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Computational Predictors of the Predominant Protein Function: SARS-CoV-2 Case
Carlos Polanco1,2*, Manlio F. Márquez3 and Gilberto Vargas-Alarcón4
1 Department of Electromechanical Instrumentation, Instituto Nacional de Cardiología “Ignacio Chávez”, México City, México
2 Department of Mathematics, Faculty of Sciences, Universidad Nacional Autónoma de México, México City, México
3 Clinical Research Center, Instituto Nacional de Cardiología “Ignacio Chávez”, México City, México
4 Research Center, Instituto Nacional de Cardiología “Ignacio Chávez”, México City, México
Abstract
In this chapter, we describe the main molecular features of SARS-CoV-2 that cause COVID-19 disease, as well as a high-efficiency computational prediction called Polarity Index Method®. We also introduce a molecular classification of the RNA virus and DNA virus families and two main classifications: supervised and non-supervised algorithms of the predictions of the predominant function of proteins. Finally, some results obtained by the proposed non-supervised method are given, as well as some particularities found about the linear representation of proteins.
Keywords: Adenoviridae, advantages, algorithms, Anelloviridae, Arenaviridae, Caliciviridae, computational predictions, Coronaviridae family, disadvantages, DNA virus, Herpesviridae, Herpesviridae, linear representation, non-supervised algorithms, Papillomaviridae, Parvoviridae, Picornaviridae, PIM® profile, Polarity Index Method®, Poxviridae, putative proteins, Reoviridae, Rhabdoviridae, RNA virus, SARS-CoV-2, supervised algorithms
3.1 Introduction
The discipline called Proteomics focuses, among other things, on the prediction of the predominant function of proteins, since this enables their construction by alteration or removal of their amino acids, either in its linear or in its three-dimensional representation.
This means some benefits for scholars of this discipline; since from these modifications, it is possible to obtain, mostly by accident, proteins with improved toxic action toward some pathogen.
Of course, it does not mean that there are no proteins or peptides in nature that have the toxic action we are looking for, it is just that in most cases, it is less expensive to try to manufacture one than to find it among the many organisms in nature.
The proteins expressing the SARS-CoV-2 that caused the COVID-19 pandemic have the particularity that their linear representation, i.e., their sequence, has a large number of amino acids, approximately 2,400 amino acids (aa). To give the reader an idea of the complexity and dimension of it, let us consider that some short peptides with antibacterial action have an average of 9aa.
Now, the capacity and robustness of the SARS-CoV-2 and all the regulatory processes can be dimensioned. Viruses, in general, have not simple mechanisms; they occupy some microns in length (a micron equals a thousand of a millimeters), but they are specialized organisms with multiple properly regulated functions that are characterized, among other things, for completing themselves when they are in contact with the RNA or DNA of the host.
This particularity suggests that they are not living organisms if we compare them with other living organisms whose species are known. Living organisms are born complete and do not get completed at birth; they have everything to reproduce themselves. This is not so with viruses; in any case, we can say that viruses are another type of life.
The SARS-CoV-2 is a virus of the group of coronaviruses, whose particularity and strength is the possibility of reproducing in any living organism. This feature is not shared by all viruses, e.g., the Ebola virus only passes to certain species, despite its lethality that is greater than 60%, it is less dangerous to our species because, when it kills its host, the virus dies with it and the damage is so fast that the number of deaths is small.
This does not occur with SARS-CoV-2 that can spread rapidly and the infected subject does not show any symptoms (asymptomatic) for 4 or up to 7 days, despite its lethality rate that is no higher than 2%.
From the above, it is clear that the definition of the lethality rate is not just a quotient, but multiple variables have to be considered. Almost as many as asking us about the lethality of a human being.
The review of the basic concepts related to viruses and particularly the SARS-CoV-2, make us think about the complexity of these organisms, not as organisms that by their small size are simple and potentially fragile, but as organisms with an auto-regulatory capacity as complex as the human species but in a few microns.
3.2 Human Coronavirus Types
Coronaviruses feature the crown-like spikes on their surface; they were first identified in the 1960s and there are seven types of coronavirus that infect people [1]:
1 1. 229E alpha coronavirus causes the common cold; it infects the upper respiratory tract, i.e., nose, throat, sinuses, and larynx. The subject presents symptoms within a couple of days of being in contact with the virus; these can be headache, runny nose, coughing, sore throat, and fever. The illness lasts a week or 10 days, but it can be extended up to three weeks. Sometimes, subjects with other health problems develop pneumonia [2].
2 2. OC43 beta coronavirus is also the cause of common cold, and just like the 229E, it infects the upper respiratory tract and affects the same organs. The symptoms are also the same as well as the recovery time. Subjects with other health problems can develop pneumonia too [2].
3 3. NL63 alpha coronavirus causes many common symptoms and diseases; it infects the upper and lower tract and can cause croup and bronchiolitis [3].
4 4. MERS-CoV, the beta coronavirus, is the cause of Middle East Respiratory Syndrome or MERS; the symptoms are coughing, shortness of breath, and fever. Sometimes, the subject can also present pneumonia and gastrointestinal symptoms, such as diarrhoea. Some laboratory-confirmed cases of MERS-CoV are reported asymptomatic, i.e., the subjects do not present symptoms. Most of these cases are detected after a thorough tracing of laboratory-confirmed cases [4].
5 5. HKU1 beta coronavirus causes upper respiratory diseases with common cold symptoms and the subject can develop pneumonia and bronchiolitis [5].
6 6. SARS-CoV, the beta coronavirus, causes severe acute respiratory syndrome (SARS), it starts with a high fever, more than 38°C, the subject presents chills, headache, and muscle pain; some cases have mild respiratory symptoms, and some patients have diarrhoea.
7 7. Within a week, the subject presents a dry cough or dyspnoea that can progress to hypoxemia. Some cases even require intubation and mechanical ventilation. The white blood cell count decreases and many people have low platelet counts [6].
8 8. SARS-CoV-2, the novel coronavirus which is the cause of COVID-19, affects people in different ways. In most cases a moderate illness is present and the subject recovers without hospitalization. The symptoms are fever, tiredness, dry coughing, aches and pains, diarrhoea, headaches, conjunctivitis, rash on the skin, and loss of taste or smell. There could also be difficulty breathing, chest pain,
