is the best for us and maintain respect for others, and as much as we can get informed it is always a good thing, but it is also important do not get overwhelmed and continue living our life in the best possible way and with a little bit of faith, God is always there if we ask for Him and let Him guide us.
I would like to try at this point a brief survey on my own just to have an idea of how things have been going since this pandemic did start.
This is the link for who kindly would like to participate.
It is important distinguish between Food Allergies, and Intolerance and/or Sensitivities, and as much as we know or believe to know more clarifications come up.
During my internship in hospital after my degree in Biology, I have had the opportunity to work in a laboratory sector where allergy’s tests were performed on serum to detect the immunoglobulins responsible for allergic reactions, the IgE, and those for intolerances, or better sensitivity as IgG and IgA and which in case of wheatcompounds, gluten and gliadin are responsible for celiac disease, these tests were called PRIST and RAST for allergies and AGA for gluten sensitivity, for I have a little bit of knowledge in this field along with the studies that have accompanied this part.
Then I have learned more from Dr. Peter D’Adamo, the Blood Type Diet founder; one of his books on allergies was my first approach to his science and to his focus on lectins in foods and ways the body reacts, antibodies productions to foods’ antigens, or allergens and of course, the involvement of blood types in this case. Then later from Dr. Tom O’Bryan, the gluten sensitivity expert who covers in his books, webinars, and public speaking great part on food sensitivities and related connections with health and diseases, inflammation, leaky gut, importance of health of microbiome, immune system, the autoimmunity process, and the different theories in regard, and much more.
But despite of all and because the material around is a large amount among books, courses, articles, etc., alternatively, I refer to the internet when in search of clarifications and validations, and for quicker results, and here is how I have found in the middle of a new confusion.
There were several articles in regard, as for everything we look on internet, but I concentrated my attention on two of these, the first one did clarify and refreshed what I already knew, but the second one, actually, a you tube video coming from a reliable source appeared to contrast everything in regard of IgG and food sensitivities, and paradoxically confirming something that I was always wondering myself.
The first article from a certified nutritionist gives a good understanding among the differences and provides accurate information.
The author, Dr. Mary Ellen, defines Food Allergy as hypersensitivity of the immune system to foods with production of IgE or immunoglobulin-E, Food Sensitivity as immune delayed reaction and which manifests with the production of IgG and IgA, and finally Food Intolerance as a non-immune reaction to foods.
Then she gives a brief explanation of what antibodies or immunoglobulins are as products of the immune system (lymphocyte B) against invaders, and that body makes different immunoglobulins to combat different antigens. There are five classes of immunoglobulins, but three are those involved with food reactions, and they are:
Immunoglobulin E or IgE, Immunoglobulin G or IgG, Immunoglobulin A, or IgA
IgE allergies are immediate responses to an antigen that has entered the body. After being exposed to an allergen, IgE antibodies attach to mast cells, where they stay until the next exposure to the food which has caused the allergic reaction. At a next exposure, the IgE antibodies stimulate the mast cells to send out histamine and other compounds cause of symptoms like inflammation, swelling and itching.
IgE food allergies -she reports- can decrease over time if an individual’s health improves. Dr. D’Adamo, instead, was talking of decreasing with age. The stronger the immune system and the healthier the gut, the better the body will be able to tolerate accidental exposure. Symptoms of an IgE allergy usually appear within seconds or minutes and can include swelling/inflammation, hives/rash, itching skin, difficulty breathing, throat tightening anaphylactic shock in severe cases.
IgE tests are performed as part of an initial screening for allergies or for confirmation of an allergy. This can be done by skin prick or patch testing which measures how much IgE is present in a person’s blood, or with test on serum-blood as I was mentioning previously.
IgG food allergies are delayed food allergies. They are often called food sensitivities.
With IgG reactions– she assesses- the immune system produces IgG antibodies which can lead to inflammatory processes. Symptoms for IgG reactions can appear up to three daysafter the consumption of a food. It is not always easy to identify exactly which food causes problems because of the delayed appearance, therefore tests or an elimination diet can help. Dr. O’Bryan, for example, at this regard, keeps repeating- as he stresses on different other part in regard of this matter- that people with allergies are “lucky” because they know what food or allergen can be a problem, while people with sensitivities cannot.
