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3.3 The SARS-CoV-2 Pandemic Impact

      The SARS-CoV-2 and the COVID-19 disease impact is a multifactorial phenomenon to measure it we have to take into account some factors (Section 3.1), so let us only take two of them for the moment; its dissemination capacity and its capacity to kill a human being.

      The propagation of viruses has to do with the possibility of passing to any organism and the SARS-CoV-2 virus gets this feature from the Coronaviridae family (Section 3.3.2), which can be considered very high; on the other hand, the lethality of the SARS-CoV-2 is no higher than 2% (Section 3.1), which is low.

      However, both factors together create a combination that strongly impacts humans, as their propagation and lethality take on a large number of lives, given the permanence of the virus in human beings.

      In this sense, the impact is very high since this coronavirus has a very similar spread to any flu; however, its lethality is very high compared to this disease, as up to date there is no effective treatment or vaccine available; unlike the A H1N1 influenza pandemic in 2009 that had an effective treatment and the vaccine was available few months later.

In this regard, any alert or official warning that the population is facing an epidemic process or a pandemic, in general, has to do with a minimum number of people infected that have had a microbiological corroboration.

      In the case of an unknown illness, this verification can take days or even weeks; this is a limitation that defers the notification. So, once this alert has been issued, the authorities should state it is a pandemic and not an epidemic event, according to the definition that at least two continents present infected cases, regardless of the number of them.

      From the epidemiological point of view, there should be an algorithm that not only considers the number of confirmed cases, as continuous improvement of the means of transport makes contagion and dissemination of illness much faster nowadays.

      3.3.1 RNA Virus vs DNA Virus

      There are two main groups in the classification of viruses and they are related to the genetic material a virus uses to replicate, whether it is in a DNA or an RNA host.

      DNA viruses are formed by the families (Source: [8]; change family by the corresponding family name): Adenoviridae, Papillomaviridae, Parvoviridae, Herpesviridae, Poxviridae, and Anelloviridae.

      While RNA viruses are formed by the families (Source: [8]; change family by the corresponding family name): Reoviridae, Picornaviridae, Caliciviridae, Arenaviridae, Rhabdoviridae, Coronaviridae, and Herpesviridae.

      Given the purpose of this chapter, the reader is invited to consult the source cited in each of the classifications, if he/she wants to delve into this topic.

3.3.2 The Coronaviridae Family

      Coronaviruses are transmitted by respiratory secretion sprays, with different incubation periods estimated between 2 days and a week, after these 2 weeks, the virus is eliminated from the body. The virus replicates in the host cell, passing to the Golgi apparatus until they are finally released by exocytosis. In general, coronaviruses induce 15% of colds and flu, and their effect intensifies in winter and early spring.

      Coronaviruses infect a large number of birds and mammals, particularly the SARS CoV-2-index-SARS-CoV-2; they are responsible for severe respiratory diseases, which can be spread even to babies; and in few cases, they are responsible for neurologic syndromes.

The virus remains in the upper respiratory tract and exhibits minimal immune response. Due to its mutation capacity, it persists in the invaded species.

3.3.3 The SARS-CoV-2 Structural Proteins

      Four structural proteins form the SARS-CoV-2, the Spike, Membrane, Envelope, and Nucleocapsid proteins; there are other groups related to SARS-CoV-2 like the non-structural proteins, and SARS-CoV-2 putative accessory factors; although, there are also protein groups with important structural differences related to it, such as those of the MERS, and SARS-CoV proteins.

      3.3.4 Protein Representations

      Proteins are formed by amino acids; they are the fundamental units of every living organism; they are transformed into tissues, muscles, skin, or nails, but they can also be converted into accelerators or retardants of chemical or physiological processes. Life could not be understood without them.

      The first representation of a protein is a succession of amino acids; it is like placing one amino acid after another, this representation is called linear representation or sequence. Then, three representations take place in the three-dimensional space that are related to the form the amino acids settle.

      When protein amino acids cluster, they take forms like alpha helices and beta sheets, this is called a secondary representation. When these small structures bind together, the protein has a tertiary representation. Finally, if the protein is so large that it is made up of two or more tertiary structures, then it is said to be a protein with a quaternary structure.

      A protein may be made up of few amino acids or thousands of them; however, their number has nothing to do with the size it adopts but with its regulation. Suffice it to say that as an example the SARS-CoV-2 structural protein (Spike) has 1283aa and yet it only has few microns.

      Note 3.1 Here, it is important to mention that viruses are formed by proteins, and although at the time being, it is still discussed whether they are living organisms or not, they are also formed by proteins.

3.4 Computational Predictors

      There is a practical interest, besides the scientific interest, in aiming efforts to determine the predominant function of a protein. Let us start by saying that proteins do not have a single action on a pathogen; on the contrary, all proteins have action on several pathogens. For this reason, when examining a database specialized in proteins, it is common to find that the same protein is reported several times, with a different predisposition.

      On the other hand, determining the action or function of a protein involves costly experiments and/or clinical trials, without mentioning that there are proteins with pathogenic action that are increasingly difficult to find in nature; as in the case of SCAAPs (selective cationic amphipathic antibacterial peptides) that are highly toxic to bacterial membrane and harmless to erythrocytes.

      SCAAPs are also very short 6aa proteins – 14aa; for all these characteristics, they are very valuable in the production of pharmaceutical drugs; however, it is increasingly difficult to find them in nature.

      In this scenario, it is very useful to have computational mathematical predictions that can identify the preponderant function of a protein only by taking its sequence. This enables the inspection of databases to search peptides with a specific function. Of course, this will not prevent experimental testing, but it will substantively reduce the proteins tested.

      There are several types of classification СКАЧАТЬ