COVID-19 LEGACY: SARS-CoV-2 clinical trials, vaccines trials and bioethics

Bibliography

Preface

In this book are analyzed topics related to COVID-19 which form the basis of the understanding of the multiple aspects related to the protection of public health, and which will allow the reader to broaden his or her understanding of how the system of preparation for the global pandemic is developed. Today, on the eve of the first fifth of the twenty-first century, we have new tools which allow us the management of pandemics. Will be described what are those tools, deepening several topics which are interrelated and which create the healthcare system. The book focuses in particular on the management of clinical studies, the pharmaceutical patent system, gene sequencing and the role of artificial intelligence in the protection of public health and fundamental human rights, observing how all this different tools are used to address the COVID-19.

CHAPTER 1

What are coronavirinae

Coronaviruses were first discovered in the 1930s, when acute respiratory infection among chickens was shown to be caused by the contagious bronchitis virus. In 1931 a new respiratory infection of chickens in North Dakota was described by A. Schalk and M. Hawn. Chick infection was characterized by laziness and prostration. The mortality rate of the chicks was 60%. In 1938 the contagious bronchitis virus was successfully isolated from F. Beaudette and C. Hudson. In the 1940s, two additional animal coronavirinae strains were isolated: the mouse hepatitis virus and the transmissible gastroenteritis virus. At that time there was no awareness of the relationships between the three viruses. We come to the discovery of human coronavirinae strains only 20 years later in the 1960s. A new cold virus called B814 was isolated in 1960 from the Common Cold Unit of the British Medical Research Council by E.C. Kendall, Malcom Byone and David Tyrrell. The virus did not seem to be easily cultivated using the common cultivation vial which, on the contrary, had been successfully used to grow rhinovirus, adenovirus and other cold viruses. Five years later, Tyrrell and Byone successfully cultivated the new virus by serially introducing strains within the cultures of the human-derived embryonic trachea. The same year at the University of Chicago a new cold virus, later called 229E by medical students, was isolated from professors D. Hamre and J. Procknow, who used a different cultural approach to grow the virus in culture. kidney tissue. The new 229E virus, such as the viral strain B814, when inoculated in volunteers caused a cold and was inactivated by the ether, indicating that both viruses had a lipid envelope. Most viruses such as HIV have the so-called viral envelope as an outer layer in their life cycle stage when they live outside the host. This happens because the envelopes are generally derived from portions of the membranes of the host cells (phospholipids and proteins), but also include some viral glycoproteins and not only those of the host. They may prefer viruses to avoid the host immune system. The glycoproteins found on the surface of the envelope are useful for identification and binding with receptor sites on the host membrane. The viral envelope eventually merges with the host membrane, which allows the capsid and viral genome to break through and infect the host. Varieties B814 and 229E were officially photographed for the first time by an electron microscope by J. Almeida, a microbiologist who worked for St Thomas Hospital in London. Thanks to electron microscopy, Dr. Almeida was able to highlight that both strains could be distinguished from the peaks like those of a club. Thanks to Dr. Almeida not only was it possible to understand the morphological relationship of the two strains that were very similar to the contagious bronchitis virus. Following the National Institute of Health of the United States of America he was able to detect another virus called OC42 which belongs to the same family. The NIH isolated the virus and was able to allow the scientific community to study these viruses and their relationships, and the conclusions thanks to the electron microscope in which these viruses had distinctive peaks similar to those of a club, each of which has its own strain. Coronaviridae are a group of viruses that can cause disease in mammals and avian species. These viruses are the causative agent of respiratory tract infections which, due to our misunderstanding of the mechanism of action, can vary from mild to lethal. In describing mild disease, they include colds, keeping in mind that they are not the only family of viruses that cause colds, which are mainly caused by the rhinovirus family. The lethal strains of coronaviridae have been found to be the causative agents of severe acute respiratory syndrome (SARS) and Middle Eastern respiratory syndrome (MERS) and coronavirinae strain 19 disease (covid-19). For all these viral diseases there is a wide range of symptoms that affect not only humans but also other mammals and avian species, as we have just anticipated above. We can observe that in chickens, these viruses cause a respiratory tract infection differently from pigs in which the same strain mainly causes diarrhea. Since 2002 there have been numerous patents on vaccines and antivirals of coronaviridae, but unfortunately it has not been possible to prevent this disease, to spread further for various reasons related both to the mutagenicity of this family of viruses, and to the patent system that must guarantee the confidentiality of data in order to protect researchers' rights and for the practical construction of the laboratories needed to produce an antiviral drug or vaccine in time.