Elimination of IgG-positive foods, under her observation- and of other nutritionists- can often improve symptoms of irritable bowel syndrome, autism, ADHD, cystic fibrosis, rheumatoid arthritis, and epilepsy, according to numerous clinical studies.
IgG antibodies– she continues- lead to inflammatory processes and are not associated with the release of histamines, for this reason there are not immediate hypersensitivity reactions. And this is what the majority of naturopaths and integrative doctors believe and sustain.
Symptoms of an IgG reaction can include anxiety, depression, bloating/gas, diarrhea, constipation, acid reflux, joint aches, fatigue, mood changes, hyperactivity, loss of breath, weakness, brain fog/memory issues, and certain conditions- she believes so as others in this field- could derive from food sensitivities such as arthritis, migraines, ear Infections, eczema, sinusitis, asthma, colitis, irritable bowel syndrome or IBS.
She also comments about the consequences of these reactions and of the damages on the intestinal wall and the emerging of leaky gut. With intestinalpermeability the intestinal wall becomes porous letting food particles, toxins, and bacteria flow into the bloodstream and causing the immune system to react and trigger inflammation and changes into the gut. Chronic, prolonged inflammation and toxicity can be a cause of autoimmune disease and other related disorders, as I personally keep bringing up, so as the doctors I refer.
For this nutritionist, as for the most I believe, it is often difficult to determine exactly which food cause problems because of the delayed appearance of IgG symptoms, and because of this, an IgG test, or Food Panel test, is the best way to find out foods to which we are sensitive, but it does not look like for allergologists as I will explain in a few.
IgA reactions are not related to food allergies and sensitivities, but they are involved with intestinal permeability. IgA, or secretory IgA are found in high concentrations in the mucous membranes of the respiratory and gastrointestinal tracts. Secretory IgA provide protection against potentially harmful microbes, they are the body’s first line of defense against bacteria, food particles, parasites, and viruses. Chronic stress, frequent antibiotic use, overload of foods like soda, coffee, alcohol, or sugar can thin the lining of the gut.
She also mentions a Secretory IgA test, called SIgA test to see how strong or thin the gut-lining is. This will show a person’s ability to defend against infections, allergies, and food reactions as well as provides guide for next steps in treatment of health issues.
Food intolerance can cause some of the same symptoms as a food allergy/sensitivity, for it is easy to be confused. Whilefood allergies trigger the immune system, food intolerances do not. Food intolerances are usually caused by a deficiency or absence of an enzyme neededto digest and process a food.
She mentions two examples in regard, lactose intolerance where people do not have enough of the enzyme lactase necessary to break down the sugar lactose found in cow’s milk, and histamine intolerance that could be due to lack of the DAO or HNMT enzymes that both lead to an excess of histamine.
People with food intolerance may be able to prevent issues related by taking the digestive enzymes that are missing. Histamine intolerance is a little different because of the buildup of histamine. She suggests better to stay away from foods that release histamine until this one level is decreased.
She then concludes saying that food intolerances do not have a specific blood test because the immune system is not involved, and immunoglobulins will not be present in the blood, and that some people are more susceptible to intolerances because of genetic polymorphisms -variations in DNA called SNPs or single nucleotide polymorphisms- In the case of histamine intolerance, DNA testing could be done to see if predisposed to impaired histamine processing. She mentions three main genes involved in processing histamine HNMT, DAO, MAO.
“Dirty Genes,” a book by Dr. Ben Lynch, who is the expert in SNPs and methylations and histamine sensitivities gives a good understanding in regard of SNPs and genetic variations and more, I refer to him and to his book in regard of all of this as more times mentioned in my blogs.
Dr. David Stukus, pediatric allergologist, is the specialist that I was talking about and that has created the confusion to myself. This doctor in a you tube video comments about the validity of Food Panel testing and values of IgG in regard of intolerances or sensitivities.
For his definition Food Allergies are dangerous immediate reactions to a food and that manifest with IgE production, while with Food Intolerances or Sensitivities the body cannot process or digest a food, and this can cause uncomfortable but not dangerous symptoms. Classic food intolerance is the lactose intolerance due to the lack of the enzyme that breaks down the lactose and that can cause, abdominal pain, bloating, gas, and other symptoms, especially if eating too much of that food; other foods may also cause brain fog, fatigue, and joint pain.
He thinks that no tests can be reliable and that tests that claim to diagnose food sensitivities are available as IgG food tests. These tests report IgG levels toward multiple foods declaring that the remove of the food responsible of raising the IgG level can improve the symptoms or can even reverse conditions like IBS, autism, rheumatoid arthritis, or epilepsy.
He sustains that there are not scientific studies in support of this and that:
“The presence of IgG is a normal response of the immune system to exposure to food,” and that “Higher levels of IgG4(a sub-class of IgG) to foods may simply be associated with tolerance to those foods”
He then continues that due to lack of evidence, many organizations including the American Academy of Allergy, Asthma, and Immunology have recommended against using IgG testing to diagnose food intolerance or sensitivities.
No words at this point, this is up siding down every believe around, maybe I just heard this for the first time, probably this is already common in the conventional medicine and functional medicine, but the believes are different and divergent.
It is true that antibodies are a rection to an antigen and that in this case is a food, or allergen, that IgG are the evidence of a past contact, or exposure, and that they testimony chronic infection, and that when there are antibodies against foreign agents that means that the immune system is reacting or has reacted and that all of this will cause a cascade of events that will lead to inflammation and from here to an infection or something else.
How come an immunologist/allergologist does not consider this, I am feeling confused myself and certainly aware that has been time that I am not in the field anymore, or practicing laboratory for I do not feel so confident to support or to argue, but I really hope that the experts will give more clarifications in regard, and especially this doctor and his philosophy of thought.
The emerging science is a new science originated with the explosion of natural and integrative medicine; it is the science of epigenetics and nutrigenomics which studies, treats, and analyzed how the environment and lifestyle can affect our genes with all the pathological consequences from related mutations, ways, and natural remedies to prevent, to address and treat the related dysfunctions.
This is the main concept of the emerging science and what most of the experts are treating and commenting in their articles, blogs, books, seminars and webinars, summits and conferences, and that bloggers and writers like myself try to report and share with the public.
But we can all feel overwhelmed from a lot of information from all kinds of sources, and we all may know already enough of these new lifestyle protocols and suggestions.
Why I chose the title of “The Emerging Science” for my blog’s site then?
One of my first blogs, titled “The World Summit” was partially describing the essential point of the “Emerging Science” and why I did get involved with that.
The purpose of the functional and integrative medicine is to find the “root cause” of a disease, and we all know this now very well.
“Every disease begins in the gut” and/or “we are what we eat” are other sentences more time repeated from naturopaths.
Hippocrates the “Father of Medicine” was mentioning these sentences and still today are so valid and true.
We now know so well that the food and ways we eat, our lifestyle and environment are the main reasons of our health issues and of the major diseases today.
The health of the microbiome is so important and the wellbeing of our digestive tract even more because- in short and simplified- if this is damaged, or leaky the bacteria and fragments of proteins and molecules, and toxins from the intestine can migrate in other systems causing variety of problems.
So, what can we do to keep our microbiome healthy and so the intestinal wall?
The food obviously is what we introduce more frequently in our body, and this is why we need to make sure first of all to pick healthy, clean and safe food, but also, we must look at our body’s tolerance. As we know there are food to which we might be sensitive or intolerant and these are those we should avoid and that will cause the problems. Or if we refer to the Blood Type Diet of Dr. Peter D’Adamo whose father was testing that a food who is medicine for one can be poison for another in a book titled “One Man’s Food”, and based on experience with his patients, we should eat following the prototypes and protocols of our blood type avoiding foods that can cause agglutinations for the presence of lectins which are substantially toxins.
I am not expert of other diets because I personally follow and refer to the Mediterranean Diet and Blood Type Diet, and which are anti-inflammatory diets with some restrictions.
If there are instead more serious digestive problems, like IBS, SIBO, or yeast infections, or others, those suggested are elimination diets, or microbiome diets, or fodmap diets which are pretty restrictive.