According to the International Committee for the Taxonomy of Viruses, the strains of coronavirinae are a subfamily of the ortho-coronavirinae, which belong to the wider family of coronaviridae, which are grouped in the order of nidovirales, which are further collected in the kingdom of riboviria (which collects all ribonucleic acid viruses). According to the Baltimore classification, coronavirinae strains are viruses wrapped with a positive-sense single-strand RNA (+ssRNA) gene pool. The genome size of the coronavirinae strains is between 26 and 32 kilobases (one kilobase - kb - means 1000 nitrogen bases), i.e. it extends from 26,000 to 32,000 nitrogen bases. The nitrogen bases that make up nucleic acids in biochemistry are one of the four components of organic life together with sugars, lipids and proteins. They have characteristic club-shaped tips that protrude from their surface, which in electronic micrographs create an image that resembles the solar crown, from which their name derives. Coronavirinae are spherical stones with spike-like protrusions that have a size of almost 17-22 nm, which make up the proteins encoded by its genome, the average diameter of these spheres is 80 nm (1 nano-meter - nm - It's one billionth of a meter, or 1 meter divided 1,000,000,000 times). To be even more correct, we must add that obviously they do not all have the same dimensions; but the size varies from 60 nm to 120 nm. To be even more precise on the size, we can consider the fact that the diameter of the envelope varies within 80 nm while the diameter of the tips, as we have just said, varies within 20 nm for this reason, we will estimate the dimensions based on the fact that we consider the peaks or if we start measuring from the internal spherical diameter. The envelope consists of a double-layer lipid membrane derived from the host during bubbling. Inside the envelope, there is the nucleocapsid, which is made up of copies of the nucleocapsid protein and those are linked to the + ssRNA of the coronavirinae. The lipid bilayer envelope and the nucleocapsid together perform the function of protecting the virus outside a host. The coronavirinae replication cycle is divided into four main phases: entry, replication, release and transmission. Contagion begins when glycoprotein (the peaks) attaches to its complementary host cell receptor. Declaring protection of the host cell divides and activates the receptor. The cleavage and activation set the entry of the virus into the host cell via a mechanism known as endocytosis (on some microbiology textbooks also called direct fusion) of the viral envelope with the host membrane. After entering the host cell, the viral chapter is more widespread, as it is uncoated and its genome floats within the cell cytoplasm. The coronavirinae genome + ssRNA has a 5 'methylated cap (containing several methyl groups); and a 3 'polyadenylated tail (also known as poly-A, containing almost 200 nitrogen bases supplied only adenine), this is necessary for the RNA to adhere to the host cell ribosome and translation begins. The host's ribosome translates the genome into a long polyprotein. This polyprotein contains its own proteases which subdivide the integrated polyprotein into several unintegrated proteins. When several unstructured proteins are formed, they aggregate to form a multiple complex of replicated-transcriptase proteins (also known as RTC - that is, replicase transcriptase complex). At this point, since the main replicase-transcriptase protein is RNA-dependent RNA polymerase (also known as RdRp), it begins to replicate and transcribe RNA from an RNA strand. The remaining unstructured proteins are believed to aid in replication and transcription, but not all functions of unsecured proteins are known to give just one example, exo-ribo-nuclease proteins, responsibilities to support replication by increasing the proofreading function of RdRp. Viral genome. RdRp media selected the synthesis of negative sense RNA from positive sense RNA followed by replication of positive sense RNA from negative sense RNA. Another important function of the complex is the transcription of the genome of the virus itself, and this process is also mediated by RdRp through the synthesis of RNA molecules of negative sense from RNA of positive sense, followed by the transcription of this story the molecules of RNA in their correspondent messenger RNA. What has just been replicated, which is the positive sense RNA at this stage, becomes the genome of future viruses, the sons and daughters of the virus. The negative-sense RNA. Another important function of the complex is the transcription of the genome of the virus itself, and also this process is mediated by RdRp through the synthesis of negative-sense RNA molecules from the positive-sense RNA, directly followed by the transcription of such negative-sense RNA molecules into their corresponding messenger RNA. What has just been replicated that is the positive-sense RNA at this stage becomes the genome of the future viruses the sons and daughters of the virus. Messenger RNAs are transcripts of the last third of the viral sequence from the initial reading frame. This messenger RNA is translated by ribosomes within the eukaryotic cell into proteins that will form the structure of the virus plus other functional proteins whose activity has yet to be fully understood. The above process occurs within the endoplasmic reticulum of eukaryotic cells in which the structural proteins of the virus continue through the secretion pathway inside the Golgi apparatus where they find the machine necessary for assembling new viruses and from the exocytosis these new carriers are finally released outside the cell. In conclusion of the replication cycle, the coronavirinae interaction of the peak protein with the receptor of the complement host cell is central in determining the tropism of the tissues, but also the infectivity.