The other way we can alter our microbiome and not simply this is with the introduction of toxins, the doctors talk incessantly about this and the number and type of these are enormous, they come with foods as poison, as lectins that agglutinate cells, with products we use for cleaning, or any other purpose, from the environment, as emissions of gas and chemicals of all types. The alternatives to these are many and mainly coming from natural products or essential oils, while in case of pollution several attempts for reduction of emissions or other type of strategies have been adopted from years and even more lately because of the world’s catastrophic damages on the environment.
When these external attacks on our body and systems reach the limit, we start to react and to get sick also based on the strength of our immune system and that depends on how we nourish and supplement and from how much inflammation there is in our body caused from these external causes. It is all connected, and one can influence another, our internal feedback systems help to alert, and repair the damages till possible, otherwise we must take action.
Here is why prevention is particularly important and must be addressed as soon as possible before these damages can initiate with serious and drastic consequences.
I am not a health coach, but a biologist, and I encourage all of whom are interested in becoming a health coach to look at the options because this is a growing field and with career opportunities at these times.
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Nitric Oxide is the molecule with the chemical formula NO. This is also known as nitrogen monoxide and is a colorless gas. When exposed to air, it reacts with oxygen, to produce much more harmful nitrogen dioxide gas or NO2. Nitric oxide is an intermediate in some chemical reactions. It is produced as a by-product in fossil fuel burning in vehicle engines and machines. This nitric oxide can cause ozone depletion together with nitrogen dioxide. Naturally, nitric oxide is produced in the air when lightening occurs. In this process, atmospheric nitrogen and oxygen are mixed to produce nitric oxide; this is a major step in the nitrogen cycle, the nitrate source for providing nutrition for plants.
Nitric oxide, or NO is also an endogenous mediator of particularly important biochemical processes, such as vasodilation and transmission of nerve impulses.
In our body the synthesis of this compound is performed from a group of enzymes belonging to the nitric oxide synthetase family, NOS, which use arginine as a substrate, an essential amino acid in children and conditionally essential in adults.
Picture by personaltrainer.it
The synthesis of nitric oxide is regulated by varied factors such as the one called “shear stress”, a parameter that measures the force applied by the flow of blood on the walls of the vessels. When blood pressure rises excessively, the body defends itself by synthesizing nitric oxide which, by dilating the walls of the vessels, contributes to the lowering of pressure. In contrast, the inhibition of nitric oxide synthesis determines an increase in peripheral resistance and a consequent increase in blood pressure.
The synthesis of nitric oxide by endothelial walls can be also promoted by molecules like norepinephrine and cytokines.
The half-life of nitric oxide is markedly short, its rapid catabolism involves binding to the eme group of hemoglobin, this process leads to the consequent production of methemoglobin, a non-functioning form, then nitrites and nitrates, NO2 and NO3, which are eliminated by the kidney.
Nitric oxide modulates nerve and neuromuscular transmission by acting as a neurotransmitter in the central nervous system and in the peripheral non-adrenergic and non-cholinergic nerve plexuses of the bronchial tree, bronchodilator- anti-asthmatic effect, and gastro-intestinal tract.
It relaxes not voluntary smooth muscle, exercises vasodilator action on the systemic, coronary, and renal vascular endothelium.
It intervenes directly in the immune system; nitric oxide is produced by some cells of the immune system that use it to defend themselves from the aggressions of antigens. In this case it is utilized its oxidant action and consequent ability to release free radicals capable of destroying the plasma membrane of microbial agents.
Nitric oxide, in addition, appears to stimulate cell proliferation of T and B lymphocytes during the immune response.
In conclusion, nitric oxide has therapeutic potential for reducing blood pressure, strengthening the immune system, preventing angina, stroke, and heart attack, and for the treatment of erectile dysfunction.
The cytotoxic effects of this molecule are mainly due to its strong oxidizing action which express with increase of the production of free radicals, the most dangerous cause of premature aging, degenerative diseases, and some forms of cancer.
The food supplementation sector is progressively expanding with products capable of increasing the endogenous synthesis of nitric oxide. In particular, the focus is on the administration of high doses of the precursor amino acid L-arginine orally. According to supporters of these supplements, regular intake of arginine would be able to increase the synthesis of nitric oxide.
In fact, the synthesis of nitric oxide is a complicated process, which responds to endocrine and mechanical factors. The stimulatory effect of arginine becomes appreciable only in case of increased need or in the presence of deficiencies induced by a diet low in this nutrient.
Recently instead of traditional arginine it has been proposed the integration of a precursor, the amino acid L-citrulline, in the form of citrulline malate with the purpose of increasing in way dose-dependent the quantity of arginine available for the synthesis of oxide nitric.
Nitric Oxide vs Nitrous Oxide
Nitric oxide and nitrous oxide are molecules of nitrogen (N) and oxygen (O2). Both are gases in the atmosphere. Today, they are emitted mostly by anthropogenic activities and affecting the environment in harmful ways.
Nitrous Oxide commonly known as laughing gas is an oxide of nitrogen with the formula N2O. At room temperature, it is a colorless non-inflammable gas. At elevated temperatures, nitrous oxide is a powerful oxidizer like molecular oxygen.
Nitrous oxide has significant medical uses, especially in surgery and dentistry, for its anesthetic and pain reducing effects. Its name as “laughing gas” is due to the euphoric effects following inhalation. It is also used as an oxidizer in rocket propellant, and in motor racing to increase the power output of engines.
Global reporting of N2O sources over the decade indicates that about 40% of the average of emissions originated from human activity and shows that emissions growth mainly come from expanding agriculture and industry sources within emerging economies. For these reasons, nitrous oxide also substantially contributes to global warming.
Additionally for Dr. Ben Lynch, molecular biologist, ND and epigenetics expert, nitrous oxide irreversibly inactivates cobalamin, the active form of vitamin B12, essential for methionine synthase activity in brain; practically inhibits cobalamin to function as a coenzyme in the methylation cycle.
Under his knowledge there have been reported exposures (~30,000) to N2O and neurological diseases among dental professionals manifesting with symptoms as numbing, tingling and muscle weakness; for those heavy exposed complications are even greater.
Still from his statement there are a wide range of people who may exhibit sensitivity to nitrous oxide, among the populations at risks there are: those with oxidative stress cause of glutathione deficiency and cellular membrane damage, inflammation and increase of TNFa factor (a tumoral factor).
Pathogens as candida, viral infections, and H. Pilory, heavy metals load, MTHFR SNPs, low or high homocysteine, methionine deficiency, SAMe, B-vitamins, selenium, glycine, and glutamine deficiency. Exposure to chemicals and post-operative dementia.
Verification of data by PubChem (nih.gov) “Nitric Oxide”
Nitric oxide appears as a colorless gas. Non-combustible but accelerates the burning of combustible material. Vapors heavier than air. It is a nitrogen oxide which is a free radical. It has a role as a neurotransmitter, a signaling molecule, a vasodilator agent, a bronchodilator agent, a radical scavenger, a human metabolite, an Escherichia coli metabolite, and a mouse metabolite.
Nitric oxide or Nitrogen monoxide is a chemical compound with chemical formula NO. This gas is an important signaling molecule in the body of mammals including humans and is an extremely important intermediate in the chemical industry. It is also a toxic airpollutant produced by automobile engines and power plants. Nitric oxide (NO) should not be confused with nitrous oxide (N2O), a general anesthetic, or with nitrogen dioxide (NO2) which is another poisonous air pollutant. Nitric Oxide as a free radical has high reactivity and reacts with NO2 in the air producing even more toxic gas.
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This abstract comprises a simple analysis and description of the virus genome.
Human coronaviruses, or HCoVs consist of HCoV-229E and HCoV-NL63 in the Alphacoronavirus family and HCoV-OC43 and HCoV-HKU1 in the Betacoronavirus family.
Four CoVs, for instance, HKU1, NL63, 229E and OC43, are mainly responsible for mild respiratory disorders in human circulation.
SARS-CoV-2 is a β-coronavirus carrying a single positive RNA strand as genetic material, it has a lipidic envelope that confers an elliptic morphology.
CoVs evolved a relatively complex multiplicationmechanism to facilitate virus reproduction. In their viral life cycle CoVs transmit genomes and subgenomicRNAs only from RNA templates, and do not need a step of DNA. CoVs use exonuclease NSP14, the first known RNA virus-encoded proofreading enzyme that in comparison with other error-prone RNA viruses, could be adapted to handle CoVs‘ large RNA genome.