Human infections in the 21st century

Coronavirinae has a wide range of variations considering the risk factor. There are strains that have reached a killing rate of 30% of infected mammals, such as MERS-CoV, while other strains are relatively harmless or completely harmless. Coronavirinae as many of you as readers already know from the news or as a personal experience if you have been infected with the coronavirinae strain and have suffered the symptoms, knows the maximum common symptomatology caused by the infection of the coronavirinae strain, which can extend from cold main symptoms, such as fever, sore throat, swollen throat, swollen adenoids dry cough, dyspnea, diarrhea etc. Coronavirinae can also cause pneumonia or bronchitis directly or indirectly. Seventeen years ago, in 2003, another coronavirinae strain, SARS-CoV, infected humans, was the causative agent of severe acute respiratory syndrome (SARS) and had the particularity of infecting both respiratory tract infections higher than lower, as is happening with SARS-Cov-2, which is the pathogen of Coronavirus 2019 (covid-19). In nature there are seven known strains of coronavirinae that can infect humans, among these four are the cause of the cold every year, the OC43 strain, the HKU1 strain, which are two beta coronaviridae; and the variety 229E and the variety NL63, which are alpha-coronaviridae. It is important to emphasize when speaking of alpha and beta coronaviridae that coronavirinae infect both animals and humans. While alpha and beta are derived from the bat gene pool, the gamma and delta genera are derived from the bird and pig gene pool. Among the seven coronavirinae known to infect three humans they can cause more severe symptoms, and those are the SARS-CoV strain, the MERS-CoV strain and the SARS-CoV-2 strain, all of which are coronaviridae beta. In 2002-2003, after the outbreak of severe acute respiratory syndrome (SARS), the World Health Organization (World Health Organization) released a press release warning that a new coronavirinae strain had been identified by a number of laboratories and who appeared to be the causative agent for SARS. The virus has been officially called the SARS coronavirinae (SARS-CoV) strain. In the 2012-2013 period, a new strain of coronavirinae was identified, and after several names where it was suggested that it was finally officially called the Middle East Respiratory Syndrome (MERS-CoV). Again, the World Health Organization has warned the world of the global alert. The World Health Organization, on September 28, 2012, stated that the virus does not seem to spread easily among the population. However, on May 12, 2013, a human transmission case in France was confirmed by the French Ministry of Health. In addition, cases of human-to-human transmission have been reported by the Ministry of Health in Tunisia. Two confirmed cases involved people who appeared to have contracted the disease from their father, who fell ill after a visit to Qatar and Saudi Arabia. Despite this, it appears that the virus had difficulty in spreading from man to man, since most of the infected people did not transmit the virus. The Dutch Erasmus Medical Center has sequenced a variety of coronavirinae which have been given a new name, Human Coronavirus - Erasmus Medical Center (HCoV-EMC). In 2015, a MERS-CoV outbreak also erupted in the Republic of Korea, when a man who had traveled to the Middle East visited four hospitals in the Seoul area to treat his illness. This caused one of the biggest MERS-CoV outbreaks outside the Middle East. By December 2019, 2,468 cases of MERS-CoV infection had been confirmed by laboratory tests, 851 of which were fatal, a mortality rate of around 34.5%. In December 2019, a pneumonia outbreak was reported in Wuhan, China. On December 31, 2019, the outbreak was traced to a new variety of coronavirinae, which received the tentative name 2019-nCoV from the World Health Organization (World Health Organization), later renamed SARS-CoV-2 by the Committee. International for Taxonomy of Viruses (ICTV). As of April 27, 2020, there have been at least 206,569 confirmed deaths and over 2,973,264 confirmed cases. The Wuhan strain has been identified as a new beta-coronavirinae strain with approximately 70% genetic similarity to SARS-CoV. The virus has a 96% similarity to a bat coronavirinae strain. The pandemic resulted in travel restrictions and national blockades in several countries. Coronaviruses have been recognized as the cause of pathological conditions in veterinary medicine since the 1930s.

Diseases caused by the coronavirinae among mammalian and aves classes

Coronavirinae mainly infect the upper respiratory tract of mammals and birds. They also cause a range of diseases in farm animals and pets, some of which can be serious and are considered a threat to the agricultural sector. In chickens, for example, the contagious bronchitis virus (IBV), which as we discussed in chapter 1 belongs to the coronavirinae, affects not only the respiratory tract but also the urogenital tract. This virus can spread to different organs around the chicken. Before the discovery of SARS-CoV, the mouse hepatitis virus (MHV) was the most studied coronavirinae strain both in vivo and in vitro. Some strains of MHV cause progressive demyelinating encephalitis in mice which has been used as a mouse model for multiple sclerosis. Significant research has aimed to clarify the viral etiopathogenesis of these mammalian coronavirinae, by experts in veterinary and zoonotic diseases. Concerning extremely economically relevant farm animals, including bovine coronavirinae strains and porcine coronavirinae strain which causes the coronavirinae strain of transmissible gastroenteritis, both of which cause diarrhea in young animals. Pathologically, feline coronavirinae strains are present in two forms, the feline enteric coronavirinae strain is a less relevant clinical pathogen, even though spontaneous mutation of the coronavirinae strain usually causes contagious feline peritonitis. (also called FIP by veterinarians), which has a high mortality rate among the felid family. There are two strains of coronavirus strain that infect ferrets and also cause a gastrointestinal syndrome known as catarrhal epizootic enteritis (classified as ECE by veterinary surgeons) and an even more lethal systemic version of the virus known as the systemic coronavirinae strain of ferret (classified as FSC by veterinarians). In addition, continuing with chips there