“Prolonged SARS-CoV-2 RNA shedding, and recurrence of PCR-positive tests have been widely reported in patients after recovery, yet these patients most commonly are non-infectious”. The researchers in this article have investigated the possibility that SARS-CoV-2 RNAs can be reverse-transcribed and integrated into the human genome and that transcription of the integrated sequences may be responsible for PCR-positive tests.
In support of this hypothesis, they found chimeric transcripts consisting of viral fused to cellularsequences in published data sets of SARS-CoV-2 infected cultured cells and primary cells of patients, consistent with the transcription of viral sequences integrated into the genome.
To experimentally corroborate the possibility of viral retro-integration, they describe evidence that SARS-CoV-2 RNAs can be reverse transcribed in human cells by reverse transcriptase, RT from LINE-1 elements or by HIV-1 RT, and that these DNA sequences can be integrated into the cell genome and subsequently be transcribed.
-This is, of course, referred to an infection with SARS-CoV-2, and not to the genetic material (mRNA) introduced with the vaccine-
In this last article slightly modified and reduced from myself also is commented about the reverse transcription of SARS-CoV-2.
The authors report that: “The researchers explored the occurrence of reverse transcription of the SARS-CoV-2 RNA into the human genome. This would result in positive PCR tests due to the continuing transcription of viral RNAs.
Reverse transcriptaseactivity has been detected within human cells, so as integration of the reverse transcription products.
The endogenous RT is potentially present in the form of human LINE-1 elements, which make up 17% of the human genome. These are autonomous retrotransposon elements that can transpose themselves as well as other elements of the genome back into the DNA of the nucleus for future transcription.
The researchers looked at the published RNA-sequences from SARS-CoV-2 infected cells, their purpose was to find chimeric transcripts, fusing human and viral RNA into the same genome. They found a good number of these in several different cell types, and from cells recovered from the bronchoalveolar lavage fluid obtained from COVID-19 patients.
The proportion of these chimeric sequences was directly correlated with the level of viralRNA in each sample. The greatest proportion was in cells recovered from the bronchoalveolar lavage fluid of severe COVID-19 patients, while there were almost none in blood cells.
Most of the host-viral chimeric protein contained the nucleocapsid sequences, as expected since this is the most abundant viral particles. This would, therefore, be the most likely to be reverse transcribed and then integrated. These findings for the researchers support the occurrence of this event within infected cells.
They conducted then an experiment inducing the overexpression of human LINE-1 elements or HIV-1 RT, in the cell line.
These cells were then infected with SARS-CoV-2. At two days post-infection, they carried out polymerase chain reaction, PCR, tests to detect the viral sequences, using the N-targetingprimer sets used in the commonly used COVID-19 PCR tests.
PCR amplification of the purified cell DNA from infected cells showed the presence of the Nprotein bands. This did not occur in non-transfected or uninfected cells.
They also conducted an in vitro RT experiment, which showed that cell lysates from cells expressing RT of either type could cause reverse transcription of purified viral RNA from infected cells.
Using fluorescent in situ hybridization, FISH, technology, they trapped down the presence and ongoing transcription of the viral N sequences within the cell nucleus with the help of N–targeting fluorescent probes. The N sequences were found in the cytoplasm, as expected of cells infected by SARS-CoV-2.
However, FISH also picked up N RNA signals from the nucleus of cells that overexpressedLINE-1, showing that integrated N sequences in the host genome were being transcribed there.
The integrated sequences are probably sub-genomic and cannot produce live infectiousvirions. This explains the positivity of later PCR tests for viral RNA in clinically recovered patients.
The authors suggest that the site of insertion and regulation by epigenetic factors, besides the existing immune state of the patient, may affect the translation of these sequences and their possible clinical consequences.
In conclusion, the study suggests that many PCR positive results could be due to viraltranscripts from chimeric sequences instead of reflecting the presence of replicating virus in the host. If validated, this will require better tests to be used when assessing the efficacy of COVID-19 therapies in clinical trials, for example, in the future.